From 32613662dfbd6c50662f7c7bab1a0578c5b0b2f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:29:47 +0100 Subject: [PATCH 0001/2133] add easyconfig file for Extrae --- .../Extrae-2.4.1-gompi-1.5.12-no-OFED.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb new file mode 100644 index 0000000000..bcb4f32de9 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb @@ -0,0 +1,63 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "Extrae" +version = "2.4.1" + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools' +description = """Extrae is the core instrumentation package developed by the Performance Tools + group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, + CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered + by Extrae typically includes timestamped events of runtime calls, performance counters and source + code references. Besides, Extrae provides its own API to allow the user to manually instrument his + or her application.""" + +toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchainopts = {"usempi": True} + +compname = 'GCC' +compver = '4.7.3' + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.22', "", (compname, compver)), + ('Boost', '1.53.0', '-serial', (compname, compver)), + ('libunwind', '1.1', "", (compname, compver)), + ('libxml2', '2.9.1', "", (compname, compver)), + ('PAPI', '5.2.0', "", (compname, compver)), +] + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = [SOURCELOWER_TAR_BZ2] + +configopts = ' --with-mpi=${EBROOTOPENMPI}' +configopts += ' --with-papi=${EBROOTPAPI} --enable-sampling' +configopts += ' --enable-xml --enable-merge-in-trace' +configopts += ' --with-unwind=${EBROOTLIBUNWIND}' +configopts += ' --without-dwarf --without-dyninst' +configopts += ' --with-boost=${EBROOTBOOST}' +# --- BM ISSUE --- +# +# Does not build with EasyChair provided binutils (libbfd/liberty not shared/compiler with -fPIC) +#configopts += ' --with-binutils=${EBROOTBINUTILS}' + +# --- BM EXTENSIONS --- +# +# Extrae also supports CUDA measurements - not yet tested +# configopts ++ ' --with-cuda=${CUDADIR} --with-cupti=${CUDADIR}/extras/CUPTI' + +# --- BM LIB64 --- +# +# On some systems libraries end up in lib/ +sanity_check_paths = { + 'files': ["bin/mpi2prv", "include/extrae_user_events.h", "lib64/libmpitrace.a"], + 'dirs': [] +} + +moduleclass = 'perf' -- GitLab From 87c41fc3fc9c005442ea8cd976bdb602b9eb8f8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:32:22 +0100 Subject: [PATCH 0002/2133] add easyconfig file for Paraver --- .../p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb new file mode 100644 index 0000000000..d62b7707a8 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb @@ -0,0 +1,70 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "Paraver" +version = "4.4.5" + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +dependencies = [ + ('wxPropertyGrid', '1.4.15'), + ('Boost', '1.53.0', '-serial'), +] + +osdependencies = ['wxWidgets-ansi-devel'] + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.gz'] + +# --- BM ISSUE --- +# +# lib64/lib linking should be avoided by patching Paraver configure/Makefiles files +# configure/Makefile assumes everything always in lib/ +preconfigopts = [ + 'cd ptools_common_files; ', + 'ln -s -f %(installdir)s/ptools/lib64 %(installdir)s/ptools/lib; cd paraver-kernel; ', + 'ln -s -f %(installdir)s/lib64 %(installdir)s/lib; cd wxparaver;' +] +premakeopts = [ + 'cd ptools_common_files; ', + 'cd paraver-kernel; ', + 'cd wxparaver;' +] +preinstallopts = [ + 'cd ptools_common_files; ', + 'cd paraver-kernel; ', + 'cd wxparaver;' +] + +configopts = [ + '--prefix=%(installdir)s/ptools', + '--with-boost=${EBROOTBOOST}' + + ' --with-ptools-common-files=%(installdir)s/ptools', + '--with-boost=${EBROOTBOOST}' + + ' --with-wxpropgrid=wxcode_gtk2_propgrid-2.8' + + ' --with-paraver=%(installdir)s' +] + +keeppreviousinstall = True + +# --- BM LIB64 --- +# +# On some systems libraries end up in lib/ +sanity_check_paths = { + 'files': ["bin/wxparaver", "include/paraverconfig.h", + "lib64/paraver-kernel/libparaver-kernel.a"], + 'dirs': [] +} + +moduleclass = 'perf' -- GitLab From fe8a6dcbd0ee0ff9222e528d105c840797b87d80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:33:39 +0100 Subject: [PATCH 0003/2133] add easyconfig file for TAU --- .../t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb | 114 ++++++++++++++++++ 1 file changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb new file mode 100644 index 0000000000..bda1e46477 --- /dev/null +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb @@ -0,0 +1,114 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +import platform + +name = "TAU" +version = "2.22.2" +# --- BM ISSUE --- +# +# Use hardcoded x86_64 here? +machine = platform.machine() + +homepage = 'http://tau.uoregon.edu' +description = """The TAU Performance System is a portable profiling and tracing toolkit + for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.""" + +toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchainopts = {"usempi": True} + +compname = 'GCC' +compver = '4.7.3' + +# compiler toolchain depencies +dependencies = [ + ('OTF', '1.12.4', "", (compname, compver)), + ('PAPI', '5.2.0', "", (compname, compver)), + ('PDT', '3.19', "", (compname, compver)), + ('Scalasca', '1.4.3'), + ('Score-P', '1.2.1'), + ('VampirTrace', '5.14.4'), +] + +# http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.22.2.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/'] + +# --- BM CONFIGOPTS --- +# +# Compiler should always be specified -- MUCH quicker and SAVER than autodetect +# -c++=[CC|KCC|g++|*xlC*|cxx|pgCC|pgcpp|FCC|guidec++|aCC|c++|ecpc| +# clang++|bgclang++|g++4|icpc|scgcc|scpathCC|pathCC|orCC] +# -cc=[cc|gcc|clang|bgclang|gcc4|scgcc|KCC|pgcc|guidec|*xlc*|ecc|pathcc|orcc] +# -fortran=[gnu|sgi|ibm|ibm64|hp|cray|pgi|absoft|fujitsu|sun|compaq|g95| +# open64|kai|nec|hitachi|intel|absoft|lahey|nagware|pathscale|gfortran|gfortran4] + +# Basic config: compiler, OpenMP, MPI +compcfgopts = ' -cc=gcc -c++=g++ -fortran=gfortran4' +ompcfgopts = ' -opari' +mpicfgopts = ' -mpiinc=${EBROOTOPENMPI}/include -mpilib=${EBROOTOPENMPI}/lib64' + +# Optional extra modes config: +scacfgopts = ' -scalasca=${EBROOTSCALASCA}' +vtcfgopts = ' -vampirtrace=${EBROOTVAMPIRTRACE}' +scocfgopts = ' -scorep=${EBROOTSCOREMINP}' + +# Optional packages config: +pdtcfgopts = ' -pdt=${EBROOTPDT}' +papicfgopts = ' -papi=${EBROOTPAPI}' +optionalcfgs = pdtcfgopts + papicfgopts # + otfcfgopts +# --- BM ISSUE --- +# +# TAU cannot handle name changes yet introduced with OTF-1.12.3 +#otfcfgopts = ' -otf=${EBROOTOTF}' + +# TAU special build procedure +prefix_opt = '-prefix=' +installopts = 'clean' +keeppreviousinstall = True +skipsteps = ['build'] + +# TAU build: Configure + make install for each combination of modes defined above +configopts = [ + # Basic TAU mode + MPI, OMP, OMPI + compcfgopts+mpicfgopts+optionalcfgs, + compcfgopts+ompcfgopts+optionalcfgs, + compcfgopts+mpicfgopts+ompcfgopts+optionalcfgs, + # Scalasca mode + MPI, OMP, OMPI + compcfgopts+mpicfgopts+scacfgopts+optionalcfgs, + compcfgopts+ompcfgopts+scacfgopts+optionalcfgs, + compcfgopts+mpicfgopts+ompcfgopts+scacfgopts+optionalcfgs, + # Vampirtrace mode + MPI, OMP, OMPI + compcfgopts+mpicfgopts+vtcfgopts+optionalcfgs, + compcfgopts+ompcfgopts+vtcfgopts+optionalcfgs, + compcfgopts+mpicfgopts+ompcfgopts+vtcfgopts+optionalcfgs, + # Score-P mode + MPI, OMP, OMPI + compcfgopts+mpicfgopts+scocfgopts+optionalcfgs, + compcfgopts+ompcfgopts+scocfgopts+optionalcfgs, + compcfgopts+mpicfgopts+ompcfgopts+scocfgopts+optionalcfgs, +] + +sanity_check_paths = { + 'files': [machine + "/bin/pprof", "include/TAU.h", machine + "/lib/libTAU.so"], + 'dirs': [] +} + +modextrapaths = { + 'PATH': machine + "/bin", + 'TAU_MF_DIR': machine + "/lib", + 'TAU_MAKEFILE': machine + "/lib/Makefile.tau-papi-mpi-pdt", +} +modextravars = { + 'TAU_PROFILE': '1', + 'TAU_TRACE': '0', + 'TAU_CALLPATH': '1', + 'TAU_CALLPATH_DEPTH': '10', + 'TAU_COMM_MATRIX': '1', +} + +moduleclass = 'perf' -- GitLab From c55d537bdc983511d29966d67e4698ba56b75682 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:35:53 +0100 Subject: [PATCH 0004/2133] add easyconfig file for VampirTrace --- ...VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb new file mode 100644 index 0000000000..304ad188de --- /dev/null +++ b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb @@ -0,0 +1,72 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "VampirTrace" +version = "5.14.4" + +homepage = 'http:/www.tu-dresden.de/zih/vampirtrace/' +description = """VampirTrace is an open source library that allows detailed logging of program + execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads). + Besides these typical parallelization paradigms, VampirTrace is capable of tracing GPU accelerated + applications and generates exact time stamps for all GPU related events. + Additional highlights are I/O event and memory allocation tracing as well as recording of counter metrics + like PAPI and external counters. + VampirTrace provides several variants to instrument the application source code, such as manual, automatic + by the compiler, binary (Dyninst) instrumentation and library wrapping. + The log data is written in the Open Trace Format (OTF), which can be analyzed and visualized by the visualization tool Vampir. + VampirTrace has established a wide user base and has become an integral part of Open MPI version 1.3 and higher.""" + +toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchainopts = {"usempi": True} + +compname = 'GCC' +compver = '4.7.3' + +# compiler toolchain depencies +dependencies = [ + ('OTF', '1.12.4', "", (compname, compver)), + ('PAPI', '5.2.0', "", (compname, compver)), + ('PDT', '3.19', "", (compname, compver)), +] + +# http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz +sources = [SOURCE_TAR_GZ] +source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get='] + +# --- BM CONFIGOPTS --- +# +# MPI suite should always be specified -- MUCH quicker and SAVER than autodetect +# --with-hpmpi | --with-pcmpi | --with-intelmpi | --with-intelmpi2 | --with-lam | --with-mpibgl | --with-mpibgp | +# --with-mpibgq | --with-mpich | --with-mpich2 | --with-mvapich | --with-mvapich2 | --with-mpisx | --with-mpisx-ew | +# --with-openmpi | --with-openmpi17 | --with-sgimpt | --with-sunmpi | --with-sunmpi-mt | --with-mpibull2 +# +# --- BM ISSUE --- +# +# MPIxx variable settings and --enable-compinst= options are ToolChain specific!!! +configopts = ' MPIFC=mpif90' +configopts += ' --with-openmpi' # quicker and saver than autodetect +configopts += ' --enable-compinst=gnu' +configopts += ' --with-papi-dir=${EBROOTPAPI}' +configopts += ' --with-extern-otf-dir=${EBROOTOTF}' +configopts += ' --with-tau-instrumentor=${EBROOTPDT}/x86_64/bin/tau_instrumentor' +configopts += ' --with-pdt-cparse=${EBROOTPDT}/x86_64/bin/cparse' +configopts += ' --with-pdt-cxxparse=${EBROOTPDT}/x86_64/bin/cxxparse' +configopts += ' --with-pdt-fparse=${EBROOTPDT}/x86_64/bin/gfparse' +# --- BM EXTENSIONS --- +# +# VamoirTrace does also support CUDA measurements - not yet tested in EasyBuild +# configopts += ' --with-cuda-dir=${CUDADIR}' + +# --- BM LIB64 --- +# +# On some systems libraries end up in lib/ +sanity_check_paths = { + 'files': ["bin/vtcc", "include/vampirtrace/vt_user.h", "lib64/libvt.a"], + 'dirs': [] +} + +moduleclass = 'perf' -- GitLab From 21b39b1378d0f4692026b3cbd3a155c63395476b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:39:07 +0100 Subject: [PATCH 0005/2133] add libunwind, libxml2 easyconfigs as deps for Extrae --- .../l/libunwind/libunwind-1.1-GCC-4.7.3.eb | 33 +++++++++++++++++ .../l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb | 35 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb new file mode 100644 index 0000000000..14a732a78d --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = 'libunwind' +version = '1.1' + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of this project is to define a portable and efficient C + programming interface (API) to determine the call-chain of a program. The API + additionally provides the means to manipulate the preserved (callee-saved) state of each + call-frame and to resume execution at any point in the call-chain (non-local goto). + The API supports both local (same-process) and remote (across-process) operation.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +# http://download.savannah.gnu.org/releases/libunwind/libunwind-1.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] + +# --- BM LIB64 --- +# +# On some systems libraries end up in lib/ +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib64/libunwind.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb new file mode 100644 index 0000000000..fd7840cbe9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +# --- BM LIB64 --- +# +# On some systems libraries end up in lib/ +sanity_check_paths = { + 'files': ['include/libxml2/libxml/SAX2.h', 'lib64/libxml2.a'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 78c0ed0d951054b835bfa17131dea4b54fc2061b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:42:32 +0100 Subject: [PATCH 0006/2133] add Boost easyconfig as dependency for Paraver --- .../b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb new file mode 100644 index 0000000000..98fbdcdb13 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb @@ -0,0 +1,20 @@ +name = 'Boost' +version = '1.53.0' +versionsuffix = '-serial' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +configopts = '--with-libraries=serialization' + +sanity_check_paths = { + 'files': ["lib/libboost_serialization.a"], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 6665eb9369001333f58db7ae70e2bbcad28b5bf2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:44:21 +0100 Subject: [PATCH 0007/2133] add wxPropertyGrid easyconfig as dependency for Paraver --- .../wxPropertyGrid-1.4.15-GCC-4.7.3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb diff --git a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb new file mode 100644 index 0000000000..859fce3a0d --- /dev/null +++ b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb @@ -0,0 +1,31 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "wxPropertyGrid" +version = "1.4.15" + +homepage = 'http://wxpropgrid.sourceforge.net/' +description = """wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is + a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +osdependencies = ['wxWidgets-ansi-devel'] + +# http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz?download +sources = ['wxpropgrid' + '-%(version)s-src.tar.gz'] +source_urls = ['http://prdownloads.sourceforge.net/wxpropgrid/'] + +sanity_check_paths = { + 'files': ["include/wx/propgrid/propgrid.h", "lib64/libwxcode_gtk2_propgrid-2.8.so"], + 'dirs': [] +} + +parallel = 1 + +moduleclass = 'devel' -- GitLab From 270485a504f4690b9d91d159ce6a7ed9fec37b53 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Nov 2013 23:41:22 +0100 Subject: [PATCH 0008/2133] redefine Extrae easyconfigs on top of gompi/1.4.12-no-OFED toolchain --- ....eb => Extrae-2.4.1-gompi-1.4.12-no-OFED.eb} | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/e/Extrae/{Extrae-2.4.1-gompi-1.5.12-no-OFED.eb => Extrae-2.4.1-gompi-1.4.12-no-OFED.eb} (82%) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb similarity index 82% rename from easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb index bcb4f32de9..c17e508f12 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb @@ -17,19 +17,16 @@ description = """Extrae is the core instrumentation package developed by the Per code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application.""" -toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {"usempi": True} -compname = 'GCC' -compver = '4.7.3' - # compiler toolchain depencies dependencies = [ - ('binutils', '2.22', "", (compname, compver)), - ('Boost', '1.53.0', '-serial', (compname, compver)), - ('libunwind', '1.1', "", (compname, compver)), - ('libxml2', '2.9.1', "", (compname, compver)), - ('PAPI', '5.2.0', "", (compname, compver)), + ('binutils', '2.22'), + ('Boost', '1.53.0'), + ('libunwind', '1.1'), + ('libxml2', '2.9.1'), + ('PAPI', '5.2.0'), ] # http://www.bsc.es/computer-sciences/performance-tools/downloads @@ -44,7 +41,7 @@ configopts += ' --without-dwarf --without-dyninst' configopts += ' --with-boost=${EBROOTBOOST}' # --- BM ISSUE --- # -# Does not build with EasyChair provided binutils (libbfd/liberty not shared/compiler with -fPIC) +# Does not build with EasyBuild provided binutils (libbfd/liberty not shared/compiler with -fPIC) #configopts += ' --with-binutils=${EBROOTBINUTILS}' # --- BM EXTENSIONS --- -- GitLab From 025aff3519f23bd7e61c43bee4e2fee6b8338cba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Nov 2013 23:43:26 +0100 Subject: [PATCH 0009/2133] redefine libunwind and libxml2-2.9.1 GCC easyconfigs for gompi/1.4.12-no-OFED toolchain --- ...-1.1-GCC-4.7.3.eb => libunwind-1.1-gompi-1.4.12-no-OFED.eb} | 2 +- ....9.1-GCC-4.7.3.eb => libxml2-2.9.1-gompi-1.4.12-no-OFED.eb} | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/l/libunwind/{libunwind-1.1-GCC-4.7.3.eb => libunwind-1.1-gompi-1.4.12-no-OFED.eb} (95%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.1-GCC-4.7.3.eb => libxml2-2.9.1-gompi-1.4.12-no-OFED.eb} (94%) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb similarity index 95% rename from easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb rename to easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb index 14a732a78d..5406346b58 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb @@ -16,7 +16,7 @@ description = """The primary goal of this project is to define a portable and ef call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation.""" -toolchain = {'name': 'GCC', 'version': '4.7.3'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} # http://download.savannah.gnu.org/releases/libunwind/libunwind-1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb similarity index 94% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb index fd7840cbe9..de3b30363f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -7,6 +7,7 @@ # http://apps.fz-juelich.de/unite/ ## easyblock = 'ConfigureMake' + name = 'libxml2' version = '2.9.1' @@ -14,7 +15,7 @@ homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" -toolchain = {'name': 'GCC', 'version': '4.7.3'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} source_urls = [ 'http://xmlsoft.org/sources/', -- GitLab From 919c6a212f20ccff681083a5502ad9651b9136db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Nov 2013 23:45:38 +0100 Subject: [PATCH 0010/2133] add Boost easyconfig required for Extrae --- .../Boost-1.53.0-gompi-1.4.12-no-OFED.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..3e994ae064 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.53.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [('bzip2', '1.0.6')] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' -- GitLab From 6a71b3ac644fe5d4d45087c7b02ee1bfc0238811 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Nov 2013 19:05:30 +0100 Subject: [PATCH 0011/2133] add alternative lib path for libunwind --- .../l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb index 5406346b58..5a47aa7676 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb @@ -26,7 +26,7 @@ source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] # # On some systems libraries end up in lib/ sanity_check_paths = { - 'files': ['include/libunwind.h', 'lib64/libunwind.a'], + 'files': ['include/libunwind.h', ('lib/libunwind.a', 'lib64/libunwind.a')], 'dirs': [], } -- GitLab From 0da7ae12501255618ba7371e674aaa710f9783e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Nov 2013 19:18:02 +0100 Subject: [PATCH 0012/2133] tweak sanity check paths for libxml2 consistently, provide alternative paths for libraries --- .../libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb | 5 +++++ .../libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb | 5 +++++ .../l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb | 5 +++++ .../l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb | 5 +++++ .../l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb | 5 +++++ .../l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb | 5 +++++ .../libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb | 5 +++++ .../libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 15 ++------------- .../l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb | 5 +++++ 15 files changed, 72 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb index c67963ba18..3d078ed6cf 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb index 3d1f3f2077..d35a5afd09 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb @@ -18,4 +18,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb index c92bb71719..111dd07ee9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb index 1a06b1ab67..8718a3c0cd 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb index 1babda58a0..5f8aa9158f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb index 9c2538dce1..df4be8cc11 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb @@ -18,4 +18,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb index 34aa5f2ec6..ddb04fedc9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb index 59de5c01a7..2d7551a78a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb index 5618053aba..f6b392b5e3 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb index 0d54f03977..d743e7f4c4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb index de3b30363f..6f75ccd50e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -1,11 +1,3 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany -# Authors:: Bernd Mohr -# License:: New BSD -# -# This work is based from experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## easyblock = 'ConfigureMake' name = 'libxml2' @@ -25,12 +17,9 @@ sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' -# --- BM LIB64 --- -# -# On some systems libraries end up in lib/ sanity_check_paths = { - 'files': ['include/libxml2/libxml/SAX2.h', 'lib64/libxml2.a'], - 'dirs': [], + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb index b46d67c8c8..35fadff4ea 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb index 02c5f8e418..51cf5a1ff9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb index b3eac90a51..28520b4f81 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb index e18bbcef3b..d80e534ea6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' -- GitLab From bc2b6e49e59174bf38b059fc3da70e78f521c5a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Nov 2013 21:44:26 +0100 Subject: [PATCH 0013/2133] add lib alternative in Extrae sanity check --- .../easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb index c17e508f12..0737ca7b22 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb @@ -53,7 +53,7 @@ configopts += ' --with-boost=${EBROOTBOOST}' # # On some systems libraries end up in lib/ sanity_check_paths = { - 'files': ["bin/mpi2prv", "include/extrae_user_events.h", "lib64/libmpitrace.a"], + 'files': ["bin/mpi2prv", "include/extrae_user_events.h", ("lib64/libmpitrace.a", "lib/libmpitrace.a")], 'dirs': [] } -- GitLab From 3e0004f2542bc99af0a43dc52f1b90a4fec5f5a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Nov 2013 17:13:35 +0100 Subject: [PATCH 0014/2133] enable -fPIC for binutils, add gompi easyconfig for binutils as dependency for Extrae --- .../binutils-2.22-goalf-1.1.0-no-OFED.eb | 8 +++-- .../binutils-2.22-gompi-1.4.12-no-OFED.eb | 33 +++++++++++++++++++ .../b/binutils/binutils-2.22-goolf-1.4.10.eb | 7 ++-- 3 files changed, 42 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index cdbab8b742..add5f24592 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -20,12 +20,14 @@ sources = ['binutils-%s.tar.bz2' % version] source_urls = ['http://ftp.gnu.org/gnu/binutils'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist], - 'dirs': [] - } + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..17866810c4 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +name = 'binutils' +version = '2.22' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils-2.22: GNU binary utilities" + +sources = ['binutils-%s.tar.bz2' % version] +source_urls = ['http://ftp.gnu.org/gnu/binutils'] + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True} + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index aa4cc4cdb0..9ccfe20342 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -24,8 +24,9 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist], - 'dirs': [] - } + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} moduleclass = 'tools' -- GitLab From 8adc0744b3c9bbfdfe0eb90759cad3d253445b57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Nov 2013 17:18:50 +0100 Subject: [PATCH 0015/2133] make sure Extrae pick up the right libbfd.a and libiberty.a libraries by patching configure and tweaking $LDFLAGS --- ...a-2.4.1_configure-no-shared-binutils.patch | 14 ++++++++++++ .../Extrae-2.4.1-gompi-1.4.12-no-OFED.eb | 22 +++++++++---------- 2 files changed, 24 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch diff --git a/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch b/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch new file mode 100644 index 0000000000..8b712760c3 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch @@ -0,0 +1,14 @@ +--- configure.orig 2013-11-11 16:38:11.872367495 +0100 ++++ configure 2013-11-11 16:38:32.872767289 +0100 +@@ -27477,9 +27477,9 @@ + BFD_LIBSDIR="${binutils_home_dir}/lib${BITS}" + elif test -r "${binutils_home_dir}/lib/libbfd.so" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" +- elif test -r "${binutils_home_dir}/lib${BITS}/libbfd.a" -a "${binutils_require_shared}" = "no" ; then ++ elif test -r "${binutils_home_dir}/lib${BITS}/libbfd.a"; then #-a "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib${BITS}" +- elif test -r "${binutils_home_dir}/lib/libbfd.a" -a "${binutils_require_shared}" = "no" ; then ++ elif test -r "${binutils_home_dir}/lib/libbfd.a"; then # -a "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" + else + if test -d ${binutils_home_dir}/lib${BITS} ; then diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb index 0737ca7b22..d8500be6ba 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb @@ -20,6 +20,12 @@ description = """Extrae is the core instrumentation package developed by the Per toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {"usempi": True} +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['Extra-2.4.1_configure-no-shared-binutils.patch'] + # compiler toolchain depencies dependencies = [ ('binutils', '2.22'), @@ -29,29 +35,21 @@ dependencies = [ ('PAPI', '5.2.0'), ] -# http://www.bsc.es/computer-sciences/performance-tools/downloads -# Requires input of email address for download -sources = [SOURCELOWER_TAR_BZ2] - configopts = ' --with-mpi=${EBROOTOPENMPI}' configopts += ' --with-papi=${EBROOTPAPI} --enable-sampling' configopts += ' --enable-xml --enable-merge-in-trace' configopts += ' --with-unwind=${EBROOTLIBUNWIND}' configopts += ' --without-dwarf --without-dyninst' configopts += ' --with-boost=${EBROOTBOOST}' -# --- BM ISSUE --- -# -# Does not build with EasyBuild provided binutils (libbfd/liberty not shared/compiler with -fPIC) -#configopts += ' --with-binutils=${EBROOTBINUTILS}' +configopts += ' --with-binutils=${EBROOTBINUTILS}' +# make sure libbfd.a/libiberty.a provided by binutils is used rather than the ones provided by GCC +preconfigopts = 'export LDFLAGS="-L${EBROOTBINUTILS}/lib -L${EBROOTBINUTILS}/lib64 $LDFLAGS" && ' # --- BM EXTENSIONS --- # # Extrae also supports CUDA measurements - not yet tested -# configopts ++ ' --with-cuda=${CUDADIR} --with-cupti=${CUDADIR}/extras/CUPTI' +# configopts += ' --with-cuda=${EBROOTCUDA} --with-cupti=${EBROOTCUDA}/extras/CUPTI' -# --- BM LIB64 --- -# -# On some systems libraries end up in lib/ sanity_check_paths = { 'files': ["bin/mpi2prv", "include/extrae_user_events.h", ("lib64/libmpitrace.a", "lib/libmpitrace.a")], 'dirs': [] -- GitLab From 25250ead1ae49ce4119f186cee3a3854e040fcf9 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 19 Nov 2013 11:48:42 +0100 Subject: [PATCH 0016/2133] add Rgputools easyconfigs Signed-off-by: Fotis Georgatos --- .../Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb | 29 ++++++++++++++++++ .../Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb | 30 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb create mode 100644 easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb diff --git a/easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb new file mode 100644 index 0000000000..ad161b3b58 --- /dev/null +++ b/easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb @@ -0,0 +1,29 @@ +name = 'Rgputools' +version = '876c10d' + +easyblock = 'RPackage' + +homepage = 'https://github.com/nullsatz/gputools/wiki' +description = """This package provides R interfaces to a handful of common functions implemented + using the Nvidia CUDA toolkit. Some of the functions require at least GPU Compute Capability 1.3.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +git_commit_id = version +sources = ['%s.tar.gz' % git_commit_id] +source_urls = ['https://github.com/nullsatz/gputools/archive'] + +r = 'R' +rver = '3.0.2' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [('CUDA', '5.5.22', '', True)] + +sanity_check_paths = { + 'files': ["gputools/libs/gputools.so"], + 'dirs': [] +} + +#options = {'modulename': name} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb new file mode 100644 index 0000000000..12159b9a1a --- /dev/null +++ b/easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb @@ -0,0 +1,30 @@ +name = 'Rgputools' +version = "e5cb024" + +easyblock = 'RPackage' + +homepage = 'https://github.com/nullsatz/gputools/wiki' +description = """This package provides R interfaces to a handful of common functions implemented + using the Nvidia CUDA toolkit. Some of the functions require at least GPU Compute Capability 1.3.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +git_commit_id = version +sources = ['%s.tar.gz' % git_commit_id] +source_urls = ['https://github.com/nullsatz/gputools/archive'] + +r = 'R' +rver = '3.0.2' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [('CUDA', '5.0.35', '-1', True)] +#premakeopts = 'R_HOME=/opt/apps/HPCBIOS.20130902/software/R/3.0.2-ictce-5.3.0-bare/lib64/R ' + +sanity_check_paths = { + 'files': ["gputools/libs/gputools.so"], + 'dirs': [] +} + +options = {'modulename': name} + +moduleclass = 'tools' -- GitLab From 142703ae8eca0370438bc1536cfea015a0f7029e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Dec 2013 16:07:34 +0100 Subject: [PATCH 0017/2133] add easyconfigs for ATSAS --- .../a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb | 23 +++++++++++++++++++ .../a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb create mode 100644 easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb new file mode 100644 index 0000000000..aaf2a2b8d8 --- /dev/null +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb @@ -0,0 +1,23 @@ +easyblock = 'Tarball' + +name = 'ATSAS' +version = '2.5.1-1.el6.x86_64' + +homepage = 'http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html' +description = """ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download via http://www.embl-hamburg.de/biosaxs/download.html +sources = ['%(namelower)s-%(version)s.tar.gz'] + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/atsas'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib64/atsas'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb new file mode 100644 index 0000000000..37cfd159dd --- /dev/null +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb @@ -0,0 +1,23 @@ +easyblock = 'Tarball' + +name = 'ATSAS' +version = '2.5.1-1.sl5.x86_64' + +homepage = 'http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html' +description = """ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download via http://www.embl-hamburg.de/biosaxs/download.html +sources = ['%(namelower)s-%(version)s.tar.gz'] + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/atsas'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib64/atsas'], +} + +moduleclass = 'bio' -- GitLab From 867a1e5b359e0374cadec7f4cc5f4bf4f642a36b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Dec 2013 07:35:42 +0100 Subject: [PATCH 0018/2133] fix remarks --- easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb | 5 +++-- easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb index aaf2a2b8d8..60a094505c 100644 --- a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb @@ -1,7 +1,8 @@ easyblock = 'Tarball' name = 'ATSAS' -version = '2.5.1-1.el6.x86_64' +version = '2.5.1-1' +versionsuffix = '.el6.x86_64' homepage = 'http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html' description = """ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.""" @@ -9,7 +10,7 @@ description = """ATSAS is a program suite for small-angle scattering data analys toolchain = {'name': 'dummy', 'version': 'dummy'} # download via http://www.embl-hamburg.de/biosaxs/download.html -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] modextrapaths = { 'LD_LIBRARY_PATH': ['lib64/atsas'], diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb index 37cfd159dd..5dc5ca2151 100644 --- a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb @@ -1,7 +1,8 @@ easyblock = 'Tarball' name = 'ATSAS' -version = '2.5.1-1.sl5.x86_64' +version = '2.5.1-1' +versionsuffix = '.sl5.x86_64' homepage = 'http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html' description = """ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.""" @@ -9,7 +10,7 @@ description = """ATSAS is a program suite for small-angle scattering data analys toolchain = {'name': 'dummy', 'version': 'dummy'} # download via http://www.embl-hamburg.de/biosaxs/download.html -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] modextrapaths = { 'LD_LIBRARY_PATH': ['lib64/atsas'], -- GitLab From 98193c5ea05da3a6bf96e527a5852fa9d3aff7f7 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 30 Dec 2013 03:28:39 +0100 Subject: [PATCH 0019/2133] make upstream version explicit in namespace Signed-off-by: Fotis Georgatos --- ...0.2.eb => Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb} | 6 +++--- ...0.2.eb => Rgputools-0.28-e5cb024-ictce-5.3.0-R-3.0.2.eb} | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/r/Rgputools/{Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb => Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb} (88%) rename easybuild/easyconfigs/r/Rgputools/{Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb => Rgputools-0.28-e5cb024-ictce-5.3.0-R-3.0.2.eb} (89%) diff --git a/easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb similarity index 88% rename from easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb rename to easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb index ad161b3b58..50a7c3c196 100644 --- a/easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb +++ b/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb @@ -1,5 +1,6 @@ name = 'Rgputools' -version = '876c10d' +version = '0.28' +versionsuffix = '-876c10d' easyblock = 'RPackage' @@ -9,8 +10,7 @@ description = """This package provides R interfaces to a handful of common funct toolchain = {'name': 'ictce', 'version': '5.3.0'} -git_commit_id = version -sources = ['%s.tar.gz' % git_commit_id] +sources = ['%s.tar.gz' % versionsuffix[1:]] source_urls = ['https://github.com/nullsatz/gputools/archive'] r = 'R' diff --git a/easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-e5cb024-ictce-5.3.0-R-3.0.2.eb similarity index 89% rename from easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb rename to easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-e5cb024-ictce-5.3.0-R-3.0.2.eb index 12159b9a1a..603ade0f36 100644 --- a/easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb +++ b/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-e5cb024-ictce-5.3.0-R-3.0.2.eb @@ -1,5 +1,6 @@ name = 'Rgputools' -version = "e5cb024" +version = '0.28' +versionsuffix = '-e5cb024' easyblock = 'RPackage' @@ -9,8 +10,7 @@ description = """This package provides R interfaces to a handful of common funct toolchain = {'name': 'ictce', 'version': '5.3.0'} -git_commit_id = version -sources = ['%s.tar.gz' % git_commit_id] +sources = ['%s.tar.gz' % versionsuffix[1:]] source_urls = ['https://github.com/nullsatz/gputools/archive'] r = 'R' -- GitLab From 7747ded2dc5df670a0bdf5108fa5bd848d243f3a Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 10 Jan 2014 03:21:15 +0100 Subject: [PATCH 0020/2133] remove rgputools/876c10d Signed-off-by: Fotis Georgatos --- ...utools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb diff --git a/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb deleted file mode 100644 index 50a7c3c196..0000000000 --- a/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb +++ /dev/null @@ -1,29 +0,0 @@ -name = 'Rgputools' -version = '0.28' -versionsuffix = '-876c10d' - -easyblock = 'RPackage' - -homepage = 'https://github.com/nullsatz/gputools/wiki' -description = """This package provides R interfaces to a handful of common functions implemented - using the Nvidia CUDA toolkit. Some of the functions require at least GPU Compute Capability 1.3.""" - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -sources = ['%s.tar.gz' % versionsuffix[1:]] -source_urls = ['https://github.com/nullsatz/gputools/archive'] - -r = 'R' -rver = '3.0.2' -versionsuffix = '-%s-%s' % (r, rver) - -dependencies = [('CUDA', '5.5.22', '', True)] - -sanity_check_paths = { - 'files': ["gputools/libs/gputools.so"], - 'dirs': [] -} - -#options = {'modulename': name} - -moduleclass = 'tools' -- GitLab From 1053847fd144db8ad893982d3cc4f564360ceafe Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 4 Feb 2014 18:07:02 +0100 Subject: [PATCH 0021/2133] CONTRAlign-2.01 goolf-1.4.10 --- .../CONTRAlign-2.01-proteins-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../CONTRAlign-2.01-rna-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../c/CONTRAlign/contralign-gcc47.patch | 21 +++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb new file mode 100644 index 0000000000..6255d5289d --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'CONTRAlign' +version = '2.01-proteins' + +easyblock = 'MakeCp' + +homepage = 'http://contra.stanford.edu/contralign/' +description = ''' CONditional TRAining for Protein Sequence Alignment ''' + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_').strip('-proteins'))] + +patches = ['contralign-gcc47.patch'] + +start_dir = 'src' + +# this option determines whether the program is being compiled for protein or RNA sequence input. +# Here we are compiling for protein input. Check docs for details +makeopts = 'MODEL_TYPE="-DRNA=0"' + +files_to_copy = [(['contralign', 'score_directory.pl',\ + 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/contralign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb new file mode 100644 index 0000000000..50d30ad789 --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'CONTRAlign' +version = '2.01-rna' + +easyblock = 'MakeCp' + +homepage = 'http://contra.stanford.edu/contralign/' +description = ''' CONditional TRAining for Protein Sequence Alignment ''' + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_').strip('-rna'))] + +patches = ['contralign-gcc47.patch'] + +start_dir = 'src' + +# this option determines whether the program is being compiled for protein or RNA sequence input. +# Here we are compiling for RNA input. Check docs for details +makeopts = 'MODEL_TYPE="-DRNA=1"' + +files_to_copy = [(['contralign', 'score_directory.pl',\ + 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/contralign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch b/easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch new file mode 100644 index 0000000000..02e1a2bc34 --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch @@ -0,0 +1,21 @@ +--- contralign.orig/src/Makefile 2008-08-15 03:06:30.000000000 +0200 ++++ contralign/src/Makefile 2014-02-04 17:25:31.364788280 +0100 +@@ -23,7 +23,7 @@ + -ffast-math -funroll-all-loops -funsafe-math-optimizations \ + -fpeel-loops -Winline --param large-function-growth=100000 \ + --param max-inline-insns-single=100000 \ +- --param inline-unit-growth=100000 ++ --param inline-unit-growth=100000 -fpermissive + + OTHER_FLAGS = + +--- contralign.orig/src/Utilities.cpp 2008-08-14 02:08:30.000000000 +0200 ++++ contralign/src/Utilities.cpp 2014-02-04 17:25:05.483971266 +0100 +@@ -2,6 +2,7 @@ + // Utilities.cpp + ////////////////////////////////////////////////////////////////////// + ++#include + #include "Utilities.hpp" + + bool toggle_error = false; -- GitLab From 199c7e07987d6d591806acbea4faafee80de0222 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 26 Feb 2014 15:00:39 +0100 Subject: [PATCH 0022/2133] Raster3D-3.0-2-goolf-1.4.10.eb --- .../r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb new file mode 100644 index 0000000000..1b41f400d7 --- /dev/null +++ b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'Raster3D' +version = '3.0-2' + +homepage = 'http://skuld.bmsc.washington.edu/raster3d/' +description = """ Raster3D is a set of tools for generating high quality raster images + of proteins or other molecules. The core program renders spheres, triangles, cylinders, + and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an + efficient software Z-buffer algorithm which is independent of any graphics hardware. + Ancillary programs process atomic coordinates from PDB files into rendering descriptions for + pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also + be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, + shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%(name)s_%(version)s.tar.gz'] + +skipsteps = ['configure'] +makeopts = ' linux && make all' +installopts = 'prefix=%(installdir)s' + +# this are RHEL/CentOS package names +osdependencies = [('libjpeg-turbo-devel', 'libpng-devel', 'libtiff-devel')] + +modextrapaths = {'R3D_LIB': 'share/Raster3D/materials'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["avs2ps", "balls", "normal3d", "rastep", "render", + "ribbon", "rings3d", "rods", "stereo3d", "worms" ]], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From e2cd85d6891a38543e1779d24f26b5f2f195a6d2 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 26 Feb 2014 19:52:46 +0100 Subject: [PATCH 0023/2133] added EB style dependencies and required eb files --- .../libjpeg-turbo-1.3.0-goolf-1.4.10.eb | 21 +++++++++++++++++++ .../r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb | 11 ++++++++-- 2 files changed, 30 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..e33c2344b7 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb @@ -0,0 +1,21 @@ +name = 'libjpeg-turbo' +version = '1.3.0' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.07'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb index 1b41f400d7..c787473f52 100644 --- a/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb @@ -25,14 +25,21 @@ skipsteps = ['configure'] makeopts = ' linux && make all' installopts = 'prefix=%(installdir)s' +dependencies = [ + ('libjpeg-turbo', '1.3.0'), + ('libpng', '1.6.2'), + ('LibTIFF', '4.0.3'), +] + # this are RHEL/CentOS package names -osdependencies = [('libjpeg-turbo-devel', 'libpng-devel', 'libtiff-devel')] +# in case you prefer to rely in OS dependencies +#osdependencies = [('libjpeg-turbo-devel', 'libpng-devel', 'libtiff-devel')] modextrapaths = {'R3D_LIB': 'share/Raster3D/materials'} sanity_check_paths = { 'files': ['bin/%s' % x for x in ["avs2ps", "balls", "normal3d", "rastep", "render", - "ribbon", "rings3d", "rods", "stereo3d", "worms" ]], + "ribbon", "rings3d", "rods", "stereo3d", "worms" ]], 'dirs': [] } -- GitLab From ab483cb47ba1cadf1908c47db776692d4156af78 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Mar 2014 13:47:41 +0100 Subject: [PATCH 0024/2133] add subversion v1.6.23 as build dep for Python 2.5.6, add easyconfigs for subversion + deps --- .../APR-util-1.5.3-goalf-1.1.0-no-OFED.eb | 23 ++++++++++++ .../APR-util-1.5.3-gompi-1.4.12-no-OFED.eb | 23 ++++++++++++ .../a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb | 23 ++++++++++++ .../a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb | 23 ++++++++++++ .../a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb | 23 ++++++++++++ .../a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb | 23 ++++++++++++ .../a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb | 23 ++++++++++++ .../a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb | 17 +++++++++ .../a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb | 17 +++++++++ .../a/APR/APR-1.5.0-goolf-1.4.10.eb | 17 +++++++++ .../a/APR/APR-1.5.0-ictce-4.0.6.eb | 17 +++++++++ .../a/APR/APR-1.5.0-ictce-4.1.13.eb | 17 +++++++++ .../a/APR/APR-1.5.0-ictce-5.2.0.eb | 17 +++++++++ .../a/APR/APR-1.5.0-ictce-5.3.0.eb | 17 +++++++++ .../libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 22 ++++++++++++ ...libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 27 ++++++++++++++ .../l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb | 22 ++++++++++++ .../n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb | 24 +++++++++++++ .../neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb | 24 +++++++++++++ .../n/neon/neon-0.30.0-goolf-1.4.10.eb | 24 +++++++++++++ .../n/neon/neon-0.30.0-ictce-4.0.6.eb | 24 +++++++++++++ .../n/neon/neon-0.30.0-ictce-4.1.13.eb | 24 +++++++++++++ .../n/neon/neon-0.30.0-ictce-5.2.0.eb | 24 +++++++++++++ .../n/neon/neon-0.30.0-ictce-5.3.0.eb | 24 +++++++++++++ .../Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 4 +++ .../Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 4 +++ .../Python/Python-2.5.6-goolf-1.4.10-bare.eb | 4 +++ .../p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 4 +++ .../Python/Python-2.5.6-ictce-4.1.13-bare.eb | 4 +++ .../p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 4 +++ .../p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 4 +++ .../SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb | 35 +++++++++++++++++++ .../SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb | 35 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb | 35 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb | 35 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb | 35 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb | 35 +++++++++++++++++++ .../subversion-1.6.23-goalf-1.1.0-no-OFED.eb | 28 +++++++++++++++ .../subversion-1.6.23-gompi-1.4.12-no-OFED.eb | 28 +++++++++++++++ .../subversion-1.6.23-goolf-1.4.10.eb | 28 +++++++++++++++ .../subversion-1.6.23-ictce-4.0.6.eb | 28 +++++++++++++++ .../subversion-1.6.23-ictce-4.1.13.eb | 28 +++++++++++++++ .../subversion-1.6.23-ictce-5.2.0.eb | 28 +++++++++++++++ .../subversion-1.6.23-ictce-5.3.0.eb | 28 +++++++++++++++ .../subversion-1.8.8-goolf-1.4.10.eb | 28 +++++++++++++++ .../subversion-1.8.8-ictce-4.1.13.eb | 28 +++++++++++++++ .../subversion-1.8.8-ictce-5.5.0.eb | 28 +++++++++++++++ .../t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb | 19 ++++++++++ .../t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb | 19 ++++++++++ .../t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb | 19 ++++++++++ .../t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb | 19 ++++++++++ .../t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb | 19 ++++++++++ 53 files changed, 1167 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb create mode 100755 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb create mode 100755 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb create mode 100755 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb create mode 100755 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..f2b2f6d4d4 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..f5f429b778 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..f2b44bb9a1 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb new file mode 100644 index 0000000000..6785705751 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb new file mode 100644 index 0000000000..ab0ac9c226 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb new file mode 100644 index 0000000000..669555d663 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb new file mode 100644 index 0000000000..5820665193 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..42d75b76df --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..c9b38d32bc --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..e069e515a2 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb new file mode 100644 index 0000000000..bb13d21a33 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb new file mode 100644 index 0000000000..c26ce2075a --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb new file mode 100644 index 0000000000..3f74bca0b9 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..7c6b787d78 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..6e4ab86218 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100755 index 0000000000..d68ae2eaee --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.5' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb new file mode 100644 index 0000000000..232c2e480f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..f111e9310e --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..212229e999 --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..dbf0e6619b --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb new file mode 100644 index 0000000000..fdf1eabe1a --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb new file mode 100644 index 0000000000..97eea6a566 --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb new file mode 100644 index 0000000000..244a91df81 --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..6dd467a1fe --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index 279bdd8c99..6bc189fb19 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -19,6 +19,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index f9f346f7bc..ba4c8ccf22 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -19,6 +19,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index 66cb466a25..9074876929 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -19,6 +19,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index 781b45ed3f..8df72e769a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -21,6 +21,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index c8bc196270..6fde08c369 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -21,6 +21,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index 79512f826c..a35457f6ec 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -19,6 +19,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index f949db90c2..99ba7a0a56 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -19,6 +19,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..1f9d380786 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..330ea91aef --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..72c8d21c52 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb new file mode 100644 index 0000000000..8ab8985748 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb new file mode 100644 index 0000000000..6948614b01 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb new file mode 100644 index 0000000000..6a16570c53 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..499e33114e --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..10fcdfa9b8 --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..18b01448ee --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb new file mode 100644 index 0000000000..c4f4b6ed90 --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb new file mode 100644 index 0000000000..cc7766f42b --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb new file mode 100644 index 0000000000..0e7556d3dd --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb new file mode 100644 index 0000000000..3dd8117f6f --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb new file mode 100644 index 0000000000..8b59c05878 --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb new file mode 100644 index 0000000000..5f9488ba6c --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.8.8' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb new file mode 100644 index 0000000000..672480bf95 --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.8.8' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb new file mode 100644 index 0000000000..17a3d6e7d2 --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.8.8' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..688b7db304 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..bf05390914 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb new file mode 100755 index 0000000000..4497a53f78 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb new file mode 100755 index 0000000000..a112f672e2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb new file mode 100755 index 0000000000..d9d3d41205 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From 3c41da9803d064e8e7ecdfafcc408551072ef28f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Mar 2014 17:02:30 +0100 Subject: [PATCH 0025/2133] drop subversion v1.8.8 ictce/5.5.0 easyconfig --- .../subversion-1.8.8-ictce-5.5.0.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb deleted file mode 100644 index 17a3d6e7d2..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.8.8' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' -- GitLab From 3af5d4d9808163bdc24b0efd4465eaa82c4b1784 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 28 Apr 2014 15:55:20 +0200 Subject: [PATCH 0026/2133] MotEvo-1.02-goolf-1.4.10.eb --- .../m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb new file mode 100644 index 0000000000..f5e5c6d50f --- /dev/null +++ b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock='MakeCp' + +name = 'MotEvo' +version = '1.02' + +homepage = 'http://swissregulon.unibas.ch/fcgi/sr/software' +description = """ MotEvo: a integrated suite of Bayesian probabilistic methods for + the prediction of TFBSs and inference of regulatory motifs from multiple alignments + of phylogenetically related DNA sequences """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.swissregulon.unibas.ch/software/motevo/'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] + +start_dir = "source" + +parallel = 1 + +# this requires glob support in MakeCp easyblock so +# be sure to use at least EasyBuild-1.12 or newer +files_to_copy = ["../*"] + +sanity_check_paths = { + 'files': ["bin/motevo", "bin/runUFE"], + 'dirs': ["weight_matrices", "trees", "weight_matrices"], +} + +moduleclass = 'bio' -- GitLab From d2b351f40e159b14b27f1cd7ccf94345cda90762 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 6 May 2014 15:23:57 +0200 Subject: [PATCH 0027/2133] added option to verify EasyBuild version is 1.12.0 or higher --- easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb index f5e5c6d50f..b2f811f92b 100644 --- a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb @@ -24,6 +24,7 @@ parallel = 1 # this requires glob support in MakeCp easyblock so # be sure to use at least EasyBuild-1.12 or newer +easybuild_version = '1.12.0' files_to_copy = ["../*"] sanity_check_paths = { -- GitLab From 06fd2565050f6769fb6d2ca83b245bf04d63f8a3 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 7 May 2014 11:55:19 +0200 Subject: [PATCH 0028/2133] mrFAST and mrsFAST easyconfigs for goolf and ictce toolchains --- .../m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb | 33 ++++++++++++ .../m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb | 35 +++++++++++++ .../m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb | 33 ++++++++++++ .../m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb | 35 +++++++++++++ .../mrsFAST-2.6.0.4-intel-compiler.patch | 17 ++++++ .../mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb | 35 +++++++++++++ .../mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb | 37 +++++++++++++ .../mrsFAST-Ultra-3.3.1-intel-compiler.patch | 52 +++++++++++++++++++ 8 files changed, 277 insertions(+) create mode 100644 easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-intel-compiler.patch diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..a66b9f116e --- /dev/null +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrFAST' +version = '2.6.0.1' + +homepage = 'http://mrfast.sourceforge.net/' +description = """ mrFAST & mrsFAST are designed to map short reads generated with the + Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +files_to_copy = [ + (['mrfast'], 'bin'), + "TODO", + "LICENSE" +] + +sanity_check_paths = { + 'files': ["bin/mrfast", "TODO", "LICENSE"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb new file mode 100644 index 0000000000..a045864ca0 --- /dev/null +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrFAST' +version = '2.6.0.1' + +homepage = 'http://mrfast.sourceforge.net/' +description = """ mrFAST & mrsFAST are designed to map short reads generated with the + Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +makeopts = ' CC=$CC' + +files_to_copy = [ + (['mrfast'], 'bin'), + "TODO", + "LICENSE" +] + +sanity_check_paths = { + 'files': ["bin/mrfast", "TODO", "LICENSE"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..994e7e7c7f --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrsFAST' +version = '2.6.0.4' + +homepage = 'http://mrsfast.sourceforge.net' +description = """ mrsFAST is designed to map short reads to reference genome assemblies + in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that + optimizes cache usage to get higher performance. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] + +parallel = 1 + +files_to_copy = [ + (['mrsfast'], 'bin'), + "Changelog", +] + +sanity_check_paths = { + 'files': ["bin/mrsfast"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb new file mode 100644 index 0000000000..acbe7af340 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrsFAST' +version = '2.6.0.4' + +homepage = 'http://mrsfast.sourceforge.net' +description = """ mrsFAST is designed to map short reads to reference genome assemblies + in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that + optimizes cache usage to get higher performance. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['mrsFAST-2.6.0.4-intel-compiler.patch'] + +parallel = 1 + +files_to_copy = [ + (['mrsfast'], 'bin'), + "Changelog", +] + +sanity_check_paths = { + 'files': ["bin/mrsfast"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch new file mode 100644 index 0000000000..085ff27bd8 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch @@ -0,0 +1,17 @@ +diff -ru mrsfast-2.6.0.4.orig/Makefile mrsfast-2.6.0.4/Makefile +--- mrsfast-2.6.0.4.orig/Makefile 2013-07-24 00:53:41.000000000 +0200 ++++ mrsfast-2.6.0.4/Makefile 2014-05-07 11:35:36.394689000 +0200 +@@ -1,3 +1,5 @@ ++CC=icc ++ + ALL: mrsfast + + LDFLAGS=-s -static +@@ -5,5 +7,5 @@ + CFLAGS= -O2 -s + + mrsfast: baseFAST.o MrsFAST.o Common.o CommandLineParser.o RefGenome.o HashTable.o Reads.o Output.o +- gcc $^ -o $@ ${LDFLAGS} ${LIBS} ++ $(CC) $^ -o $@ ${LDFLAGS} ${LIBS} + rm *.o +Only in mrsfast-2.6.0.4: mrsfast diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..7f663058f9 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrsFAST-Ultra' +version = '3.3.1' + +homepage = 'http://mrsfast.sourceforge.net' +description = """ mrsFAST is designed to map short reads to reference genome assemblies + in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that + optimizes cache usage to get higher performance. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/mrsfast/files/', 'download')] +sources = [SOURCELOWER_ZIP] + +parallel = 1 + +files_to_copy = [ + (['mrsfast', 'snp_indexer'], 'bin'), + "HELP", + "Changelog", + "LICENSE" +] + +sanity_check_paths = { + 'files': ["bin/mrsfast", "bin/snp_indexer"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb new file mode 100644 index 0000000000..70a21c5c28 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrsFAST-Ultra' +version = '3.3.1' + +homepage = 'http://mrsfast.sourceforge.net' +description = """ mrsFAST is designed to map short reads to reference genome assemblies + in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that + optimizes cache usage to get higher performance. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = [('http://sourceforge.net/projects/mrsfast/files/', 'download')] +sources = [SOURCELOWER_ZIP] + +patches = ['mrsFAST-Ultra-3.3.1-intel-compiler.patch'] + +parallel = 1 + +files_to_copy = [ + (['mrsfast', 'snp_indexer'], 'bin'), + "HELP", + "Changelog", + "LICENSE" +] + +sanity_check_paths = { + 'files': ["bin/mrsfast", "bin/snp_indexer"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-intel-compiler.patch b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-intel-compiler.patch new file mode 100644 index 0000000000..2c61c608c2 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-intel-compiler.patch @@ -0,0 +1,52 @@ +diff -ru mrsfast-ultra-3.3.1.orig/Makefile mrsfast-ultra-3.3.1/Makefile +--- mrsfast-ultra-3.3.1.orig/Makefile 2014-03-31 10:36:25.000000000 +0200 ++++ mrsfast-ultra-3.3.1/Makefile 2014-05-07 11:44:59.677675000 +0200 +@@ -1,3 +1,4 @@ ++CC=icc + DEBUG := 0 + PROFILE := 0 + MRSFAST_VERSION := "3.3.1" +@@ -18,13 +19,13 @@ + + mrsfast: + ifeq ($(shell uname -s),Linux) +- gcc -w $(objects) -o $@ ${LDFLAGS} ${LIBS} ++ $(CC) -w $(objects) -o $@ ${LDFLAGS} ${LIBS} + else +- gcc -Wl,-no_pie -fno-pic -w $(objects) -o $@ ${LDFLAGS} ${LIBS} ++ $(CC) -Wl,-no_pie -fno-pic -w $(objects) -o $@ ${LDFLAGS} ${LIBS} + endif + + snp_indexer: SNPIndexer.o +- gcc $^ -o $@ ${LDFLAGS} ${LIBS} ++ $(CC) $^ -o $@ ${LDFLAGS} ${LIBS} + + clean: + @rm -f $(objects) +@@ -41,7 +42,7 @@ + @ld -r -b binary -o HELP.o HELP + else + @touch HELPstub.c +- gcc -o HELPstub.o -c HELPstub.c ++ $(CC) -o HELPstub.o -c HELPstub.c + ld -r -o HELP.o -sectcreate binary HELP HELP HELPstub.o + endif + +@@ -62,7 +63,7 @@ + $(shell echo "-DSSE4=0") + else + $(eval CFLAGS = $(CFLAGS) \ +- $(shell gv=`gcc -dumpversion`; \ ++ $(shell gv=`$(CC) -dumpversion`; \ + sc=`grep -c "sse4" /proc/cpuinfo`; \ + echo $$sc.$$gv | awk -F. '{if($$1>0 && $$2>=4 && $$3>=4) print "-DSSE4=1 -msse4.2"; else print "-DSSE4=0"}')) + endif +@@ -71,7 +72,7 @@ + $(shell echo "-DSSE4=0") + else + $(eval CFLAGS = $(CFLAGS) \ +- $(shell gv=`gcc -dumpversion`; \ ++ $(shell gv=`$(CC) -dumpversion`; \ + sc=`sysctl -n machdep.cpu.features | grep -c "SSE4"` ;\ + echo $$sc.$$gv | awk -F. '{if($$1>0 && $$2>=4 && $$3>=4) print "-DSSE4=1 -msse4.2"; else print "-DSSE4=0"}')) + endif -- GitLab From 5fc261e843dda742a0e3554e18237cce85c1ddf1 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 7 May 2014 14:31:33 +0200 Subject: [PATCH 0029/2133] drFAST easyconfigs for goolf and ictce toolchains --- .../d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 32 +++++++++++++++++ .../d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 34 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..571b8bd17f --- /dev/null +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'drFAST' +version = '1.0.0.0' + +homepage = 'http://drfast.sourceforge.net/' +description = """ drFAST is designed to map di-base reads (SOLiD color space reads) + to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_ZIP] + +parallel = 1 + +files_to_copy = [ + (['drfast'], 'bin'), + "README.txt" +] + +sanity_check_paths = { + 'files': ["bin/drfast", "README.txt"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb new file mode 100644 index 0000000000..6036f2cf05 --- /dev/null +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'drFAST' +version = '1.0.0.0' + +homepage = 'http://drfast.sourceforge.net/' +description = """ drFAST is designed to map di-base reads (SOLiD color space reads) + to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_ZIP] + +parallel = 1 + +makeopts = ' CC=$CC' + +files_to_copy = [ + (['drfast'], 'bin'), + "README.txt" +] + +sanity_check_paths = { + 'files': ["bin/drfast", "README.txt"], + 'dirs': [""], +} + +moduleclass = 'bio' -- GitLab From 798b23874b34465652569391971949979fe545fd Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 20 May 2014 19:45:00 +0200 Subject: [PATCH 0030/2133] MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb --- .../MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb new file mode 100644 index 0000000000..04b13ba339 --- /dev/null +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'MOSAIK' +version = '2.2.28' +versionsuffix = '_2014-04-25' + +homepage = 'https://code.google.com/p/mosaik-aligner/' +description = """ MOSAIK is a reference-guided aligner for next-generation + sequencing technologies """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] +# first six digits of the commit id we will download from github +git_commit_id = '24cf06' +sources = ['%s.tar.gz' % (git_commit_id)] + +parallel = 1 + +start_dir = "src" + +makeopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' + +files_to_copy = ["bin", "../README", "demo"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], + 'dirs': [""], +} + +moduleclass = 'bio' + -- GitLab From 1f32bf41c0ae03bf32a9b2eec17c52bf8677b2f4 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 3 Jun 2014 23:25:22 +0200 Subject: [PATCH 0031/2133] added makeopts to both easyconfigs --- easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index 571b8bd17f..69bc7179e6 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -17,6 +17,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_ZIP] +makeopts = ' CC="$CC"' + parallel = 1 files_to_copy = [ diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb index 6036f2cf05..e6d4edb800 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -17,9 +17,9 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_ZIP] -parallel = 1 +makeopts = ' CC="$CC"' -makeopts = ' CC=$CC' +parallel = 1 files_to_copy = [ (['drfast'], 'bin'), -- GitLab From 7919d401a3865e2f35b7f9c81fec98447ea5cb62 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 4 Jun 2014 15:27:12 +0200 Subject: [PATCH 0032/2133] added missing zlib dependency --- easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index 69bc7179e6..0e1f21cdae 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -17,6 +17,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_ZIP] +dependencies = [('zlib', '1.2.8')] + makeopts = ' CC="$CC"' parallel = 1 diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb index e6d4edb800..7931bee0d2 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -17,6 +17,8 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_ZIP] +dependencies = [('zlib', '1.2.8')] + makeopts = ' CC="$CC"' parallel = 1 -- GitLab From 45b77c59fba479457a6b725e643620ff3d0bf829 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 4 Jun 2014 23:50:52 +0200 Subject: [PATCH 0033/2133] small style fixes --- .../easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 7 ++----- .../easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 7 ++----- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index 0e1f21cdae..9488117544 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -23,14 +23,11 @@ makeopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ - (['drfast'], 'bin'), - "README.txt" -] +files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb index 7931bee0d2..226f9d0f9b 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -23,14 +23,11 @@ makeopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ - (['drfast'], 'bin'), - "README.txt" -] +files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' -- GitLab From f7bfbbd0835ae7108ebf6f83fb741415bffcb1cd Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 4 Jun 2014 23:56:59 +0200 Subject: [PATCH 0034/2133] added git_commit_id to versionsuffix --- .../m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb index 04b13ba339..690619ca2b 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'MOSAIK' version = '2.2.28' -versionsuffix = '_2014-04-25' +versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' description = """ MOSAIK is a reference-guided aligner for next-generation -- GitLab From ae317c6a0ecf5902129a9881c1607d01f1fb0154 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 4 Jun 2014 23:57:19 +0200 Subject: [PATCH 0035/2133] style fix in sanity_check --- .../m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb index 690619ca2b..5440998f01 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -30,7 +30,7 @@ files_to_copy = ["bin", "../README", "demo"] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' -- GitLab From 348e144e077fed8529b3329038720ecbb24a56ab Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Jun 2014 00:05:59 +0200 Subject: [PATCH 0036/2133] moved git_commit_id up --- .../m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb index 5440998f01..491953beff 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -7,6 +7,7 @@ easyblock = 'MakeCp' name = 'MOSAIK' version = '2.2.28' +git_commit_id = '24cf06' #first six digits of the commit id we will download from github versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' @@ -16,8 +17,6 @@ description = """ MOSAIK is a reference-guided aligner for next-generation toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] -# first six digits of the commit id we will download from github -git_commit_id = '24cf06' sources = ['%s.tar.gz' % (git_commit_id)] parallel = 1 -- GitLab From ee32022c3258f592b06bbd52ee42deccb42bdf8a Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Jun 2014 00:06:51 +0200 Subject: [PATCH 0037/2133] added ictce easyconfig --- .../MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb new file mode 100644 index 0000000000..d420812af7 --- /dev/null +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'MOSAIK' +version = '2.2.28' +git_commit_id = '24cf06' #first six digits of the commit id we will download from github +versionsuffix = '-20140425-%s' % git_commit_id + +homepage = 'https://code.google.com/p/mosaik-aligner/' +description = """ MOSAIK is a reference-guided aligner for next-generation + sequencing technologies """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] +sources = ['%s.tar.gz' % (git_commit_id)] + +parallel = 1 + +start_dir = "src" + +makeopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' + +files_to_copy = ["bin", "../README", "demo"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From b7a9ad31bb2bd7a2a7049bffaf74db4c6b23a7e9 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Jun 2014 00:27:54 +0200 Subject: [PATCH 0038/2133] files_to_copy in single line. style fixes --- .../m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb | 8 ++------ .../easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb | 10 +++------- .../m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb | 7 ++----- .../m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb | 7 ++----- .../m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb | 9 ++------- .../m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb | 9 ++------- 6 files changed, 13 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb index a66b9f116e..83547d99c7 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb @@ -19,15 +19,11 @@ sources = [SOURCELOWER_TAR_GZ] parallel = 1 -files_to_copy = [ - (['mrfast'], 'bin'), - "TODO", - "LICENSE" -] +files_to_copy = [ (['mrfast'], 'bin'), "TODO", "LICENSE" ] sanity_check_paths = { 'files': ["bin/mrfast", "TODO", "LICENSE"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb index a045864ca0..a2eafd5a27 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb @@ -19,17 +19,13 @@ sources = [SOURCELOWER_TAR_GZ] parallel = 1 -makeopts = ' CC=$CC' +makeopts = ' CC="$CC"' -files_to_copy = [ - (['mrfast'], 'bin'), - "TODO", - "LICENSE" -] +files_to_copy = [ (['mrfast'], 'bin'), "TODO", "LICENSE" ] sanity_check_paths = { 'files': ["bin/mrfast", "TODO", "LICENSE"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb index 994e7e7c7f..b2b767778f 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb @@ -20,14 +20,11 @@ sources = [SOURCELOWER_ZIP] parallel = 1 -files_to_copy = [ - (['mrsfast'], 'bin'), - "Changelog", -] +files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] sanity_check_paths = { 'files': ["bin/mrsfast"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb index acbe7af340..9b11e23227 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb @@ -22,14 +22,11 @@ patches = ['mrsFAST-2.6.0.4-intel-compiler.patch'] parallel = 1 -files_to_copy = [ - (['mrsfast'], 'bin'), - "Changelog", -] +files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] sanity_check_paths = { 'files': ["bin/mrsfast"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb index 7f663058f9..a714d32adb 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb @@ -20,16 +20,11 @@ sources = [SOURCELOWER_ZIP] parallel = 1 -files_to_copy = [ - (['mrsfast', 'snp_indexer'], 'bin'), - "HELP", - "Changelog", - "LICENSE" -] +files_to_copy = [ (['mrsfast', 'snp_indexer'], 'bin'), "HELP", "Changelog", "LICENSE" ] sanity_check_paths = { 'files': ["bin/mrsfast", "bin/snp_indexer"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb index 70a21c5c28..6ed2b7907b 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb @@ -22,16 +22,11 @@ patches = ['mrsFAST-Ultra-3.3.1-intel-compiler.patch'] parallel = 1 -files_to_copy = [ - (['mrsfast', 'snp_indexer'], 'bin'), - "HELP", - "Changelog", - "LICENSE" -] +files_to_copy = [ (['mrsfast', 'snp_indexer'], 'bin'), "HELP", "Changelog", "LICENSE" ] sanity_check_paths = { 'files': ["bin/mrsfast", "bin/snp_indexer"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' -- GitLab From 5eeb648a54378bec4b955d158305ca202b4dba2b Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 10 Jun 2014 17:05:31 +0200 Subject: [PATCH 0039/2133] added missing zlib dependency --- .../m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 2 ++ .../easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb index 491953beff..afc62c9a6c 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -19,6 +19,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] sources = ['%s.tar.gz' % (git_commit_id)] +dependencies = [('zlib', '1.2.8')] + parallel = 1 start_dir = "src" diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb index d420812af7..47308d8d3d 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb @@ -19,6 +19,8 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] sources = ['%s.tar.gz' % (git_commit_id)] +dependencies = [('zlib', '1.2.8')] + parallel = 1 start_dir = "src" -- GitLab From cdd449fa5c9f5cf84367c90889c333efd770b7c6 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 11 Jun 2014 14:27:30 +0200 Subject: [PATCH 0040/2133] BLASR-2.1-goolf-1.4.10.eb --- .../b/BLASR/BLASR-2.1-goolf-1.4.10.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..756b674e3a --- /dev/null +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'BLASR' +version = '2.1' + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """ BLASR (Basic Local Alignment with Successive Refinement) rapidly maps + reads to genomes by finding the highest scoring local alignment or set of local alignments + between the read and the genome. Optimized for PacBio's extraordinarily long reads and + taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] +sources = ['smrtanalysis-%(version)s.tar.gz'] + +dependencies = [('HDF5', '1.8.11')] + +skipsteps = ['configure'] + +# the STATIC= option is a workaround. Check details here: +# https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 +makeopts = ' STATIC= ' + +installopts = ' INSTALL_BIN_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ["bin/blasr"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 2478e8f498e3f9528db6f9f2fb58b15f8be54296 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 29 Jun 2014 13:24:50 +0200 Subject: [PATCH 0041/2133] splitRef-0.0.2.eb --- .../easyconfigs/s/splitRef/splitRef-0.0.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb diff --git a/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb new file mode 100644 index 0000000000..f997865645 --- /dev/null +++ b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'splitRef' +version = '0.0.2' + +homepage = 'http://www.sph.umich.edu/csg/yli/splitRef/index.html' +description = """ splitRef splits a reference haplotype file into smaller files + with subsets of markers. The current version is a pre-release. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.sph.umich.edu/csg/yli/splitRef/download/'] +sources = ['%s.V%s.tgz' % (name, version.replace(".",""))] + +sanity_check_paths = { + 'files': ["splitRef_V002/splitRef.pl"], + 'dirs': ["examples"] +} + +# add folder splitRef_V002 to PATH +modextrapaths = { + 'PATH': '%s_V%s' % (name, version.replace(".","")) +} + +moduleclass = 'bio' + -- GitLab From 8d87638c6dd193e9b7950b4bfdf5f929f624b150 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 12:25:14 +0300 Subject: [PATCH 0042/2133] Adding CP2K v.2.4.0 and CP2K with i-pi --- .../c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 37 ++ .../c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb | 35 ++ .../easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch | 509 ++++++++++++++++++ .../c/CP2K/fix_compile_date_lastcvs.patch | 11 +- 4 files changed, 585 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb new file mode 100644 index 0000000000..8c26b632c2 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -0,0 +1,37 @@ +name = 'CP2K' +version = '2.4.0' +versionsuffix = '-ipi' + +homepage = 'http://www.cp2k.org' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, + to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. + It provides a general framework for different methods such as e.g. density functional theory (DFT) + using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/cp2k/files/'] + +sources = ['%s-%s.tar.bz2' % (name.lower(), version)] + +patches = [ + 'cp2k-2.4.0_ipi.patch', + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' + ] + +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5') + ] + +dependencies = [('Libint', '1.1.4')] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# about 100 tests fail +ignore_regtest_fails=True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..9389d88e83 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +name = 'CP2K' +version = '2.4.0' + +homepage = 'http://www.cp2k.org' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, + to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. + It provides a general framework for different methods such as e.g. density functional theory (DFT) + using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/cp2k/files/'] + +sources = ['%s-%s.tar.bz2' % (name.lower(), version)] + +patches = [ + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' + ] + +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5') + ] + +dependencies = [('Libint', '1.1.4')] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# about 100 tests fail +ignore_regtest_fails=True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch b/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch new file mode 100644 index 0000000000..ba7ceaf26e --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch @@ -0,0 +1,509 @@ +diff -rupN cp2k-2.4.0_ref/makefiles/Makefile cp2k-2.4.0/makefiles/Makefile +--- cp2k-2.4.0_ref/makefiles/Makefile 2013-08-15 10:46:04.535899216 +0100 ++++ cp2k-2.4.0/makefiles/Makefile 2013-08-15 10:53:45.827911028 +0100 +@@ -354,7 +354,7 @@ else + LIB_OBJECTS = + endif + +-$(LIB_CP2K_ARCHIVE): $(OBJECTS) ++$(LIB_CP2K_ARCHIVE): $(OBJECTS) sockets.o + $(AR) $(LIB_CP2K_ARCHIVE) $? + ifneq ($(RANLIB),) + $(RANLIB) $(LIB_CP2K_ARCHIVE) +diff -rupN cp2k-2.4.0_ref/src/cp2k_runs.F cp2k-2.4.0/src/cp2k_runs.F +--- cp2k-2.4.0_ref/src/cp2k_runs.F 2013-08-15 10:46:04.091899205 +0100 ++++ cp2k-2.4.0/src/cp2k_runs.F 2013-08-15 10:56:31.715915275 +0100 +@@ -73,10 +73,10 @@ MODULE cp2k_runs + USE input_constants, ONLY: & + bsse_run, cell_opt_run, debug_run, do_atom, do_band, do_cp2k, do_ep, & + do_farming, do_fist, do_mixed, do_opt_basis, do_optimize_input, & +- do_qmmm, do_qs, do_tamc, do_test, ehrenfest, electronic_spectra_run, & +- energy_force_run, energy_run, geo_opt_run, linear_response_run, & +- mol_dyn_run, mon_car_run, none_run, pint_run, real_time_propagation, & +- vib_anal ++ do_qmmm, do_qs, do_tamc, do_test, driver_run, ehrenfest, & ++ electronic_spectra_run, energy_force_run, energy_run, geo_opt_run, & ++ linear_response_run, mol_dyn_run, mon_car_run, none_run, pint_run, & ++ real_time_propagation, vib_anal + USE input_cp2k, ONLY: create_cp2k_input_reading,& + create_cp2k_root_section,& + create_global_section,& +@@ -117,6 +117,7 @@ MODULE cp2k_runs + USE timings, ONLY: timeset,& + timestop + USE vibrational_analysis, ONLY: vb_anal ++ USE driver, ONLY: run_driver + #include "cp_common_uses.h" + + IMPLICIT NONE +@@ -362,6 +363,8 @@ CONTAINS + error=suberror) + CASE (mol_dyn_run) + CALL qs_mol_dyn ( force_env, globenv, error=suberror ) ++ CASE (driver_run) ++ CALL run_driver ( force_env, globenv, error=suberror ) + CASE (geo_opt_run) + CALL cp_geo_opt(force_env,globenv,error=suberror) + CASE (cell_opt_run) +diff -rupN cp2k-2.4.0_ref/src/driver.F cp2k-2.4.0/src/driver.F +--- cp2k-2.4.0_ref/src/driver.F 1970-01-01 01:00:00.000000000 +0100 ++++ cp2k-2.4.0/src/driver.F 2013-08-15 15:43:44.895650242 +0100 +@@ -0,0 +1,216 @@ ++! ***************************************************************************** ++!> \brief Driver mode - To communicate with i-PI Python wrapper ++!> \par History ++!> none ++!> \author Michele Ceriotti 03.2012 ++! ***************************************************************************** ++MODULE driver ++ ++ USE force_env_methods, ONLY: force_env_calc_energy_force ++ USE force_env_types, ONLY: force_env_get,& ++ force_env_type, & ++ force_env_set_cell ++ USE kinds, ONLY: default_path_length,& ++ dp ++ USE input_section_types, ONLY: section_vals_get_subs_vals,& ++ section_vals_type,& ++ section_vals_val_get ++ ++ USE cell_types, ONLY: cell_clone,& ++ cell_create,& ++ cell_release,& ++ cell_type,& ++ compare_cells,& ++ init_cell,& ++ real_to_scaled,& ++ scaled_to_real ++ USE global_types, ONLY: global_environment_type ++ USE f77_interface, ONLY: default_para_env ++ USE cp_external_control, ONLY: external_control ++ USE message_passing, ONLY: mp_bcast, mp_sync ++ USE cp_subsys_types, ONLY: cp_subsys_release,& ++ cp_subsys_type ++ USE iso_c_binding ++ USE virial_types, ONLY: virial_type ++#include "cp_common_uses.h"t ++ ++ IMPLICIT NONE ++ ++ interface ++ subroutine usleep(useconds) bind(C) ++ ! integer(c_int) function usleep(useconds) bind(C) ++ use iso_c_binding ++ implicit none ++ integer(c_int32_t), value :: useconds ++ ! end function ++ end subroutine ++ end interface ++ ++ CONTAINS ++ SUBROUTINE run_driver ( force_env, globenv, error ) ++ TYPE(force_env_type), POINTER :: force_env ++ TYPE(global_environment_type), POINTER :: globenv ++ TYPE(cp_error_type), INTENT(inout) :: error ++ ++ TYPE(section_vals_type), POINTER :: drv_section, motion_section ++ TYPE(virial_type), POINTER :: virial ++ ++ CHARACTER(len=default_path_length) :: drv_hostname, c_hostname ++ INTEGER :: drv_port ++ LOGICAL :: drv_unix ++ ++ !MIK DRIVER ++ ! server address parsing ++ CHARACTER*1024 :: serveraddr, host ++ INTEGER socket, port, inet, nread, readbuffer, slock, swait, uwait ++ ! buffers and temporaries for communication ++ INTEGER, PARAMETER :: MSGLEN=12 ++ LOGICAL :: isinit=.true., hasdata=.false., ionode=.false. ++ CHARACTER*12 :: header ++ CHARACTER*1024 :: parbuffer ++ INTEGER nat ++ REAL *8 :: cellh(3,3), cellih(3,3), vir(3,3), pot ++ REAL*8, ALLOCATABLE :: combuf(:) ++ REAL*8 :: sigma(3,3) ++ ! access cp2k structures ++ TYPE(cp_subsys_type), POINTER :: subsys ++ integer ip, ii, idir ++ TYPE(cell_type), POINTER :: cpcell ++ logical should_stop ++ ionode=(default_para_env%source==default_para_env%mepos) ++ ++ ! reads driver parameters from input ++ motion_section => section_vals_get_subs_vals(force_env%root_section,"MOTION",error=error) ++ drv_section => section_vals_get_subs_vals(motion_section,"DRIVER",error=error) ++ ++ CALL section_vals_val_get(drv_section,"HOST",c_val=drv_hostname,error=error) ++ CALL section_vals_val_get(drv_section,"PORT",i_val=drv_port,error=error) ++ CALL section_vals_val_get(drv_section,"UNIX",l_val=drv_unix,error=error) ++ ++ ++ ! opens the socket ++ socket=0 ++ inet=1 ++ if (ionode) then ++ write(*,*) "@ i-PI DRIVER BEING LOADED" ++ write(*,*) "@ INPUT DATA: ", TRIM(drv_hostname), drv_port, drv_unix ++ c_hostname=TRIM(drv_hostname)//achar(0) ++ CALL open_socket(socket, .not. drv_unix, drv_port, c_hostname) ++ endif ++ ++ !now we have a socket, so we can initialize the CP2K environments. ++ NULLIFY(cpcell) ++ call cell_create(cpcell,error=error) ++ uwait=10000 ! number of MICROseconds to be waited in filesystem lock ++ driver_loop: DO ++ ! do communication on master node only... ++ header = "" ++ ++ ! this syncs the processes, possibly (see sockets.c) without calling MPI_Barrier, ++ ! which is nice as MPI_barrier eats up a lot of CPU for nothing ++ inet=slock(default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ ++ if (ionode) nread=readbuffer(socket, header, MSGLEN) ++ if (ionode) write(0,*) "returned from readbuffer" ++ ++ inet=swait(uwait, default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ ++ call mp_bcast(nread,default_para_env%source, default_para_env%group) ++ if (nread .eq. 0) then ++ if (ionode) write(*,*) " @ DRIVER MODE: Could not read from socket, exiting now." ++ exit ++ endif ++ ++ call mp_bcast(header,default_para_env%source, default_para_env%group) ++ ++ if (ionode) write(*,*) " @ DRIVER MODE: Message from server: ", trim(header) ++ if (trim(header) == "STATUS") then ++ ++ inet=slock(default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ if (ionode) then ! does not need init (well, maybe it should, just to check atom numbers and the like... ) ++ if (hasdata) then ++ call writebuffer(socket,"HAVEDATA ",MSGLEN) ++ else ++ call writebuffer(socket,"READY ",MSGLEN) ++ endif ++ endif ++ inet=swait(uwait,default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ else if (trim(header) == "POSDATA") then ++ if (ionode) then ++ nread=readbuffer(socket, cellh, 9*8) ++ nread=readbuffer(socket, cellih, 9*8) ++ nread=readbuffer(socket, nat, 4) ++ cellh=transpose(cellh) ++ cellih=transpose(cellih) ++ endif ++ call mp_bcast(cellh,default_para_env%source, default_para_env%group) ++ call mp_bcast(cellih,default_para_env%source, default_para_env%group) ++ call mp_bcast(nat,default_para_env%source, default_para_env%group) ++ if (.not.allocated(combuf)) allocate(combuf(3*nat)) ++ if (ionode) nread=readbuffer(socket, combuf, nat*3*8) ++ call mp_bcast(combuf,default_para_env%source, default_para_env%group) ++ ++ CALL force_env_get(force_env,subsys=subsys,error=error) ++ if (nat/=subsys%particles%n_els) WRITE(*,*) " @DRIVER MODE: Uh-oh! Particle number mismatch between i-pi and cp2k input!" ++ ii=0 ++ DO ip=1,subsys%particles%n_els ++ DO idir=1,3 ++ ii=ii+1 ++ subsys%particles%els(ip)%r(idir)=combuf(ii) ++ END DO ++ END DO ++ CALL init_cell(cpcell, hmat=cellh) ++ CALL force_env_set_cell(force_env,cell=cpcell,error=error) ++ ++ CALL force_env_calc_energy_force(force_env,calc_force=.TRUE. ,error=error) ++ ++ if (ionode) write(*,*) " @ DRIVER MODE: Received positions " ++ ++ combuf=0 ++ ii=0 ++ DO ip=1,subsys%particles%n_els ++ DO idir=1,3 ++ ii=ii+1 ++ combuf(ii)=subsys%particles%els(ip)%f(idir) ++ END DO ++ END DO ++ CALL force_env_get(force_env, potential_energy=pot, error=error) ++ CALL force_env_get(force_env,cell=cpcell, virial=virial, error=error) ++ vir = transpose(virial%pv_virial) ++ ++ CALL external_control(should_stop,"DPI",globenv=globenv,error=error) ++ IF (should_stop) EXIT ++ ++ hasdata=.true. ++ else if (trim(header)=="GETFORCE") then ++ if (ionode) write(*,*) " @ DRIVER MODE: Returning v,forces,stress " ++ if (ionode) then ++ call writebuffer(socket,"FORCEREADY ",MSGLEN) ++ call writebuffer(socket,pot,8) ++ call writebuffer(socket,nat,4) ++ call writebuffer(socket,combuf,3*nat*8) ++ call writebuffer(socket,vir,9*8) ++ ++ ! i-pi can also receive an arbitrary string, that will be printed out to the "extra" ++ ! trajectory file. this is useful if you want to return additional information, e.g. ++ ! atomic charges, wannier centres, etc. one must return the number of characters, then ++ ! the string. here we just send back zero characters. ++ nat=0 ++ call writebuffer(socket,nat,4) ! writes out zero for the length of the "extra" field (not implemented yet!) ++ endif ++ hasdata=.false. ++ else ++ if (ionode) write(*,*) " @DRIVER MODE: Socket disconnected, time to exit. " ++ exit ++ endif ++ ENDDO driver_loop ++ ++ END SUBROUTINE run_driver ++ ++END MODULE driver ++ ++ +diff -rupN cp2k-2.4.0_ref/src/input_constants.F cp2k-2.4.0/src/input_constants.F +--- cp2k-2.4.0_ref/src/input_constants.F 2013-08-15 10:46:04.107899205 +0100 ++++ cp2k-2.4.0/src/input_constants.F 2013-08-15 10:53:45.839911028 +0100 +@@ -135,7 +135,8 @@ MODULE input_constants + cell_opt_run=14,& + real_time_propagation=15,& + ehrenfest=16, & +- do_tamc=17 ++ do_tamc=17, & ++ driver_run=18 + + ! Run Types of Atom Code + INTEGER, PARAMETER, PUBLIC :: atom_no_run=1,& +diff -rupN cp2k-2.4.0_ref/src/input_cp2k.F cp2k-2.4.0/src/input_cp2k.F +--- cp2k-2.4.0_ref/src/input_cp2k.F 2013-08-15 10:46:04.131899206 +0100 ++++ cp2k-2.4.0/src/input_cp2k.F 2013-08-15 10:53:45.843911028 +0100 +@@ -422,13 +422,13 @@ CONTAINS + "BAND", "CELL_OPT", "WFN_OPT", "WAVEFUNCTION_OPTIMIZATION",& + "MOLECULAR_DYNAMICS", "GEOMETRY_OPTIMIZATION", "MONTECARLO",& + "ELECTRONIC_SPECTRA", "LINEAR_RESPONSE", "NORMAL_MODES","RT_PROPAGATION",& +- "EHRENFEST_DYN","TAMC" ),& ++ "EHRENFEST_DYN","TAMC","DRIVER" ),& + enum_i_vals=(/ none_run, energy_run, energy_force_run, mol_dyn_run,& + geo_opt_run, mon_car_run, electronic_spectra_run, debug_run,& + bsse_run, linear_response_run, pint_run, vib_anal,do_band,& + cell_opt_run, energy_run, energy_run, mol_dyn_run, geo_opt_run,& + mon_car_run, electronic_spectra_run, linear_response_run,& +- vib_anal,real_time_propagation,ehrenfest,do_tamc/),& ++ vib_anal,real_time_propagation,ehrenfest,do_tamc,driver_run/),& + enum_desc=s2a("Perform no tasks", "Computes energy","Computes energy and forces",& + "Molecular Dynamics","Geometry Optimization","Monte Carlo", "Computes absorption Spectra",& + "Performs a Debug analysis","Basis set superposition error","Linear Response",& +@@ -437,7 +437,7 @@ CONTAINS + "Alias for MC","Alias for SPECTRA","Alias for LR","Alias for VIBRATIONAL_ANALYSIS",& + "Real Time propagation run (fixed ionic positions)",& + "Ehrenfest dynamics (using real time propagation of the wavefunction)",& +- "TAMC"),& ++ "TAMC","i-PI driver mode"),& + supported_feature=.TRUE.,error=error) + CALL section_add_keyword(section,keyword,error=error) + CALL keyword_release(keyword,error=error) +diff -rupN cp2k-2.4.0_ref/src/input_cp2k_motion.F cp2k-2.4.0/src/input_cp2k_motion.F +--- cp2k-2.4.0_ref/src/input_cp2k_motion.F 2013-08-15 10:46:04.095899205 +0100 ++++ cp2k-2.4.0/src/input_cp2k_motion.F 2013-08-15 10:53:45.843911028 +0100 +@@ -103,6 +103,10 @@ CONTAINS + CALL section_add_subsection(section,subsection,error=error) + CALL section_release(subsection,error=error) + ++ CALL create_driver_section(subsection,error=error) ++ CALL section_add_subsection(section,subsection,error=error) ++ CALL section_release(subsection,error=error) ++ + CALL create_fe_section(subsection,error=error) + CALL section_add_subsection(section, subsection, error=error) + CALL section_release(subsection,error=error) +@@ -1713,6 +1717,59 @@ CONTAINS + END SUBROUTINE create_md_section + + ! ***************************************************************************** ++!> \param section will contain the driver section ++!> \param error variable to control error logging, stopping,... ++!> see module cp_error_handling ++!> \author mceriotti ++! ***************************************************************************** ++ SUBROUTINE create_driver_section(section,error) ++ TYPE(section_type), POINTER :: section ++ TYPE(cp_error_type), INTENT(inout) :: error ++ ++ CHARACTER(len=*), PARAMETER :: routineN = 'create_driver_section', & ++ routineP = moduleN//':'//routineN ++ ++ LOGICAL :: failure ++ TYPE(keyword_type), POINTER :: keyword ++ ++ failure=.FALSE. ++ ++ CPPrecondition(.NOT.ASSOCIATED(section),cp_failure_level,routineP,error,failure) ++ IF (.NOT. failure) THEN ++ CALL section_create(section,name="DRIVER",& ++ description="This section defines the parameters needed to run in i-PI driver mode.",& ++ n_keywords=3, n_subsections=0, repeats=.FALSE., required=.TRUE.,& ++ error=error) ++ ++ NULLIFY(keyword) ++ CALL keyword_create(keyword, name="unix",& ++ description="Use a UNIX socket rather than an INET socket.",& ++ usage="unix LOGICAL",& ++ default_l_val=.FALSE., lone_keyword_l_val=.TRUE., error=error) ++ CALL section_add_keyword(section,keyword,error=error) ++ CALL keyword_release(keyword,error=error) ++ ++ CALL keyword_create(keyword, name="port",& ++ description="Port number for the i-PI server.",& ++ usage="port ",& ++ default_i_val=12345, error=error) ++ CALL section_add_keyword(section,keyword,error=error) ++ CALL keyword_release(keyword,error=error) ++ ++ ++ CALL keyword_create(keyword, name="host",& ++ description="Host name for the i-PI server.",& ++ usage="host ",& ++ default_c_val="localhost", error=error) ++ CALL section_add_keyword(section,keyword,error=error) ++ CALL keyword_release(keyword,error=error) ++ ++ END IF ++ ++ END SUBROUTINE create_driver_section ++ ++ ++! ***************************************************************************** + !> \brief Defines AVERAGES section + !> \param error variable to control error logging, stopping,... + !> see module cp_error_handling +diff -rupN cp2k-2.4.0_ref/src/OBJECTDEFS cp2k-2.4.0/src/OBJECTDEFS +--- cp2k-2.4.0_ref/src/OBJECTDEFS 2013-08-15 10:46:04.091899205 +0100 ++++ cp2k-2.4.0/src/OBJECTDEFS 2013-08-15 10:53:45.843911028 +0100 +@@ -180,6 +180,7 @@ OBJECTS_GENERIC =\ + dm_ls_scf.o\ + dm_ls_scf_qs.o\ + dm_ls_scf_types.o\ ++ driver.o\ + efield_utils.o\ + eigenvalueproblems.o\ + eip_environment.o\ +diff -rupN cp2k-2.4.0_ref/src/sockets.c cp2k-2.4.0/src/sockets.c +--- cp2k-2.4.0_ref/src/sockets.c 1970-01-01 01:00:00.000000000 +0100 ++++ cp2k-2.4.0/src/sockets.c 2013-08-15 15:27:36.971625458 +0100 +@@ -0,0 +1,112 @@ ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++ ++ ++//#define FS_WAIT 1 // uncomment to use a file system lock rather than mpi_barrier. ++ ++void error(const char *msg) ++{ perror(msg); } ++ ++void open_socket_(int *psockfd, int* inet, int* port, char* host) // the darn fortran passes an extra argument for the string length. here I just ignore it ++{ ++ int sockfd, portno, n; ++ struct hostent *server; ++ ++ fprintf(stderr, "Connection requested %s, %d, %d\n", host, *port, *inet); ++ struct sockaddr * psock; int ssock; ++ if (*inet!=0) ++ { ++ struct sockaddr_in serv_addr; psock=(struct sockaddr *)&serv_addr; ssock=sizeof(serv_addr); ++ sockfd = socket(AF_INET, SOCK_STREAM, 0); ++ if (sockfd < 0) error("ERROR opening socket"); ++ ++ server = gethostbyname(host); ++ if (server == NULL) ++ { ++ fprintf(stderr, "ERROR, no such host %s \n", host); ++ exit(-1); ++ } ++ ++ bzero((char *) &serv_addr, sizeof(serv_addr)); ++ serv_addr.sin_family = AF_INET; ++ bcopy((char *)server->h_addr, (char *)&serv_addr.sin_addr.s_addr, server->h_length); ++ serv_addr.sin_port = htons(*port); ++ } ++ else ++ { ++ struct sockaddr_un serv_addr; psock=(struct sockaddr *)&serv_addr; ssock=sizeof(serv_addr); ++ sockfd = socket(AF_UNIX, SOCK_STREAM, 0); ++ bzero((char *) &serv_addr, sizeof(serv_addr)); ++ serv_addr.sun_family = AF_UNIX; ++ strcpy(serv_addr.sun_path, "/tmp/ipi_"); ++ strcpy(serv_addr.sun_path+9, host); ++ } ++ ++ if (connect(sockfd, psock, ssock) < 0) error("ERROR connecting"); ++ ++ *psockfd=sockfd; ++} ++ ++void writebuffer_(int *psockfd, char *data, int* plen) ++{ ++ int n; ++ int sockfd=*psockfd; ++ int len=*plen; ++ ++ n = write(sockfd,data,len); ++ if (n < 0) error("ERROR writing to socket\n"); ++} ++ ++ ++int readbuffer_(int *psockfd, char *data, int* plen) ++{ ++ int n, nr; ++ int sockfd=*psockfd; ++ int len=*plen; ++ ++ n = nr = read(sockfd,data,len); ++ ++ while (nr>0 && n Date: Thu, 7 Aug 2014 14:37:19 +0300 Subject: [PATCH 0043/2133] Adding modified configs and patch file --- .../c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 20 +++++++++---------- .../c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb | 18 ++++++++--------- .../easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch | 1 + 3 files changed, 20 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index 8c26b632c2..567f926654 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -4,9 +4,9 @@ versionsuffix = '-ipi' homepage = 'http://www.cp2k.org' description = """CP2K is a freely available (GPL) program, written in Fortran 95, - to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. - It provides a general framework for different methods such as e.g. density functional theory (DFT) - using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ + to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. + It provides a general framework for different methods such as e.g. density functional theory (DFT) + using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -15,15 +15,15 @@ source_urls = ['http://sourceforge.net/projects/cp2k/files/'] sources = ['%s-%s.tar.bz2' % (name.lower(), version)] patches = [ - 'cp2k-2.4.0_ipi.patch', - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch' - ] + 'cp2k-2.4.0_ipi.patch', + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' + ] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') + ] dependencies = [('Libint', '1.1.4')] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb index 9389d88e83..d44d72b4be 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb @@ -3,9 +3,9 @@ version = '2.4.0' homepage = 'http://www.cp2k.org' description = """CP2K is a freely available (GPL) program, written in Fortran 95, - to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. - It provides a general framework for different methods such as e.g. density functional theory (DFT) - using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ + to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. + It provides a general framework for different methods such as e.g. density functional theory (DFT) + using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -14,14 +14,14 @@ source_urls = ['http://sourceforge.net/projects/cp2k/files/'] sources = ['%s-%s.tar.bz2' % (name.lower(), version)] patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch' - ] + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' + ] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') + ] dependencies = [('Libint', '1.1.4')] diff --git a/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch b/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch index ba7ceaf26e..b8115df6c5 100644 --- a/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch +++ b/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch @@ -1,3 +1,4 @@ +#This patch makes CP2K source code compatible with i-pi diff -rupN cp2k-2.4.0_ref/makefiles/Makefile cp2k-2.4.0/makefiles/Makefile --- cp2k-2.4.0_ref/makefiles/Makefile 2013-08-15 10:46:04.535899216 +0100 +++ cp2k-2.4.0/makefiles/Makefile 2013-08-15 10:53:45.827911028 +0100 -- GitLab From 6d5ab1a5269f91edace9031576fd66789f3ba1bb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Sep 2014 13:10:39 +0200 Subject: [PATCH 0044/2133] add easyconfigs for pplacer and OCaml deps --- .../batteries-2.2-ictce-5.5.0-OCaml-4.01.0.eb | 32 ++++++++++++++ .../CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb | 36 +++++++++++++++ .../csv/csv-1.3.3-ictce-5.5.0-OCaml-4.01.0.eb | 35 +++++++++++++++ .../findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb | 29 ++++++++++++ ...SL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb | 35 +++++++++++++++ ...L-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb | 32 ++++++++++++++ ...L-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb | 31 +++++++++++++ .../o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 3 ++ .../o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 44 +++++++++++++++++++ .../o/OCaml/OCaml-4.01.0_icc-fixes.patch | 11 +++++ ...er-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb | 41 +++++++++++++++++ .../s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb | 35 +++++++++++++++ ...e3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb | 32 ++++++++++++++ .../t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb | 19 ++++++++ .../Xmlm-1.2.0-ictce-5.5.0-OCaml-4.01.0.eb | 20 +++++++++ 15 files changed, 435 insertions(+) create mode 100644 easybuild/easyconfigs/b/batteries/batteries-2.2-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/c/csv/csv-1.3.3-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch create mode 100644 easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/x/Xmlm/Xmlm-1.2.0-ictce-5.5.0-OCaml-4.01.0.eb diff --git a/easybuild/easyconfigs/b/batteries/batteries-2.2-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/b/batteries/batteries-2.2-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..42ce7ca6fb --- /dev/null +++ b/easybuild/easyconfigs/b/batteries/batteries-2.2-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,32 @@ +name = 'batteries' +version = '2.2' + +homepage = 'http://batteries.forge.ocamlcore.org/' +description = """OCaml Batteries included (or simply "Batteries") is a community-driven effort to standardize on an + consistent, documented, and comprehensive development platform for the OCaml programming language.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://forge.ocamlcore.org/frs/download.php/1363/'] +sources = [SOURCE_TAR_GZ] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) + +builddependencies = [('findlib', '1.5.2', versionsuffix)] +dependencies = [(ocaml, ocamlver)] + +skipsteps = ['configure'] + +buildopts = 'all' +preinstallopts = "mkdir -p %(installdir)s/site-lib && OCAMLFIND_DESTDIR=%(installdir)s/site-lib" + +modextrapaths = {'OCAMLPATH': 'site-lib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['site-lib/batteries'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..29ce049ecc --- /dev/null +++ b/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,36 @@ +name = 'CamlZIP' +version = '1.05' + +homepage = 'https://forge.ocamlcore.org/projects/camlzip/' +description = """This OCaml library provides easy access to compressed files in ZIP + and GZIP format, as well as to Java JAR files. It provides functions + for reading from and writing to compressed files in these formats.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://forge.ocamlcore.org/frs/download.php/1037/'] +sources = [SOURCE_TAR_GZ] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) + +builddependencies = [('findlib', '1.5.2', versionsuffix)] +dependencies = [ + (ocaml, ocamlver), + ('zlib', '1.2.7'), +] + +skipsteps = ['configure', 'install'] + +prebuildopts = "mkdir -p %(installdir)s/site-lib && " +buildopts = 'all && make allopt && OCAMLFIND_DESTDIR=%(installdir)s/site-lib make install-findlib' + +modextrapaths = {'OCAMLPATH': 'site-lib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['site-lib/zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/csv/csv-1.3.3-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/c/csv/csv-1.3.3-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..4b85bf3dd4 --- /dev/null +++ b/easybuild/easyconfigs/c/csv/csv-1.3.3-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,35 @@ +name = 'csv' +version = '1.3.3' + +homepage = 'https://forge.ocamlcore.org/projects/csv/' +description = """This is a pure OCaml library to read and write CSV files, including all extensions used by Excel -- + e.g., quotes, newlines, 8 bit characters in fields, "0 etc.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://forge.ocamlcore.org/frs/download.php/1376/'] +sources = [SOURCE_TAR_GZ] + +patches = ['csv-%(version)s_prefix.patch'] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) + +builddependencies = [('findlib', '1.5.2', versionsuffix)] +dependencies = [(ocaml, ocamlver)] + +skipsteps = ['configure', 'build'] + +preinstallopts = "mkdir -p %(installdir)s/site-lib && OCAMLFIND_DESTDIR=%(installdir)s/site-lib PREFIX=%(installdir)s " + +parallel = 1 + +modextrapaths = {'OCAMLPATH': 'site-lib'} + +sanity_check_paths = { + 'files': ['bin/csvtool'], + 'dirs': ['site-lib/csv'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..d5d33d89fc --- /dev/null +++ b/easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,29 @@ +name = 'findlib' +version = '1.5.2' + +homepage = 'http://projects.camlcity.org/projects/findlib.html' +description = """Findlib is a library manager for Objective Caml. It provides a convention how to store libraries, + and a file format ("META") to describe the properties of libraries. There is also a tool (ocamlfind) for interpreting + the META files, so that it is very easy to use libraries in programs and scripts.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://download.camlcity.org/download/'] +sources = [SOURCE_TAR_GZ] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) +dependencies = [(ocaml, ocamlver)] + +skipsteps = ['configure'] + +premakeopts = "./configure -bindir %(installdir)s/bin && " +preinstallopts = "mkdir %(installdir)s/site-lib && PATH=%(installdir)s/bin:$PATH" + +sanity_check_paths = { + 'files': ['bin/ocamlfind', 'bin/safe_camlp4'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..3ea3a84e5e --- /dev/null +++ b/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,35 @@ +name = 'GSL-OCaml' +version = '0.6.3' + +homepage = 'http://mmottl.github.io/gsl-ocaml/' +description = "OCaml bindings to the GSL (GNU Scientific Library)." + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://github.com/mmottl/gsl-ocaml/archive/'] +sources = ['v%(version)s.tar.gz'] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) + +builddependencies = [('findlib', '1.5.2', versionsuffix)] +dependencies = [ + (ocaml, ocamlver), + ('GSL', '1.16'), +] + +skipsteps = ['configure'] +prebuildopts = "OCAML_BACKEND=gcc" +preinstallopts = "mkdir -p %(installdir)s/site-lib && OCAML_BACKEND=gcc OCAMLFIND_DESTDIR=%(installdir)s/site-lib" + +parallel = 1 + +modextrapaths = {'OCAMLPATH': 'site-lib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ["site-lib/gsl"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..8ebdaa8e3c --- /dev/null +++ b/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,32 @@ +name = 'GSL-OCaml' +version = '1.17.2' + +homepage = 'http://mmottl.github.io/gsl-ocaml/' +description = "OCaml bindings to the GSL (GNU Scientific Library)." + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://github.com/mmottl/gsl-ocaml/archive/'] +sources = ['v%(version)s.tar.gz'] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) + +builddependencies = [('findlib', '1.5.2', versionsuffix)] +dependencies = [ + (ocaml, ocamlver), + ('GSL', '1.16'), +] + +configopts = "--destdir=%(installdir)s" +preinstallopts = "mkdir -p %(installdir)s/site-lib && OCAMLFIND_DESTDIR=%(installdir)s/site-lib" + +modextrapaths = {'OCAMLPATH': 'site-lib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ["site-lib/gsl"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..87454947cb --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,31 @@ +name = 'MCL' +version = '12-068oasis4' + +homepage = 'https://github.com/fhcrc/mcl' +description = """Graph clustering by flow simulation.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fhcrc/mcl/archive/'] +sources = ['%(version)s.tar.gz'] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) +builddependencies = [('findlib', '1.5.2', versionsuffix)] +dependencies = [(ocaml, ocamlver)] + +preconfigopts = "ocaml setup.ml -configure --prefix %(installdir)s && " +buildopts = "&& ocaml setup.ml -build" +preinstallopts = "mkdir -p %(installdir)s/site-lib &&" +installopts = "&& OCAMLFIND_DESTDIR=%(installdir)s/site-lib ocaml setup.ml -install" + +modextrapaths = {'OCAMLPATH': 'site-lib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb index ce145c9209..00d6056acc 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -26,11 +26,14 @@ builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] prefix_opt = "-prefix " +configopts = '-cc "$CC $CFLAGS"' buildopts = "world.opt" # parallel build tends to break parallel = 1 +modextrapaths = {'CAML_LD_LIBRARY_PATH': 'lib'} + sanity_check_paths = { 'files': ["bin/ocaml", "bin/ocamlc"], 'dirs': [] diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb new file mode 100644 index 0000000000..1c91aeafaa --- /dev/null +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +name = "OCaml" +version = "4.01.0" + +homepage = 'http://ocaml.org/' +description = """OCaml is a general purpose industrial-strength programming language + with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria + it benefits from one of the most advanced type systems and supports functional, + imperative and object-oriented styles of programming.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +sources = ['ocaml-%(version)s.tar.gz'] +sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) +source_urls = ['http://caml.inria.fr/pub/distrib/%s' % sourcedir] + +patches = ['OCaml-%(version)s_icc-fixes.patch'] + +builddependencies = [('Autoconf', '2.69')] +dependencies = [('ncurses', '5.9')] + +prefix_opt = "-prefix " +configopts = '-cc "$CC $CFLAGS"' +buildopts = "world.opt" + +# parallel build tends to break +parallel = 1 + +modextrapaths = {'CAML_LD_LIBRARY_PATH': 'lib'} + +sanity_check_paths = { + 'files': ["bin/ocaml", "bin/ocamlc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch new file mode 100644 index 0000000000..595505634a --- /dev/null +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch @@ -0,0 +1,11 @@ +--- ocaml-4.01.0/configure.orig 2014-08-19 12:26:23.008974288 +0200 ++++ ocaml-4.01.0/configure 2014-08-19 12:27:15.800298562 +0200 +@@ -1015,7 +1015,7 @@ + fi + + has_select=no +-if sh ./hasgot select && \ ++if cc="$cc -wd165" sh ./hasgot select && \ + sh ./hasgot -i sys/types.h $select_include -t fd_set ; then + echo "select() found." + echo "#define HAS_SELECT" >> s.h diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..48464d06a1 --- /dev/null +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'pplacer' +version = '1.1.alpha16' + +homepage = 'http://matsen.fhcrc.org/pplacer/' +description = """Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic + likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give + useful information about uncertainty, and to offer advanced visualization and downstream analysis.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://github.com/matsen/pplacer/archive/'] +sources = ['v%(version)s.tar.gz'] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) +builddependencies = [('findlib', '1.5.2', versionsuffix)] +dependencies = [ + (ocaml, ocamlver), + ('batteries', '2.2', versionsuffix), + ('CamlZIP', '1.05', versionsuffix), + ('GSL-OCaml', '0.6.3', versionsuffix), + ('csv', '1.3.3', versionsuffix), + ('SQLite3-OCaml', '2.0.6', versionsuffix), + ('Xmlm', '1.2.0', versionsuffix), + ('MCL', '12-068oasis4', versionsuffix), +] + +prebuildopts = "echo 'let version = \"v1.1.alpha16-9-g78ea126\"\n' > common_src/version.ml && " +parallel = 1 + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/guppy', 'bin/pplacer', 'bin/rppr'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb new file mode 100644 index 0000000000..ab3d1ec5e2 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.6' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..d08ea78903 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,32 @@ +name = 'SQLite3-OCaml' +version = '2.0.6' + +homepage = 'https://github.com/mmottl/sqlite3-ocaml' +description = "OCaml bindings to the SQLite3 database.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://github.com/mmottl/sqlite3-ocaml/archive/'] +sources = ['v%(version)s.tar.gz'] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) + +builddependencies = [('findlib', '1.5.2', versionsuffix)] +dependencies = [ + (ocaml, ocamlver), + ('SQLite', '3.8.6'), +] + +configopts = "--destdir=%(installdir)s" +preinstallopts = "mkdir -p %(installdir)s/site-lib && OCAMLFIND_DESTDIR=%(installdir)s/site-lib" + +modextrapaths = {'OCAMLPATH': 'site-lib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ["site-lib/sqlite3"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb new file mode 100644 index 0000000000..19a137231e --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/Xmlm/Xmlm-1.2.0-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/x/Xmlm/Xmlm-1.2.0-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..7c572b469c --- /dev/null +++ b/easybuild/easyconfigs/x/Xmlm/Xmlm-1.2.0-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,20 @@ +name = 'Xmlm' +version = '1.2.0' + +homepage = 'http://erratique.ch/software/xmlm' +description = """Xmlm is an OCaml streaming codec to decode and encode the XML data format. It can process XML + documents without a complete in-memory representation of the data.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://erratique.ch/software/xmlm/releases'] +sources = ['%(namelower)s-%(version)s.tbz'] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) + +builddependencies = [('findlib', '1.5.2', versionsuffix)] +dependencies = [(ocaml, ocamlver)] + +moduleclass = 'lib' -- GitLab From fc5be4489ad03f74f3d96f64582bb266f8d3f495 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Sep 2014 09:08:06 +0200 Subject: [PATCH 0045/2133] ad missing patch file for csv --- easybuild/easyconfigs/c/csv/csv-1.3.3_prefix.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/c/csv/csv-1.3.3_prefix.patch diff --git a/easybuild/easyconfigs/c/csv/csv-1.3.3_prefix.patch b/easybuild/easyconfigs/c/csv/csv-1.3.3_prefix.patch new file mode 100644 index 0000000000..d76bf10483 --- /dev/null +++ b/easybuild/easyconfigs/c/csv/csv-1.3.3_prefix.patch @@ -0,0 +1,11 @@ +--- csv-1.3.3/Makefile.orig 2014-08-25 14:32:19.026905764 +0200 ++++ csv-1.3.3/Makefile 2014-08-25 14:32:33.607257131 +0200 +@@ -16,7 +16,7 @@ + ocaml setup.ml -build + + configure: setup.ml +- ocaml $< -configure --enable-tests ++ ocaml $< -configure --enable-tests --prefix $(PREFIX) + + setup.ml: _oasis + oasis setup -setup-update dynamic -- GitLab From 42760da1a91bed74172b2bb0d725b18d5ad9288c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Sep 2014 09:34:26 +0200 Subject: [PATCH 0046/2133] add zlib dependency for pplacer --- .../p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb index 48464d06a1..935d5edab7 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb @@ -18,6 +18,7 @@ ocamlver = '4.01.0' versionsuffix = '-%s-%s' % (ocaml, ocamlver) builddependencies = [('findlib', '1.5.2', versionsuffix)] dependencies = [ + ('zlib', '1.2.7'), (ocaml, ocamlver), ('batteries', '2.2', versionsuffix), ('CamlZIP', '1.05', versionsuffix), -- GitLab From 9c13932ce72143051fe757a4700d7b19527302e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Sep 2014 09:48:43 +0200 Subject: [PATCH 0047/2133] Revert "add zlib dependency for pplacer" This reverts commit 42760da1a91bed74172b2bb0d725b18d5ad9288c. --- .../p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb index 935d5edab7..48464d06a1 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb @@ -18,7 +18,6 @@ ocamlver = '4.01.0' versionsuffix = '-%s-%s' % (ocaml, ocamlver) builddependencies = [('findlib', '1.5.2', versionsuffix)] dependencies = [ - ('zlib', '1.2.7'), (ocaml, ocamlver), ('batteries', '2.2', versionsuffix), ('CamlZIP', '1.05', versionsuffix), -- GitLab From 81722803bfb713021130fbb7760b51de6e738b86 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Sep 2014 11:27:54 +0200 Subject: [PATCH 0048/2133] fix location of findlib.conf --- .../f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb index d5d33d89fc..e9f92f5302 100644 --- a/easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb @@ -18,11 +18,13 @@ dependencies = [(ocaml, ocamlver)] skipsteps = ['configure'] -premakeopts = "./configure -bindir %(installdir)s/bin && " +premakeopts = "./configure -bindir %(installdir)s/bin -config %(installdir)s/findlib.conf && " preinstallopts = "mkdir %(installdir)s/site-lib && PATH=%(installdir)s/bin:$PATH" +modextravars = {'OCAMLFIND_CONF': '%(installdir)s/findlib.conf'} + sanity_check_paths = { - 'files': ['bin/ocamlfind', 'bin/safe_camlp4'], + 'files': ['bin/ocamlfind', 'bin/safe_camlp4', 'findlib.conf'], 'dirs': [], } -- GitLab From 9f73f3d64912e83a53eb5bde17eea4d9c3239c3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 16:48:31 +0200 Subject: [PATCH 0049/2133] get rid of unnecessary patch for OCaml with ictce --- .../easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 2 -- .../easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch | 11 ----------- 2 files changed, 13 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb index 1c91aeafaa..6ad336f36b 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -22,8 +22,6 @@ sources = ['ocaml-%(version)s.tar.gz'] sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) source_urls = ['http://caml.inria.fr/pub/distrib/%s' % sourcedir] -patches = ['OCaml-%(version)s_icc-fixes.patch'] - builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch deleted file mode 100644 index 595505634a..0000000000 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ocaml-4.01.0/configure.orig 2014-08-19 12:26:23.008974288 +0200 -+++ ocaml-4.01.0/configure 2014-08-19 12:27:15.800298562 +0200 -@@ -1015,7 +1015,7 @@ - fi - - has_select=no --if sh ./hasgot select && \ -+if cc="$cc -wd165" sh ./hasgot select && \ - sh ./hasgot -i sys/types.h $select_include -t fd_set ; then - echo "select() found." - echo "#define HAS_SELECT" >> s.h -- GitLab From 53128ed575b3c95c43ca2a811bd65edd31d0482a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 17:21:57 +0200 Subject: [PATCH 0050/2133] Revert "get rid of unnecessary patch for OCaml with ictce" This reverts commit 9f73f3d64912e83a53eb5bde17eea4d9c3239c3a. --- .../easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 2 ++ .../easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch | 11 +++++++++++ 2 files changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb index 6ad336f36b..1c91aeafaa 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -22,6 +22,8 @@ sources = ['ocaml-%(version)s.tar.gz'] sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) source_urls = ['http://caml.inria.fr/pub/distrib/%s' % sourcedir] +patches = ['OCaml-%(version)s_icc-fixes.patch'] + builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch new file mode 100644 index 0000000000..595505634a --- /dev/null +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch @@ -0,0 +1,11 @@ +--- ocaml-4.01.0/configure.orig 2014-08-19 12:26:23.008974288 +0200 ++++ ocaml-4.01.0/configure 2014-08-19 12:27:15.800298562 +0200 +@@ -1015,7 +1015,7 @@ + fi + + has_select=no +-if sh ./hasgot select && \ ++if cc="$cc -wd165" sh ./hasgot select && \ + sh ./hasgot -i sys/types.h $select_include -t fd_set ; then + echo "select() found." + echo "#define HAS_SELECT" >> s.h -- GitLab From 8b85e2f64d3e0a3ceed8e38ce49f973f50b7219e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Dec 2014 19:34:11 +0100 Subject: [PATCH 0051/2133] add easyconfig for ROOT v5.30.06 with goolf toolchain --- ...libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 27 ++++++++++++++ .../r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb | 35 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb create mode 100755 easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..d68ae2eaee --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.5' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb new file mode 100755 index 0000000000..9a78780f34 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +name = 'ROOT' +version = 'v5.30.06' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] + +python = 'Python' +pyver = '2.7.5' + +dependencies = [ + ('GSL', '1.16'), + ('libxml2', '2.9.1', '-%s-%s' % (python, pyver)), + (python, pyver), +] + +# architecture +arch = 'linuxx8664gcc' + +# disable features +configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_DIR' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' + +moduleclass = 'data' -- GitLab From 29f76ad33050d5b831f116f64b79eb4dab79ef87 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 12 Jan 2015 13:52:07 +1300 Subject: [PATCH 0052/2133] New easyconfigs for GROMOS++ and gromosXX --- .../g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb | 30 +++++++++++++++++++ .../g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..1da3cc48d3 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'GROMOS++' +version = '1.0' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = ['%(namelower)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +sanity_check_paths = { + 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", + "lib/gromosplugin.a", "lib/libgromos.a"], + 'dirs': ["include", "share/gromos++"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..9b0643940a --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = ['%(name)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + #'files': ["bin/md", "bin/md_mpi"], + 'dirs': ['include/md++'], +} + +moduleclass = 'bio' -- GitLab From 744b58f10247ff8f494f6baa568b945b1eade69b Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 12 Jan 2015 16:37:06 +1300 Subject: [PATCH 0053/2133] Added support for a Linux group for restricting to licensed users --- easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb index 1da3cc48d3..557a5258d6 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb @@ -27,4 +27,5 @@ sanity_check_paths = { 'dirs': ["include", "share/gromos++"], } +group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb index 9b0643940a..428ee43e0b 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb @@ -27,4 +27,5 @@ sanity_check_paths = { 'dirs': ['include/md++'], } +group = 'gromos' moduleclass = 'bio' -- GitLab From bd538b2ddcdae6590ec32ba6297f94009b130ea2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 14 Jan 2015 14:09:44 +1300 Subject: [PATCH 0054/2133] Improved version numbering and OpenMP and MPI variants of GROMOS --- .../GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb | 36 +++++++++++++++++++ ... GROMOS++-1.0.2211-goolf-1.5.14-serial.eb} | 8 +++-- .../gromosXX-1.0.1737-goolf-1.5.14-mpi.eb | 36 +++++++++++++++++++ .../gromosXX-1.0.1737-goolf-1.5.14-openmp.eb | 36 +++++++++++++++++++ ... gromosXX-1.0.1737-goolf-1.5.14-serial.eb} | 8 +++-- 5 files changed, 120 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb rename easybuild/easyconfigs/g/GROMOS++/{GROMOS++-1.0-goolf-1.5.14.eb => GROMOS++-1.0.2211-goolf-1.5.14-serial.eb} (84%) create mode 100644 easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb create mode 100644 easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb rename easybuild/easyconfigs/g/gromosXX/{gromosXX-1.0-goolf-1.5.14.eb => gromosXX-1.0.1737-goolf-1.5.14-serial.eb} (83%) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb new file mode 100644 index 0000000000..f8faf80988 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'GROMOS++' +version = '1.0.2211' +versionsuffix = '-openmp' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': True, 'usempi': False} + +sources = ['%(namelower)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", + "lib/gromosplugin.a", "lib/libgromos.a"], + 'dirs': ["include", "share/gromos++"], +} + +group = 'gromos' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb similarity index 84% rename from easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb rename to easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb index 557a5258d6..31c8c80c13 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -6,7 +6,8 @@ easyblock = 'ConfigureMake' name = 'GROMOS++' -version = '1.0' +version = '1.0.2211' +versionsuffix = '-serial' homepage = 'http://www.gromos.net/' description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation @@ -16,11 +17,14 @@ Netherlands, and since then at the ETH, the Swiss Federal Institute of Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': False} -sources = ['%(namelower)s.tar.bz2'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] dependencies = [('GSL', '1.16')] +preconfigopts = './Config.sh &&' + sanity_check_paths = { 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", "lib/gromosplugin.a", "lib/libgromos.a"], diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb new file mode 100644 index 0000000000..1ca0239cec --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0.1737' +versionsuffix = '-mpi' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': True} + +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-mpi' + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + #'files': ["bin/md", "bin/md_mpi"], + 'dirs': ['include/md++'], +} + +group = 'gromos' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb new file mode 100644 index 0000000000..0845c8a493 --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0.1737' +versionsuffix = '-openmp' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': True, 'usempi': False} + +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + #'files': ["bin/md", "bin/md_mpi"], + 'dirs': ['include/md++'], +} + +group = 'gromos' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb similarity index 83% rename from easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb rename to easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb index 428ee43e0b..d48f6a0b1f 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -6,7 +6,8 @@ easyblock = 'ConfigureMake' name = 'gromosXX' -version = '1.0' +version = '1.0.1737' +versionsuffix = '-serial' homepage = 'http://www.gromos.net/' description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation @@ -16,11 +17,14 @@ Netherlands, and since then at the ETH, the Swiss Federal Institute of Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': False} -sources = ['%(name)s.tar.bz2'] +sources = ['%(name)s-%(version)s.tar.bz2'] dependencies = [('GSL', '1.16')] +preconfigopts = './Config.sh &&' + sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], #'files': ["bin/md", "bin/md_mpi"], -- GitLab From 750e44a9c09fafb64469a8e5a02000ded699cf85 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jan 2015 14:09:58 +1300 Subject: [PATCH 0055/2133] Updates as per comments --- .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb | 4 ++-- .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb | 4 ++-- .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb | 1 - 5 files changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb index f8faf80988..b0cbb9b351 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -19,7 +19,7 @@ Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'openmp': True, 'usempi': False} -sources = ['%(namelower)s-%(version)s.tar.bz2'] +sources = [SOURCELOWER_TAR_BZ2] dependencies = [('GSL', '1.16')] @@ -28,7 +28,7 @@ configopts = '--enable-openmp' sanity_check_paths = { 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", - "lib/gromosplugin.a", "lib/libgromos.a"], + "lib/gromosplugin.a", "lib/libgromos.a"], 'dirs': ["include", "share/gromos++"], } diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb index 31c8c80c13..9d4e1b8c63 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -19,7 +19,7 @@ Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'openmp': False, 'usempi': False} -sources = ['%(namelower)s-%(version)s.tar.bz2'] +sources = [SOURCELOWER_TAR_BZ2] dependencies = [('GSL', '1.16')] @@ -27,7 +27,7 @@ preconfigopts = './Config.sh &&' sanity_check_paths = { 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", - "lib/gromosplugin.a", "lib/libgromos.a"], + "lib/gromosplugin.a", "lib/libgromos.a"], 'dirs': ["include", "share/gromos++"], } diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb index 1ca0239cec..323c0f50ec 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -28,7 +28,6 @@ configopts = '--enable-mpi' sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], - #'files': ["bin/md", "bin/md_mpi"], 'dirs': ['include/md++'], } diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb index 0845c8a493..b47b02b824 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -28,7 +28,6 @@ configopts = '--enable-openmp' sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], - #'files': ["bin/md", "bin/md_mpi"], 'dirs': ['include/md++'], } diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb index d48f6a0b1f..d0b7ca517a 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -27,7 +27,6 @@ preconfigopts = './Config.sh &&' sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], - #'files': ["bin/md", "bin/md_mpi"], 'dirs': ['include/md++'], } -- GitLab From 0f4d7484b84e888d4fd319d6fbf39bcd07a653e1 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 28 Jan 2015 10:21:21 +0100 Subject: [PATCH 0056/2133] mview easyconfigs added --- .../MView-1.49-goolf-1.4.10-Perl-5.16.3.eb | 30 ++++++++++++++++++ .../MView-1.57-goolf-1.4.10-Perl-5.16.3.eb | 31 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb create mode 100644 easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..1d8d750921 --- /dev/null +++ b/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'MView' +version = '1.49' +versionsuffix = '-Perl-5.16.3' + +homepage = 'http://sourceforge.net/projects/bio-mview/' +description = """ MView reformats the results of a sequence database search or a + multiple alignment, optionally adding HTML markup.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/mview"], + 'dirs': ["lib"], +} + +modextravars = { + 'PERL5LIB': '$root/lib' + } + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..f5fb2d82e3 --- /dev/null +++ b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'MView' +version = "1.57" +versionsuffix = '-Perl-5.16.3' + +homepage = 'http://sourceforge.net/projects/bio-mview/' +description = """ MView reformats the results of a sequence database search or a + multiple alignment, optionally adding HTML markup.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/mview"], + 'dirs': ["lib"], +} + +modextravars = { + 'PERL5LIB': '$root/lib' + } + +moduleclass = 'bio' + -- GitLab From 7c4969f9e8a9a13dc6ab37cfca17d734de6024bb Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 28 Jan 2015 10:39:21 +0100 Subject: [PATCH 0057/2133] added missing Perl deps --- .../easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb | 2 ++ .../easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb index 1d8d750921..3e83426be9 100644 --- a/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] sources = [SOURCELOWER_TAR_GZ] +dependencies = [('Perl', '5.16.3')] + sanity_check_paths = { 'files': ["bin/mview"], 'dirs': ["lib"], diff --git a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb index f5fb2d82e3..0d93edc825 100644 --- a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] sources = [SOURCELOWER_TAR_GZ] +dependencies = [('Perl', '5.16.3')] + sanity_check_paths = { 'files': ["bin/mview"], 'dirs': ["lib"], -- GitLab From 873923b04ca2661d61be0993d2088332e2757f9f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 29 Jan 2015 10:51:00 +1300 Subject: [PATCH 0058/2133] Removed group directive per request from user @boegel --- .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb | 1 - .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb | 1 - .../easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb | 1 - 5 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb index b0cbb9b351..cd7029cdae 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -32,5 +32,4 @@ sanity_check_paths = { 'dirs': ["include", "share/gromos++"], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb index 9d4e1b8c63..2b1345c99b 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -31,5 +31,4 @@ sanity_check_paths = { 'dirs': ["include", "share/gromos++"], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb index 323c0f50ec..3020c00623 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -31,5 +31,4 @@ sanity_check_paths = { 'dirs': ['include/md++'], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb index b47b02b824..8cae45f338 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -31,5 +31,4 @@ sanity_check_paths = { 'dirs': ['include/md++'], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb index d0b7ca517a..075812f642 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -30,5 +30,4 @@ sanity_check_paths = { 'dirs': ['include/md++'], } -group = 'gromos' moduleclass = 'bio' -- GitLab From e87b43b89df58f55569c014a4852f7bbbb216d58 Mon Sep 17 00:00:00 2001 From: "Dominik L. Borkowski" Date: Mon, 23 Feb 2015 12:04:39 -0500 Subject: [PATCH 0059/2133] added libopenssl-devel to the list of acceptable OS dependencies for openssl devel A lot of existing easyconfigs used 'openssl-devel' and 'libssl-dev' under osdependencies to indicate the need to have development files for openssl. SLES 11 uses 'libopenssl-devel', so we add that as a third option. --- easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb | 2 +- .../easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb | 2 +- .../p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 2 +- .../p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb | 2 +- .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb | 2 +- 45 files changed, 45 insertions(+), 45 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb index 3b257ff22b..90466f7075 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] #dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb index 39773d3294..b14d94df84 100644 --- a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] dependencies = [ ('libevent', '2.0.21'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index 279bdd8c99..a0f450f70f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index f9f346f7bc..53b6064132 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index 66cb466a25..ed1944c3f2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index 781b45ed3f..d9118da106 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -21,6 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index c8bc196270..da9bd1c2a4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -21,6 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index 79512f826c..ae0e9d0e08 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index f949db90c2..6d976f526f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 7a975980fe..1774b27146 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index c0a121ef71..c9112a0795 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -78,6 +78,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index 2e5b1c3cc2..b580f1c96b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index 3cc5940708..bc9c8df4f8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -78,6 +78,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index f8a7666f78..afc1ee4239 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 262c91f061..9bfd01b319 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index c22d902c71..f057b47357 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index 4e3149189f..a1b17c0b65 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 0f28917f5c..d89dd01c51 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 678cacbe75..fbdb6f6118 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 11ffa16a41..ad5cb03e20 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index 97c9a23292..5a7796659d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 79e4bbcd67..db0b052ea7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -78,6 +78,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 1ccc5c12ca..090ba3d58e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -78,6 +78,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index 3a167c9f92..0b5a6610e5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index 1ad8450e3d..773802dfae 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -84,6 +84,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index df55e62340..cc6f960e75 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -78,6 +78,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index 968045a415..f08dc7f7bf 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index 464a9c0441..ad0d7286f0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -83,6 +83,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index 54b6d1a65f..f576d9f1dd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -81,6 +81,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index d513f80632..b32a7b9444 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -81,6 +81,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index 4a7605ab2c..0c3b0edee6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -85,6 +85,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index 44158cd159..df97eca668 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index 6a17a47968..74a0ab5c69 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -83,6 +83,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index af561484ae..bc1bc26e4c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -83,6 +83,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 6594db177f..721a9d7c3b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -87,6 +87,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index dd7a8d8f1e..2f65dc0b7a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -92,6 +92,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 64f8e11174..3cd030d43c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -89,6 +89,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index 236304395e..d1ff8b9e48 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -64,6 +64,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index fbb78f9e84..11d4899222 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -64,6 +64,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index c6cedb61ef..913671b48a 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -66,6 +66,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 38875e2a4f..252ce755ac 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -64,6 +64,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index 73c3832a10..9c7858f00d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -42,6 +42,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb index 8cd8056d73..56769b0734 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb @@ -44,6 +44,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index 27461c4521..de3765e4a6 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -44,6 +44,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index df2e52ef20..223b5aa45c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -91,6 +91,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' -- GitLab From a00e0f8eaca41d380e590bec6d8c5ec3cfc0fc96 Mon Sep 17 00:00:00 2001 From: "Dominik L. Borkowski" Date: Mon, 23 Feb 2015 21:29:19 -0500 Subject: [PATCH 0060/2133] Revert "added libopenssl-devel to the list of acceptable OS dependencies for openssl devel" This reverts commit e87b43b89df58f55569c014a4852f7bbbb216d58. --- easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb | 2 +- .../easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb | 2 +- .../p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 2 +- .../p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb | 2 +- .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb | 2 +- 45 files changed, 45 insertions(+), 45 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb index 90466f7075..3b257ff22b 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] #dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] sanity_check_paths = { 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb index b14d94df84..39773d3294 100644 --- a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] dependencies = [ ('libevent', '2.0.21'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index a0f450f70f..279bdd8c99 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index 53b6064132..f9f346f7bc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index ed1944c3f2..66cb466a25 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index d9118da106..781b45ed3f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -21,6 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index da9bd1c2a4..c8bc196270 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -21,6 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index ae0e9d0e08..79512f826c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index 6d976f526f..f949db90c2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 1774b27146..7a975980fe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index c9112a0795..c0a121ef71 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -78,6 +78,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index b580f1c96b..2e5b1c3cc2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index bc9c8df4f8..3cc5940708 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -78,6 +78,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index afc1ee4239..f8a7666f78 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 9bfd01b319..262c91f061 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index f057b47357..c22d902c71 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index a1b17c0b65..4e3149189f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index d89dd01c51..0f28917f5c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index fbdb6f6118..678cacbe75 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index ad5cb03e20..11ffa16a41 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index 5a7796659d..97c9a23292 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index db0b052ea7..79e4bbcd67 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -78,6 +78,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 090ba3d58e..1ccc5c12ca 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -78,6 +78,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index 0b5a6610e5..3a167c9f92 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index 773802dfae..1ad8450e3d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -84,6 +84,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index cc6f960e75..df55e62340 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -78,6 +78,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index f08dc7f7bf..968045a415 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index ad0d7286f0..464a9c0441 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -83,6 +83,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index f576d9f1dd..54b6d1a65f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -81,6 +81,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index b32a7b9444..d513f80632 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -81,6 +81,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index 0c3b0edee6..4a7605ab2c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -85,6 +85,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index df97eca668..44158cd159 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -80,6 +80,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index 74a0ab5c69..6a17a47968 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -83,6 +83,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index bc1bc26e4c..af561484ae 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -83,6 +83,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 721a9d7c3b..6594db177f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -87,6 +87,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index 2f65dc0b7a..dd7a8d8f1e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -92,6 +92,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 3cd030d43c..64f8e11174 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -89,6 +89,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index d1ff8b9e48..236304395e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -64,6 +64,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index 11d4899222..fbb78f9e84 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -64,6 +64,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index 913671b48a..c6cedb61ef 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -66,6 +66,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 252ce755ac..38875e2a4f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -64,6 +64,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index 9c7858f00d..73c3832a10 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -42,6 +42,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb index 56769b0734..8cd8056d73 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb @@ -44,6 +44,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index de3765e4a6..27461c4521 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -44,6 +44,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 223b5aa45c..df2e52ef20 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -91,6 +91,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' -- GitLab From a65d6c402c3b2788c13ba869d26b3a12d5c5dca1 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 24 Feb 2015 15:57:01 +0100 Subject: [PATCH 0061/2133] trinity 2.0.4 --- .../t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..9259406d80 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'Trinity' +version = '2.0.4' + +homepage = 'http://trinityrnaseq.github.io/' +description = """ Trinity assembles transcript sequences from Illumina RNA-Seq data. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] +sources = ['v%(version)s.tar.gz'] + +java = 'Java' +javaver = '1.7.0_21' + +dependencies = [ + (java, javaver, '', True) + ] + +parallel = 1 + +buildopts = ' && make plugins' + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ["Chrysalis/Chrysalis", "Inchworm/bin/inchworm", "trinity-plugins/rsem/rsem-run-em"], + 'dirs': [""], +} + +# add install dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + -- GitLab From a3d8f3e0cfa3c884202871c5c20ddc8bf2259a98 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 24 Feb 2015 16:24:06 +0100 Subject: [PATCH 0062/2133] MM-align --- .../m/MM-align/MM-align-1.0-goolf-1.4.10.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/MM-align/MM-align-1.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/m/MM-align/MM-align-1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MM-align/MM-align-1.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..94bf357f14 --- /dev/null +++ b/easybuild/easyconfigs/m/MM-align/MM-align-1.0-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'CmdCp' + +name = 'MM-align' +version = '1.0' # no version info provided. I decide it's 1.0 + +homepage = 'http://zhanglab.ccmb.med.umich.edu/MM-align/' +description = """ MM-align is an algorithm for structurally aligning + multiple-chain protein-protein complexes. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://zhanglab.ccmb.med.umich.edu/MM-align/'] +sources = ['MMalign.f'] + +skipsteps = ['source'] + +cmds_map = [('MMalign.f', '$F77 -static -O3 -ffast-math -lm -o MMalign %(source)s')] + +files_to_copy = [(['MMalign'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/MMalign'], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From b7a9da861043eb87f6519823a05253022134e40e Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Thu, 26 Mar 2015 11:12:41 +1300 Subject: [PATCH 0063/2133] itac-9.0.3.051 --- .../easyconfigs/i/itac/itac-9.0.3.051.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb diff --git a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb new file mode 100644 index 0000000000..42551d67c6 --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb @@ -0,0 +1,21 @@ +name = 'itac' +version = '9.0.3.051' + +homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_itac_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +preferredmpi = 'impi5' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'tools' -- GitLab From 3311fdb947e0d8f6377ce95b604142aea6052bb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2015 16:51:24 +0200 Subject: [PATCH 0064/2133] fix Paraver/wxPropertyGrid --- .../p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb | 42 ------------------- .../wxPropertyGrid-1.4.15-GCC-4.7.3.eb | 2 +- 2 files changed, 1 insertion(+), 43 deletions(-) diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb index d62b7707a8..801bff930d 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb @@ -21,50 +21,8 @@ dependencies = [ ('Boost', '1.53.0', '-serial'), ] -osdependencies = ['wxWidgets-ansi-devel'] - # http://www.bsc.es/computer-sciences/performance-tools/downloads # Requires input of email address for download sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.gz'] -# --- BM ISSUE --- -# -# lib64/lib linking should be avoided by patching Paraver configure/Makefiles files -# configure/Makefile assumes everything always in lib/ -preconfigopts = [ - 'cd ptools_common_files; ', - 'ln -s -f %(installdir)s/ptools/lib64 %(installdir)s/ptools/lib; cd paraver-kernel; ', - 'ln -s -f %(installdir)s/lib64 %(installdir)s/lib; cd wxparaver;' -] -premakeopts = [ - 'cd ptools_common_files; ', - 'cd paraver-kernel; ', - 'cd wxparaver;' -] -preinstallopts = [ - 'cd ptools_common_files; ', - 'cd paraver-kernel; ', - 'cd wxparaver;' -] - -configopts = [ - '--prefix=%(installdir)s/ptools', - '--with-boost=${EBROOTBOOST}' - + ' --with-ptools-common-files=%(installdir)s/ptools', - '--with-boost=${EBROOTBOOST}' - + ' --with-wxpropgrid=wxcode_gtk2_propgrid-2.8' - + ' --with-paraver=%(installdir)s' -] - -keeppreviousinstall = True - -# --- BM LIB64 --- -# -# On some systems libraries end up in lib/ -sanity_check_paths = { - 'files': ["bin/wxparaver", "include/paraverconfig.h", - "lib64/paraver-kernel/libparaver-kernel.a"], - 'dirs': [] -} - moduleclass = 'perf' diff --git a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb index 859fce3a0d..b4eceecafb 100644 --- a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb @@ -15,7 +15,7 @@ description = """wxPropertyGrid is a property sheet control for wxWidgets. In ot toolchain = {'name': 'GCC', 'version': '4.7.3'} -osdependencies = ['wxWidgets-ansi-devel'] +osdependencies = [('wxGTK-devel', 'libwxgtk2.8-dev', 'wxWidgets-ansi-devel')] # http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz?download sources = ['wxpropgrid' + '-%(version)s-src.tar.gz'] -- GitLab From 874893040bf5edbc636328421fffb7d308a91194 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2015 00:38:06 +0200 Subject: [PATCH 0065/2133] Tau tweaks --- .../t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb index bda1e46477..008012a78d 100644 --- a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb @@ -30,9 +30,15 @@ dependencies = [ ('OTF', '1.12.4', "", (compname, compver)), ('PAPI', '5.2.0', "", (compname, compver)), ('PDT', '3.19', "", (compname, compver)), - ('Scalasca', '1.4.3'), - ('Score-P', '1.2.1'), - ('VampirTrace', '5.14.4'), + #('Scalasca', '1.4.3'), # requires enabling scalasca1 as extra backend + #('Score-P', '1.2.1'), # requires enabling scorep as extra backend + ('VampirTrace', '5.14.4'), # requires enabling vampirtrace as extra backend +] + +extra_backends = [ + #'scalasca1', # deprecated, use scorep backend instead (requires Scalasca v1.x as dependency) + #'vampirtrace', # deprecated, use scorep backend instead (requires VampirTrace as dependency) + 'scorep', # requires Score-P as dependency ] # http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.22.2.tar.gz @@ -98,12 +104,10 @@ sanity_check_paths = { 'dirs': [] } -modextrapaths = { - 'PATH': machine + "/bin", - 'TAU_MF_DIR': machine + "/lib", - 'TAU_MAKEFILE': machine + "/lib/Makefile.tau-papi-mpi-pdt", -} + +# default measurement settings modextravars = { + 'TAU_MAKEFILE': '%(installdir)s/lib/Makefile.tau-papi-mpi-pdt', 'TAU_PROFILE': '1', 'TAU_TRACE': '0', 'TAU_CALLPATH': '1', -- GitLab From b9f6e36fe37d60e768e3c8a11290d4ccad3541c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 May 2015 23:02:17 +0200 Subject: [PATCH 0066/2133] include extensions in OCaml easyconfigs --- .../csv/csv-1.3.3-ictce-5.5.0-OCaml-4.01.0.eb | 35 ------------------ .../easyconfigs/c/csv/csv-1.3.3_prefix.patch | 11 ------ .../findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb | 31 ---------------- .../o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 33 +++++++++-------- .../o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 37 ++++++++++--------- .../Xmlm-1.2.0-ictce-5.5.0-OCaml-4.01.0.eb | 20 ---------- 6 files changed, 37 insertions(+), 130 deletions(-) delete mode 100644 easybuild/easyconfigs/c/csv/csv-1.3.3-ictce-5.5.0-OCaml-4.01.0.eb delete mode 100644 easybuild/easyconfigs/c/csv/csv-1.3.3_prefix.patch delete mode 100644 easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb delete mode 100644 easybuild/easyconfigs/x/Xmlm/Xmlm-1.2.0-ictce-5.5.0-OCaml-4.01.0.eb diff --git a/easybuild/easyconfigs/c/csv/csv-1.3.3-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/c/csv/csv-1.3.3-ictce-5.5.0-OCaml-4.01.0.eb deleted file mode 100644 index 4b85bf3dd4..0000000000 --- a/easybuild/easyconfigs/c/csv/csv-1.3.3-ictce-5.5.0-OCaml-4.01.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -name = 'csv' -version = '1.3.3' - -homepage = 'https://forge.ocamlcore.org/projects/csv/' -description = """This is a pure OCaml library to read and write CSV files, including all extensions used by Excel -- - e.g., quotes, newlines, 8 bit characters in fields, "0 etc.""" - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ['https://forge.ocamlcore.org/frs/download.php/1376/'] -sources = [SOURCE_TAR_GZ] - -patches = ['csv-%(version)s_prefix.patch'] - -ocaml = 'OCaml' -ocamlver = '4.01.0' -versionsuffix = '-%s-%s' % (ocaml, ocamlver) - -builddependencies = [('findlib', '1.5.2', versionsuffix)] -dependencies = [(ocaml, ocamlver)] - -skipsteps = ['configure', 'build'] - -preinstallopts = "mkdir -p %(installdir)s/site-lib && OCAMLFIND_DESTDIR=%(installdir)s/site-lib PREFIX=%(installdir)s " - -parallel = 1 - -modextrapaths = {'OCAMLPATH': 'site-lib'} - -sanity_check_paths = { - 'files': ['bin/csvtool'], - 'dirs': ['site-lib/csv'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/csv/csv-1.3.3_prefix.patch b/easybuild/easyconfigs/c/csv/csv-1.3.3_prefix.patch deleted file mode 100644 index d76bf10483..0000000000 --- a/easybuild/easyconfigs/c/csv/csv-1.3.3_prefix.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- csv-1.3.3/Makefile.orig 2014-08-25 14:32:19.026905764 +0200 -+++ csv-1.3.3/Makefile 2014-08-25 14:32:33.607257131 +0200 -@@ -16,7 +16,7 @@ - ocaml setup.ml -build - - configure: setup.ml -- ocaml $< -configure --enable-tests -+ ocaml $< -configure --enable-tests --prefix $(PREFIX) - - setup.ml: _oasis - oasis setup -setup-update dynamic diff --git a/easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb deleted file mode 100644 index e9f92f5302..0000000000 --- a/easybuild/easyconfigs/f/findlib/findlib-1.5.2-ictce-5.5.0-OCaml-4.01.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'findlib' -version = '1.5.2' - -homepage = 'http://projects.camlcity.org/projects/findlib.html' -description = """Findlib is a library manager for Objective Caml. It provides a convention how to store libraries, - and a file format ("META") to describe the properties of libraries. There is also a tool (ocamlfind) for interpreting - the META files, so that it is very easy to use libraries in programs and scripts.""" - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ['http://download.camlcity.org/download/'] -sources = [SOURCE_TAR_GZ] - -ocaml = 'OCaml' -ocamlver = '4.01.0' -versionsuffix = '-%s-%s' % (ocaml, ocamlver) -dependencies = [(ocaml, ocamlver)] - -skipsteps = ['configure'] - -premakeopts = "./configure -bindir %(installdir)s/bin -config %(installdir)s/findlib.conf && " -preinstallopts = "mkdir %(installdir)s/site-lib && PATH=%(installdir)s/bin:$PATH" - -modextravars = {'OCAMLFIND_CONF': '%(installdir)s/findlib.conf'} - -sanity_check_paths = { - 'files': ['bin/ocamlfind', 'bin/safe_camlp4', 'findlib.conf'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb index b4bc7ba9b4..eef25b2450 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -6,9 +6,6 @@ # License:: MIT/GPL # $Id$ ## - -easyblock = 'ConfigureMake' - name = "OCaml" version = "4.01.0" @@ -20,25 +17,29 @@ description = """OCaml is a general purpose industrial-strength programming lang toolchain = {'version': '1.4.10', 'name': 'goolf'} -sources = ['ocaml-%(version)s.tar.gz'] -sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) -source_urls = ['http://caml.inria.fr/pub/distrib/%s' % sourcedir] +ocaml_sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) +opam_ver = '1.2.2' +source_urls = [ + 'http://caml.inria.fr/pub/distrib/%s' % ocaml_sourcedir, + 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, +] +sources = [ + 'ocaml-%(version)s.tar.gz', + 'opam-full-%s.tar.gz' % opam_ver, +] builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] -prefix_opt = "-prefix " -configopts = '-cc "$CC $CFLAGS"' -buildopts = "world.opt" - # parallel build tends to break parallel = 1 -modextrapaths = {'CAML_LD_LIBRARY_PATH': 'lib'} - -sanity_check_paths = { - 'files': ["bin/ocaml", "bin/ocamlc"], - 'dirs': [] -} +# handled by OPAM, order matters! +exts_list = [ + ('ocamlfind', '1.5.5'), + ('batteries', '2.3.1'), + ('csv', '1.3.4'), + ('xmlm', '1.2.0'), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb index 1c91aeafaa..5c9d36e6b7 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -1,12 +1,11 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ ## - name = "OCaml" version = "4.01.0" @@ -16,29 +15,33 @@ description = """OCaml is a general purpose industrial-strength programming lang it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming.""" -toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchain = {'version': '1.4.10', 'name': 'goolf'} -sources = ['ocaml-%(version)s.tar.gz'] -sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) -source_urls = ['http://caml.inria.fr/pub/distrib/%s' % sourcedir] +ocaml_sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) +opam_ver = '1.2.2' +source_urls = [ + 'http://caml.inria.fr/pub/distrib/%s' % ocaml_sourcedir, + 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, +] +sources = [ + 'ocaml-%(version)s.tar.gz', + 'opam-full-%s.tar.gz' % opam_ver, +] patches = ['OCaml-%(version)s_icc-fixes.patch'] builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] -prefix_opt = "-prefix " -configopts = '-cc "$CC $CFLAGS"' -buildopts = "world.opt" - # parallel build tends to break parallel = 1 -modextrapaths = {'CAML_LD_LIBRARY_PATH': 'lib'} - -sanity_check_paths = { - 'files': ["bin/ocaml", "bin/ocamlc"], - 'dirs': [] -} +# handled by OPAM, order matters! +exts_list = [ + ('ocamlfind', '1.5.5'), + ('batteries', '2.3.1'), + ('csv', '1.3.4'), + ('xmlm', '1.2.0'), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/Xmlm/Xmlm-1.2.0-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/x/Xmlm/Xmlm-1.2.0-ictce-5.5.0-OCaml-4.01.0.eb deleted file mode 100644 index 7c572b469c..0000000000 --- a/easybuild/easyconfigs/x/Xmlm/Xmlm-1.2.0-ictce-5.5.0-OCaml-4.01.0.eb +++ /dev/null @@ -1,20 +0,0 @@ -name = 'Xmlm' -version = '1.2.0' - -homepage = 'http://erratique.ch/software/xmlm' -description = """Xmlm is an OCaml streaming codec to decode and encode the XML data format. It can process XML - documents without a complete in-memory representation of the data.""" - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ['http://erratique.ch/software/xmlm/releases'] -sources = ['%(namelower)s-%(version)s.tbz'] - -ocaml = 'OCaml' -ocamlver = '4.01.0' -versionsuffix = '-%s-%s' % (ocaml, ocamlver) - -builddependencies = [('findlib', '1.5.2', versionsuffix)] -dependencies = [(ocaml, ocamlver)] - -moduleclass = 'lib' -- GitLab From c823fac1f8b1cba955f4cdd0a00037b161279003 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 19:40:52 +0200 Subject: [PATCH 0067/2133] switch to configure/make and build in install_dir --- .../t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 9 ++-- .../t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb | 44 +++++++++++++++++++ 2 files changed, 49 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb index 9259406d80..f148f469c9 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'Trinity' version = '2.0.4' @@ -23,12 +23,14 @@ dependencies = [ (java, javaver, '', True) ] +skipsteps = ['configure', 'install'] + parallel = 1 +buildininstalldir = True + buildopts = ' && make plugins' -files_to_copy = ["*"] - sanity_check_paths = { 'files': ["Chrysalis/Chrysalis", "Inchworm/bin/inchworm", "trinity-plugins/rsem/rsem-run-em"], 'dirs': [""], @@ -40,4 +42,3 @@ modextrapaths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb new file mode 100644 index 0000000000..69e40a1027 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'Trinity' +version = '2.0.6' + +homepage = 'http://trinityrnaseq.github.io/' +description = """ Trinity assembles transcript sequences from Illumina RNA-Seq data. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] +sources = ['v%(version)s.tar.gz'] + +java = 'Java' +javaver = '1.7.0_21' + +dependencies = [ + (java, javaver, '', True) + ] + +skipsteps = ['configure', 'install'] + +parallel = 1 + +buildininstalldir = True + +buildopts = ' && make plugins' + +sanity_check_paths = { + 'files': ["Chrysalis/Chrysalis", "Inchworm/bin/inchworm", "trinity-plugins/rsem/rsem-run-em"], + 'dirs': [""], +} + +# add install dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' -- GitLab From 7fac4f5121e0453b16f67d2861f735e9d3704436 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 20:02:32 +0200 Subject: [PATCH 0068/2133] added jellyfish to sanity checking --- .../easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb index f148f469c9..079422c025 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -16,6 +16,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] sources = ['v%(version)s.tar.gz'] +unpack_options = '--strip-components=1' + java = 'Java' javaver = '1.7.0_21' @@ -32,7 +34,8 @@ buildininstalldir = True buildopts = ' && make plugins' sanity_check_paths = { - 'files': ["Chrysalis/Chrysalis", "Inchworm/bin/inchworm", "trinity-plugins/rsem/rsem-run-em"], + 'files': ["Chrysalis/Chrysalis", "Inchworm/bin/inchworm", + "trinity-plugins/rsem/rsem-run-em", "trinity-plugins/jellyfish/bin/jellyfish"], 'dirs': [""], } -- GitLab From 7768cb96870a86711dd42062c6f0beb148d34848 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Thu, 4 Jun 2015 09:24:31 +0200 Subject: [PATCH 0069/2133] bump java version to 1.7.0_80 --- easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb index 079422c025..d17305cb3c 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -19,7 +19,7 @@ sources = ['v%(version)s.tar.gz'] unpack_options = '--strip-components=1' java = 'Java' -javaver = '1.7.0_21' +javaver = '1.7.0_80' dependencies = [ (java, javaver, '', True) -- GitLab From 50d854e85c1c9b2db7b51002cbaf82844b776f0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 13:21:51 +0200 Subject: [PATCH 0070/2133] fix remove license header line in binutils easyconfig --- .../easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 6923d84abe..037eea64d6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -3,6 +3,7 @@ # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos +# License:: MIT/GPL # $Id$ # # This work implements a part of the HPCBIOS project and is a component of the policy: -- GitLab From 8febcc4dcee4b8aa71bb8b6315bae23de1ef8f6f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 29 Jul 2015 13:38:10 +1200 Subject: [PATCH 0071/2133] Added environment variable to force no CPU binding in Slurm --- easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb | 1 + 5 files changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index 76be1035a7..1082a356d5 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -30,3 +30,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb index 3b66a977f7..4fa5665414 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb @@ -31,3 +31,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb index c63048d89b..dc0616d42c 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb @@ -33,3 +33,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb index 5a28bbce0d..b2f34f7977 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb @@ -33,3 +33,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb index b63bd53de9..4c2e30db07 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb @@ -33,3 +33,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } -- GitLab From 29450f0d39654c8cf4ccaba1f97bab304e96d306 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 29 Jul 2015 15:57:32 +1200 Subject: [PATCH 0072/2133] ORCA 3.0.x is compiled against only OpenMPI 1.6.5 on linux --- ...nmpi_165.eb => ORCA-3_0_0-linux_x86-64.eb} | 6 ++-- .../ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb | 36 ------------------- ...PI-1.6.5.eb => ORCA-3_0_2-linux_x86-64.eb} | 6 ++-- ...PI-1.6.5.eb => ORCA-3_0_3-linux_x86-64.eb} | 6 ++-- 4 files changed, 7 insertions(+), 47 deletions(-) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_0-linux_x86-64_openmpi_165.eb => ORCA-3_0_0-linux_x86-64.eb} (90%) delete mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb => ORCA-3_0_2-linux_x86-64.eb} (91%) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb => ORCA-3_0_3-linux_x86-64.eb} (91%) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb similarity index 90% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb index 4fa5665414..1d969f2204 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb @@ -1,8 +1,7 @@ easyblock = "PackedBinary" name = "ORCA" -openmpiversion = '1.6.5' -version = '3_0_0-linux_x86-64_openmpi_%s' % ''.join(openmpiversion.split('.')) +version = '3_0_0-linux_x86-64' homepage = 'http://www.thch.uni-bonn.de/tc/orca/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry @@ -15,7 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] +# ORCA 3.0.0 is compiled only against OpenMPI 1.6.5 for Linux +dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb deleted file mode 100644 index b2f34f7977..0000000000 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = "PackedBinary" - -name = "ORCA" -version = '3_0_2-linux_x86-64' - -openmpiversion = '1.8.1' -versionsuffix = '-OpenMPI-%s' % openmpiversion - -homepage = 'http://cec.mpg.de/forum/' -description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry - with specific emphasis on spectroscopic properties of open-shell molecules. - It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- - and multireference correlated ab initio methods. - It can also treat environmental and relativistic effects.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] - -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.8.3')] - -sanity_check_paths = { - 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] - for y in ["", "_mpi"]] + \ - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', - 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ - ['orca', 'otool_cosmo'], - 'dirs': [], -} - -moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb similarity index 91% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb index dc0616d42c..39d6350aed 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -3,9 +3,6 @@ easyblock = "PackedBinary" name = "ORCA" version = '3_0_2-linux_x86-64' -openmpiversion = '1.6.5' -versionsuffix = '-OpenMPI-%s' % openmpiversion - homepage = 'http://cec.mpg.de/forum/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. @@ -17,7 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] +# ORCA 3.0.2 is compiled only against OpenMPI 1.6.5 for Linux +dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb similarity index 91% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb index 4c2e30db07..adeb3b2fac 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb @@ -3,9 +3,6 @@ easyblock = "PackedBinary" name = "ORCA" version = '3_0_3-linux_x86-64' -openmpiversion = '1.6.5' -versionsuffix = '-OpenMPI-%s' % openmpiversion - homepage = 'http://cec.mpg.de/forum/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. @@ -17,7 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] +# ORCA 3.0.3 is compiled only against OpenMPI 1.6.5 for Linux +dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', -- GitLab From 7dc818b916057265ce6b10caee13fc97abab87ea Mon Sep 17 00:00:00 2001 From: "Dominik L. Borkowski" Date: Wed, 12 Aug 2015 14:14:40 -0400 Subject: [PATCH 0073/2133] added easyconfig for MACS2 --- .../MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/m/MACS2/MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/MACS2/MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..5be84c881c --- /dev/null +++ b/easybuild/easyconfigs/m/MACS2/MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2015 Virginia Bioinformatics Institute at Virginia Tech +# Authors:: Dominik L. Borkowski +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = "PythonPackage" + +name = "MACS2" +version = "2.1.0.20150731" + +homepage = "https://github.com/taoliu/MACS/" +description = "Model Based Analysis for ChIP-Seq data" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = ["%s-%s.tar.gz" % (name, version)] + +python = "Python" +pyver = "2.7.3" +pyshortver = '.'.join(pyver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pyshortver +versionsuffix = "-%s-%s" % (python, pyver) + + +dependencies = [(python, pyver), + ('numpy', '1.7.1', versionsuffix)] + + +sanity_check_paths = { + 'files': ['bin/macs2', + '%s/%s-%s-py%s-linux-x86_64.egg' % (pylibdir, name, version, pyshortver)], + 'dirs':[] + } + +# specify that this asyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_commands = [('%(namelower)s --version')] + + +# default sanity check for importing module fails, because EB guesses with name.lower(). +# to work around that, we explicitly request using the original name +# options = {'modulename': 'MACS2'} +options = {'modulename': '%s' % name } + +moduleclass = 'bio' + -- GitLab From de40c2e86ced4deb5e1eb87bca7ffe92e9475a85 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 00:15:31 +0200 Subject: [PATCH 0074/2133] fix style issues in MACS2 easyconfig --- .../MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb | 40 ++++++++----------- 1 file changed, 17 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/MACS2/MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb index 5be84c881c..5ab68f3355 100644 --- a/easybuild/easyconfigs/m/MACS2/MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MACS2/MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb @@ -8,46 +8,40 @@ # ## -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "MACS2" -version = "2.1.0.20150731" +name = 'MACS2' +version = '2.1.0.20150731' -homepage = "https://github.com/taoliu/MACS/" +homepage = 'https://github.com/taoliu/MACS/' description = "Model Based Analysis for ChIP-Seq data" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [PYPI_SOURCE] -sources = ["%s-%s.tar.gz" % (name, version)] +sources = [SOURCE_TAR_GZ] -python = "Python" -pyver = "2.7.3" +python = 'Python' +pyver = '2.7.3' pyshortver = '.'.join(pyver.split('.')[0:2]) pylibdir = 'lib/python%s/site-packages' % pyshortver versionsuffix = "-%s-%s" % (python, pyver) +dependencies = [ + (python, pyver), + ('numpy', '1.7.1', versionsuffix), +] -dependencies = [(python, pyver), - ('numpy', '1.7.1', versionsuffix)] - - -sanity_check_paths = { - 'files': ['bin/macs2', - '%s/%s-%s-py%s-linux-x86_64.egg' % (pylibdir, name, version, pyshortver)], - 'dirs':[] - } +options = {'modulename': name } # specify that this asyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -sanity_check_commands = [('%(namelower)s --version')] - +sanity_check_paths = { + 'files': ['bin/macs2', '%s/%s-%s-py%s-linux-x86_64.egg' % (pylibdir, name, version, pyshortver)], + 'dirs': [], +} -# default sanity check for importing module fails, because EB guesses with name.lower(). -# to work around that, we explicitly request using the original name -# options = {'modulename': 'MACS2'} -options = {'modulename': '%s' % name } +sanity_check_commands = [('%(namelower)s --version')] moduleclass = 'bio' - -- GitLab From 38b7e620113a578a6ce459538610858fb6809fc2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 09:31:18 +0200 Subject: [PATCH 0075/2133] {tools}[intel/2015a] IPython 4.0.0 (WIP) --- ...IPython-4.0.0-intel-2015a-Python-2.7.10.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..865d2c3f16 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,74 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '4.0.0' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +python = 'Python' +pyver = '2.7.10' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +# this is a bundle of Python packages +# override extensions sanity check for IPython, importing a Python module doesn't work there +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c "import %(ext_name)s" || ipython -h', '') + +exts_list = [ + ('traitlets', '4.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pexpect', '3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('path.py', '7.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + }), + ('pickleshare', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('testpath', '0.2', { + 'source_urls': ['https://github.com/jupyter/testpath/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest', '')] + +moduleclass = 'tools' -- GitLab From 4c433fc27f1f85b4743387e68cdec549b5588596 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 09:48:14 +0200 Subject: [PATCH 0076/2133] fix exts_filter, enhance sanity check --- .../IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb index 865d2c3f16..f5a2e2e413 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -25,7 +25,7 @@ dependencies = [ # this is a bundle of Python packages # override extensions sanity check for IPython, importing a Python module doesn't work there exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s" || ipython -h', '') +exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('traitlets', '4.0.0', { @@ -56,6 +56,7 @@ exts_list = [ }), ('ipython', version, { 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', }), ] @@ -65,10 +66,13 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} full_sanity_check = True sanity_check_paths = { - 'files': [], + 'files': [bin/ipython], 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], } -sanity_check_commands = [('iptest', '')] +sanity_check_commands = [ + ('ipython -h', ''), + ('iptest', ''), +] moduleclass = 'tools' -- GitLab From e63fc5d25f081b721910b1062526813c49a11b4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 10:08:09 +0200 Subject: [PATCH 0077/2133] fix typo --- .../i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb index f5a2e2e413..aee1a02648 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -66,7 +66,7 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} full_sanity_check = True sanity_check_paths = { - 'files': [bin/ipython], + 'files': ['bin/ipython'], 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], } -- GitLab From f89592f6ea067db995c91321f82e52d06e42d3cc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 9 Sep 2015 15:00:52 +0100 Subject: [PATCH 0078/2133] Update IMPUTE2 to 2.3.2 --- .../i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb | 32 +++++++++++++++++++ .../i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb create mode 100644 easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb new file mode 100644 index 0000000000..115f19d847 --- /dev/null +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'IMPUTE2' +version = '2.3.2' +versionsuffix = '_x86_64_dynamic' + +homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' +description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation + and haplotype phasing program based on ideas from Howie et al. 2009 """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] +sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["impute2"], + 'dirs': ["Example"] +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb new file mode 100644 index 0000000000..fe290f068e --- /dev/null +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'IMPUTE2' +version = '2.3.2' +versionsuffix = '_x86_64_static' + +homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' +description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation + and haplotype phasing program based on ideas from Howie et al. 2009 """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] +sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["impute2"], + 'dirs': ["Example"] +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + -- GitLab From 1d979ba9139bf6c729cc1e532614ce3e8723c564 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Sep 2015 15:14:08 +0300 Subject: [PATCH 0079/2133] Adding modified configs --- .../c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 12 ++++++------ .../easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb | 8 ++++---- .../{cp2k-2.4.0_ipi.patch => CP2K-2.4.0_ipi.patch} | 0 3 files changed, 10 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/c/CP2K/{cp2k-2.4.0_ipi.patch => CP2K-2.4.0_ipi.patch} (100%) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index 567f926654..b708ab38e5 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -12,18 +12,18 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://sourceforge.net/projects/cp2k/files/'] -sources = ['%s-%s.tar.bz2' % (name.lower(), version)] +sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'cp2k-2.4.0_ipi.patch', - 'fix_compile_date_lastcvs.patch', + 'CP2K-2.4.0_ipi.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', 'do_regtest_nocompile.patch' - ] +] builddependencies = [ ('flex', '2.5.35'), ('Bison', '2.5') - ] +] dependencies = [('Libint', '1.1.4')] @@ -34,4 +34,4 @@ parallel = 1 # about 100 tests fail ignore_regtest_fails=True -moduleclass = 'chem' + diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb index d44d72b4be..d3bcea99ca 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb @@ -11,17 +11,17 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://sourceforge.net/projects/cp2k/files/'] -sources = ['%s-%s.tar.bz2' % (name.lower(), version)] +sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'fix_compile_date_lastcvs.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', 'do_regtest_nocompile.patch' - ] +] builddependencies = [ ('flex', '2.5.35'), ('Bison', '2.5') - ] +] dependencies = [('Libint', '1.1.4')] diff --git a/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch similarity index 100% rename from easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch rename to easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch -- GitLab From 3e1f8943e1ff8924bee86a1ca13c0b4527d18352 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Sep 2015 15:16:30 +0300 Subject: [PATCH 0080/2133] last changes --- .../easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 2 +- .../easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch | 11 ----------- 2 files changed, 1 insertion(+), 12 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index b708ab38e5..aa550ff0b9 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -34,4 +34,4 @@ parallel = 1 # about 100 tests fail ignore_regtest_fails=True - +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch deleted file mode 100644 index a50d6e9cf4..0000000000 --- a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- makefiles/Makefile.orig 2012-08-21 14:35:17.000000000 +0300 -+++ makefiles/Makefile 2013-11-12 12:41:29.361582641 +0200 -@@ -194,7 +194,7 @@ - # - ifeq ($(CPPSHELL),) - CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ -- -D__COMPILE_DATE="\"$(shell date)\""\ -+ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g')\""\ - -D__COMPILE_HOST="\"$(shell hostname)\""\ - -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" - endif -- GitLab From e61aac2fab0c11ba2dda71871b89e71c2e632e60 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Sep 2015 16:04:42 +0300 Subject: [PATCH 0081/2133] Adding accidentally deleted patch --- .../easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch new file mode 100644 index 0000000000..a50d6e9cf4 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch @@ -0,0 +1,11 @@ +--- makefiles/Makefile.orig 2012-08-21 14:35:17.000000000 +0300 ++++ makefiles/Makefile 2013-11-12 12:41:29.361582641 +0200 +@@ -194,7 +194,7 @@ + # + ifeq ($(CPPSHELL),) + CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ +- -D__COMPILE_DATE="\"$(shell date)\""\ ++ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g')\""\ + -D__COMPILE_HOST="\"$(shell hostname)\""\ + -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" + endif -- GitLab From 6dfa12bbcd946d3eab429cf96037dc8fcb6ced3b Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 22 Sep 2015 15:06:43 +0300 Subject: [PATCH 0082/2133] Making changes according to comments --- .../easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 6 +++--- .../easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch | 2 ++ .../easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch | 11 ----------- 4 files changed, 6 insertions(+), 15 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index aa550ff0b9..5716e9f33a 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -15,8 +15,8 @@ source_urls = ['http://sourceforge.net/projects/cp2k/files/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'CP2K-2.4.0_ipi.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', + 'CP2K-%(version)s_ipi.patch', + 'CP2K-%(version)s-fix_compile_date_lastsvn.patch', 'do_regtest_nocompile.patch' ] @@ -34,4 +34,4 @@ parallel = 1 # about 100 tests fail ignore_regtest_fails=True -moduleclass = 'chem' + diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb index d3bcea99ca..5c6f21e195 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb @@ -14,7 +14,7 @@ source_urls = ['http://sourceforge.net/projects/cp2k/files/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', + 'CP2K-%(version)s-fix_compile_date_lastsvn.patch', 'do_regtest_nocompile.patch' ] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch index b8115df6c5..3c7cc4aaec 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch @@ -1,4 +1,6 @@ #This patch makes CP2K source code compatible with i-pi +#It was created by the CP2K team and can be found in the following link: +#https://github.com/i-pi/i-pi/tree/master/patches diff -rupN cp2k-2.4.0_ref/makefiles/Makefile cp2k-2.4.0/makefiles/Makefile --- cp2k-2.4.0_ref/makefiles/Makefile 2013-08-15 10:46:04.535899216 +0100 +++ cp2k-2.4.0/makefiles/Makefile 2013-08-15 10:53:45.827911028 +0100 diff --git a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch deleted file mode 100644 index a50d6e9cf4..0000000000 --- a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- makefiles/Makefile.orig 2012-08-21 14:35:17.000000000 +0300 -+++ makefiles/Makefile 2013-11-12 12:41:29.361582641 +0200 -@@ -194,7 +194,7 @@ - # - ifeq ($(CPPSHELL),) - CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ -- -D__COMPILE_DATE="\"$(shell date)\""\ -+ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g')\""\ - -D__COMPILE_HOST="\"$(shell hostname)\""\ - -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" - endif -- GitLab From 1c99c6b8f1c70ce1f5d6bd21d959ef4c592ece44 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 22 Sep 2015 15:31:55 +0300 Subject: [PATCH 0083/2133] adding back original patch file --- .../c/CP2K/fix_compile_date_lastcvs.patch | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch new file mode 100644 index 0000000000..97dca5d868 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch @@ -0,0 +1,14 @@ +--- makefiles/Makefile.orig 2010-12-10 05:35:15.000000000 +0100 ++++ makefiles/Makefile 2011-01-24 10:14:35.000000000 +0100 +@@ -149,9 +149,9 @@ + # + ifeq ($(CPPSHELL),) + CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ +- -D__COMPILE_DATE="\"$(shell date)\""\ ++ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g')\""\ + -D__COMPILE_HOST="\"$(shell hostname)\""\ +- -D__COMPILE_LASTCVS="\"$(shell tail -n1 $(SRCDIR)/CVS/Entries)\"" ++ -D__COMPILE_LASTCVS="\"$(shell tail -n1 $(SRCDIR)/CVS/Entries | sed 's/ /_/g')\"" + endif + + ifneq ($(CPP),) -- GitLab From 362a6d3cb7afa719253aafe12c3aeb8a8cfe88ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 14:56:37 +0200 Subject: [PATCH 0084/2133] remove old svnversion build dep in Python 2.5.6 easyconfigs (patch makes it uneccesary) --- .../p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 4 ---- .../p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 4 ---- .../easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 4 ---- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 4 ---- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 4 ---- .../easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 4 ---- .../easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 4 ---- 7 files changed, 28 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index 7756ecc5cf..43ff3feba7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -21,10 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index 6f7b7074bb..f825fd87bd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -21,10 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index 2b86e4f482..18d0d4a8df 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -21,10 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index ad5a259b72..23ddabe854 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -24,10 +24,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index 061722f46e..f747214b5c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -24,10 +24,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index cfb317b18e..0228eae5be 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -21,10 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index ad8051da17..fc44c37e78 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -21,10 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' -- GitLab From 29cf2032b0d98eaa677c83aa38f5907f600c570d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 16:42:32 +0200 Subject: [PATCH 0085/2133] fix conflict --- .../l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb index f473597909..96f39c944c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -4,13 +4,8 @@ name = 'libxml2' version = '2.9.1' homepage = 'http://xmlsoft.org/' -<<<<<<< HEAD -description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable -outside of the Gnome platform).""" -======= description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" ->>>>>>> develop toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -- GitLab From 05cfc4122c9ea2ddcd7c5502bb5bad82ed9708c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 16:46:30 +0200 Subject: [PATCH 0086/2133] trash easyconfigs with different toolchains, stick to just goolf/1.4.10 --- .../APR-util-1.5.3-goalf-1.1.0-no-OFED.eb | 23 ------------ .../APR-util-1.5.3-gompi-1.4.12-no-OFED.eb | 23 ------------ .../a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb | 23 ------------ .../a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb | 23 ------------ .../a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb | 23 ------------ .../a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb | 23 ------------ .../a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb | 17 --------- .../a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb | 17 --------- .../a/APR/APR-1.5.0-ictce-4.0.6.eb | 17 --------- .../a/APR/APR-1.5.0-ictce-4.1.13.eb | 17 --------- .../a/APR/APR-1.5.0-ictce-5.2.0.eb | 17 --------- .../a/APR/APR-1.5.0-ictce-5.3.0.eb | 17 --------- .../n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb | 24 ------------- .../neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb | 24 ------------- .../n/neon/neon-0.30.0-ictce-4.0.6.eb | 24 ------------- .../n/neon/neon-0.30.0-ictce-4.1.13.eb | 24 ------------- .../n/neon/neon-0.30.0-ictce-5.2.0.eb | 24 ------------- .../n/neon/neon-0.30.0-ictce-5.3.0.eb | 24 ------------- .../Python-2.5.6-gompi-1.5.12-no-OFED-bare.eb | 26 -------------- .../SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb | 35 ------------------- .../SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb | 35 ------------------- .../s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb | 35 ------------------- .../s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb | 35 ------------------- .../s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb | 35 ------------------- .../s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb | 35 ------------------- .../subversion-1.6.23-goalf-1.1.0-no-OFED.eb | 28 --------------- .../subversion-1.6.23-gompi-1.4.12-no-OFED.eb | 28 --------------- .../subversion-1.6.23-ictce-4.0.6.eb | 28 --------------- .../subversion-1.6.23-ictce-4.1.13.eb | 28 --------------- .../subversion-1.6.23-ictce-5.2.0.eb | 28 --------------- .../subversion-1.6.23-ictce-5.3.0.eb | 28 --------------- .../subversion-1.8.8-ictce-4.1.13.eb | 28 --------------- .../t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb | 19 ---------- .../t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb | 19 ---------- .../t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb | 19 ---------- .../t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb | 19 ---------- .../t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb | 19 ---------- 37 files changed, 911 deletions(-) delete mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb delete mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb delete mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb delete mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb delete mode 100644 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/dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index f5f429b778..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb deleted file mode 100644 index 6785705751..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb deleted file mode 100644 index ab0ac9c226..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb deleted file mode 100644 index 669555d663..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb deleted file mode 100644 index 5820665193..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index 42d75b76df..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index c9b38d32bc..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb deleted file mode 100644 index bb13d21a33..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb deleted file mode 100644 index c26ce2075a..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb deleted file mode 100644 index 3f74bca0b9..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb deleted file mode 100644 index 7c6b787d78..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index f111e9310e..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index 212229e999..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb deleted file mode 100644 index fdf1eabe1a..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb deleted file mode 100644 index 97eea6a566..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb deleted file mode 100644 index 244a91df81..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb deleted file mode 100644 index 6dd467a1fe..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.5.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.5.12-no-OFED-bare.eb deleted file mode 100644 index fbb6fb607f..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.5.12-no-OFED-bare.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'Python' -version = '2.5.6' -versionsuffix = '-bare' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -patches = ['Python-%(version)s_svnversion-cmd.patch'] - -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.7'), - ('libreadline', '6.2'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index 1f9d380786..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index 330ea91aef..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb deleted file mode 100644 index 8ab8985748..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb deleted file mode 100644 index 6948614b01..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb deleted file mode 100644 index 6a16570c53..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb deleted file mode 100644 index 499e33114e..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index 10fcdfa9b8..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index 18b01448ee..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb deleted file mode 100644 index cc7766f42b..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb deleted file mode 100644 index 0e7556d3dd..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb deleted file mode 100644 index 3dd8117f6f..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb deleted file mode 100644 index 8b59c05878..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb deleted file mode 100644 index 672480bf95..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.8.8' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index 688b7db304..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Tcl' -version = '8.6.1' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index bf05390914..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Tcl' -version = '8.6.1' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb deleted file mode 100755 index 4497a53f78..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Tcl' -version = '8.6.1' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb deleted file mode 100755 index a112f672e2..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Tcl' -version = '8.6.1' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb deleted file mode 100755 index d9d3d41205..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Tcl' -version = '8.6.1' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' -- GitLab From 173a810ac34382286a46d66d706adab97a9bcf49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 16:48:49 +0200 Subject: [PATCH 0087/2133] add missing 'easyblock' line --- .../a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb | 2 ++ .../easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb | 2 ++ .../easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb | 2 ++ .../s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb | 1 + .../s/subversion/subversion-1.6.23-goolf-1.4.10.eb | 12 +++++++----- 5 files changed, 14 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb index f2b44bb9a1..1a3a23018b 100644 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'APR-util' version = '1.5.3' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb index e069e515a2..bbe4a3f6c2 100644 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'APR' version = '1.5.0' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb index dbf0e6619b..2732f2ab74 100644 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'neon' version = '0.30.0' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb index 72c8d21c52..5d1c89464a 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb @@ -9,6 +9,7 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/ ## +easyblock = 'ConfigureMake' name = 'SQLite' version = '3.8.4.1' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb index c4f4b6ed90..e53ac64a5b 100644 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'subversion' version = '1.6.23' @@ -9,11 +11,6 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://archive.apache.org/dist/subversion/'] sources = [SOURCE_TAR_GZ] -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - dependencies = [ ('APR', '1.5.0'), ('APR-util', '1.5.3'), @@ -25,4 +22,9 @@ dependencies = [ configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + moduleclass = 'tools' -- GitLab From 7b78413357e94593a19d8b7e13dca2ac90077da1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 16:51:21 +0200 Subject: [PATCH 0088/2133] remove easyconfig for subversion 1.8.8 (see #1970) --- .../subversion-1.8.8-goolf-1.4.10.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb deleted file mode 100644 index 5f9488ba6c..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.8.8' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' -- GitLab From 067f1e9ebdab00845652acaaa2f562358e9d279d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 16:52:24 +0200 Subject: [PATCH 0089/2133] trash extra libxml2 easyconfig --- ...libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100755 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb deleted file mode 100755 index d68ae2eaee..0000000000 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'libxml2' -version = '2.9.1' - -homepage = 'http://xmlsoft.org/' -description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable - outside of the Gnome platform).""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] - -configopts = 'CC="$CC" CXX="$CXX" --with-pic' - -pythonver = '2.7.5' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - -dependencies = [ - ('zlib', '1.2.8'), - ('Python', pythonver), -] - -moduleclass = 'lib' -- GitLab From 08257022563059a4d3c0c1134a8ce44174015542 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 18:40:14 +0200 Subject: [PATCH 0090/2133] subversion -> Subversion --- .../Subversion-1.6.23-goolf-1.4.10.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/{subversion/subversion-1.6.23-goolf-1.4.10.eb => Subversion/Subversion-1.6.23-goolf-1.4.10.eb} (97%) diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb similarity index 97% rename from easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb rename to easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb index e53ac64a5b..fc1179c894 100644 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'subversion' +name = 'Subversion' version = '1.6.23' homepage = 'http://subversion.apache.org/' -- GitLab From ea7c25c2cb7c2dcd8b20623199891abf407712ab Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 23 Sep 2015 10:35:34 +0300 Subject: [PATCH 0091/2133] Adding moduleclass --- easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index 5716e9f33a..7188e62917 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -34,4 +34,4 @@ parallel = 1 # about 100 tests fail ignore_regtest_fails=True - +moduleclass = 'chem' -- GitLab From 0910263c6bee90238409a546eb9cf6ee75db5991 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 11:06:17 +0200 Subject: [PATCH 0092/2133] fix filename of MACS2 easyconfig --- ...2.7.3.eb => MACS2-2.1.0-20150731-goolf-1.4.10-Python-2.7.3.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MACS2/{MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb => MACS2-2.1.0-20150731-goolf-1.4.10-Python-2.7.3.eb} (100%) diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0-20150731-goolf-1.4.10-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/MACS2/MACS2-1.1.3-goolf-1.4.10-Python-2.7.3.eb rename to easybuild/easyconfigs/m/MACS2/MACS2-2.1.0-20150731-goolf-1.4.10-Python-2.7.3.eb -- GitLab From 98d4e2d24f4a8dab9c9b5dfd0edf58ea60d6e240 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 12:03:12 +0200 Subject: [PATCH 0093/2133] fix sources spec --- .../easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb index fc1179c894..07b1072638 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = " Subversion is an open source version control system." toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('APR', '1.5.0'), -- GitLab From 06f61427222eaf3893ee869bb2dfcc885f49863e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 16:23:05 +0200 Subject: [PATCH 0094/2133] fix remarks --- .../CONTRAlign-2.01-proteins-goolf-1.4.10.eb | 14 +++++++------- .../CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb | 14 +++++++------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb index 6255d5289d..7ebcd2512d 100644 --- a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb @@ -3,18 +3,19 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -name = 'CONTRAlign' -version = '2.01-proteins' - easyblock = 'MakeCp' +name = 'CONTRAlign' +version = '2.01' +versionsuffix = '-proteins' + homepage = 'http://contra.stanford.edu/contralign/' -description = ''' CONditional TRAining for Protein Sequence Alignment ''' +description = """CONditional TRAining for Protein Sequence Alignment""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] -sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_').strip('-proteins'))] +sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] patches = ['contralign-gcc47.patch'] @@ -24,8 +25,7 @@ start_dir = 'src' # Here we are compiling for protein input. Check docs for details makeopts = 'MODEL_TYPE="-DRNA=0"' -files_to_copy = [(['contralign', 'score_directory.pl',\ - 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] +files_to_copy = [(['contralign', 'score_directory.pl', 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] sanity_check_paths = { 'files': ['bin/contralign'], diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb index 50d30ad789..bf7c0a545b 100644 --- a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb @@ -3,18 +3,19 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -name = 'CONTRAlign' -version = '2.01-rna' - easyblock = 'MakeCp' +name = 'CONTRAlign' +version = '2.01' +versionsuffix = '-rna' + homepage = 'http://contra.stanford.edu/contralign/' -description = ''' CONditional TRAining for Protein Sequence Alignment ''' +description = """CONditional TRAining for Protein Sequence Alignment""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] -sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_').strip('-rna'))] +sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] patches = ['contralign-gcc47.patch'] @@ -24,8 +25,7 @@ start_dir = 'src' # Here we are compiling for RNA input. Check docs for details makeopts = 'MODEL_TYPE="-DRNA=1"' -files_to_copy = [(['contralign', 'score_directory.pl',\ - 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] +files_to_copy = [(['contralign', 'score_directory.pl', 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] sanity_check_paths = { 'files': ['bin/contralign'], -- GitLab From 105da2f6b4e12edd29a50d2d1bc144daa4be63c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 16:24:24 +0200 Subject: [PATCH 0095/2133] change name of patch file for CONTRAlign --- .../c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb | 2 +- .../c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb | 2 +- .../{contralign-gcc47.patch => CONTRAlign-2.01_gcc47.patch} | 0 3 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/CONTRAlign/{contralign-gcc47.patch => CONTRAlign-2.01_gcc47.patch} (100%) diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb index 7ebcd2512d..84f7e76a78 100644 --- a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] -patches = ['contralign-gcc47.patch'] +patches = ['CONTRAlign-%(version)s_gcc47.patch'] start_dir = 'src' diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb index bf7c0a545b..e483634c15 100644 --- a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] -patches = ['contralign-gcc47.patch'] +patches = ['CONTRAlign-%(version)s_gcc47.patch'] start_dir = 'src' diff --git a/easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01_gcc47.patch similarity index 100% rename from easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch rename to easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01_gcc47.patch -- GitLab From 7987f0f06dd5afbb96270deed7559ba12d974379 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 23 Sep 2015 15:31:19 +0100 Subject: [PATCH 0096/2133] Fix macros for source and remove blank line --- .../easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb | 3 +-- easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb index 115f19d847..4a7086b810 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb @@ -16,7 +16,7 @@ description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputa toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] -sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] +sources = ['%s_v%%(version)s%%(versionsuffix)s.tgz' % name.lower()[:-1]] sanity_check_paths = { 'files': ["impute2"], @@ -29,4 +29,3 @@ modextrapaths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb index fe290f068e..2f68d383ff 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb @@ -16,7 +16,7 @@ description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputa toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] -sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] +sources = ['%s_v%%(version)s%%(versionsuffix)s.tgz' % name.lower()[:-1]] sanity_check_paths = { 'files': ["impute2"], @@ -29,4 +29,3 @@ modextrapaths = { } moduleclass = 'bio' - -- GitLab From b52b5f9dd4ae7a935bfebc2529857c32a51f536d Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 17:40:27 +0200 Subject: [PATCH 0097/2133] fixed identation --- .../l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb index e33c2344b7..df64a5cb98 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb @@ -2,8 +2,9 @@ name = 'libjpeg-turbo' version = '1.3.0' homepage = 'http://sourceforge.net/libjpeg-turbo/' -description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG -compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +description = """ libjpeg-turbo is a fork of the original IJG libjpeg which + uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg + is a library that implements JPEG image encoding, decoding and transcoding. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 46f373893e82e1b8e8502bfa610a1656a6159d3b Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 18:04:34 +0200 Subject: [PATCH 0098/2133] removed uneeded lines --- easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb index b2f811f92b..ce172894c9 100644 --- a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb @@ -22,9 +22,6 @@ start_dir = "source" parallel = 1 -# this requires glob support in MakeCp easyblock so -# be sure to use at least EasyBuild-1.12 or newer -easybuild_version = '1.12.0' files_to_copy = ["../*"] sanity_check_paths = { -- GitLab From 248f6b10b1e0f4506f01d529fa18ee3ea5afa660 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 18:13:21 +0200 Subject: [PATCH 0099/2133] added easyblock = 'ConfigureMake' --- easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb index 756b674e3a..9b5746011a 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb @@ -3,6 +3,8 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' + name = 'BLASR' version = '2.1' -- GitLab From 250219c48f3d03795f4875cb35c781c6b2fb0c98 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 18:23:08 +0200 Subject: [PATCH 0100/2133] switch to buildops and removed empty line --- .../m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 3 +-- .../m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb index afc62c9a6c..04ab889eab 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -25,7 +25,7 @@ parallel = 1 start_dir = "src" -makeopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' +buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' files_to_copy = ["bin", "../README", "demo"] @@ -35,4 +35,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb index 47308d8d3d..c0347a9308 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb @@ -25,7 +25,7 @@ parallel = 1 start_dir = "src" -makeopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' +buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' files_to_copy = ["bin", "../README", "demo"] @@ -35,4 +35,3 @@ sanity_check_paths = { } moduleclass = 'bio' - -- GitLab From 2cfb04cc3a8a161032657ee1f57a6720583ed747 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 18:27:53 +0200 Subject: [PATCH 0101/2133] switch to buildopts and added easyblock = 'ConfigureMake' --- .../easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb index c787473f52..435d596a7e 100644 --- a/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb @@ -3,6 +3,8 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' + name = 'Raster3D' version = '3.0-2' @@ -22,7 +24,7 @@ source_urls = [homepage] sources = ['%(name)s_%(version)s.tar.gz'] skipsteps = ['configure'] -makeopts = ' linux && make all' +buildopts = ' linux && make all' installopts = 'prefix=%(installdir)s' dependencies = [ -- GitLab From 1765d52bf7b85ae8d8c6851a4078e002fa54cc5f Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 19:58:06 +0200 Subject: [PATCH 0102/2133] switch to buildopts --- easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb index 9b5746011a..7b47764f47 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb @@ -25,7 +25,7 @@ skipsteps = ['configure'] # the STATIC= option is a workaround. Check details here: # https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 -makeopts = ' STATIC= ' +buildopts = ' STATIC= ' installopts = ' INSTALL_BIN_DIR=%(installdir)s/bin' -- GitLab From f5ea289e46eaf584a678f1edd0f7c3cfc5a1e22b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Oct 2015 13:35:11 +0200 Subject: [PATCH 0103/2133] bump to OCaml 4.02.3 and foss/2015a (2015b yields problems?) --- .../Autotools/Autotools-20150215-GCC-4.9.2.eb | 17 ++++++++++ .../batteries-2.2-ictce-5.5.0-OCaml-4.01.0.eb | 32 ------------------- .../CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb | 1 - ...SL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb | 1 - ...L-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb | 1 - .../l/libtool/libtool-2.4.6-GCC-4.9.2.eb | 17 ++++++++++ ...L-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb | 1 - .../o/OCaml/OCaml-4.01.0_icc-fixes.patch | 11 ------- ...ce-5.5.0.eb => OCaml-4.02.3-foss-2015a.eb} | 10 +++--- ...er-1.1.alpha17-foss-2015a-OCaml-4.02.3.eb} | 12 +++---- ...e3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb | 1 - 11 files changed, 43 insertions(+), 61 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb delete mode 100644 easybuild/easyconfigs/b/batteries/batteries-2.2-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.2.eb delete mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch rename easybuild/easyconfigs/o/OCaml/{OCaml-4.01.0-ictce-5.5.0.eb => OCaml-4.02.3-foss-2015a.eb} (85%) rename easybuild/easyconfigs/p/pplacer/{pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb => pplacer-1.1.alpha17-foss-2015a-OCaml-4.02.3.eb} (74%) diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb new file mode 100644 index 0000000000..9fe586bfbb --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/batteries/batteries-2.2-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/b/batteries/batteries-2.2-ictce-5.5.0-OCaml-4.01.0.eb deleted file mode 100644 index 42ce7ca6fb..0000000000 --- a/easybuild/easyconfigs/b/batteries/batteries-2.2-ictce-5.5.0-OCaml-4.01.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'batteries' -version = '2.2' - -homepage = 'http://batteries.forge.ocamlcore.org/' -description = """OCaml Batteries included (or simply "Batteries") is a community-driven effort to standardize on an - consistent, documented, and comprehensive development platform for the OCaml programming language.""" - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ['http://forge.ocamlcore.org/frs/download.php/1363/'] -sources = [SOURCE_TAR_GZ] - -ocaml = 'OCaml' -ocamlver = '4.01.0' -versionsuffix = '-%s-%s' % (ocaml, ocamlver) - -builddependencies = [('findlib', '1.5.2', versionsuffix)] -dependencies = [(ocaml, ocamlver)] - -skipsteps = ['configure'] - -buildopts = 'all' -preinstallopts = "mkdir -p %(installdir)s/site-lib && OCAMLFIND_DESTDIR=%(installdir)s/site-lib" - -modextrapaths = {'OCAMLPATH': 'site-lib'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['site-lib/batteries'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb index 29ce049ecc..6a52cf9add 100644 --- a/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb @@ -15,7 +15,6 @@ ocaml = 'OCaml' ocamlver = '4.01.0' versionsuffix = '-%s-%s' % (ocaml, ocamlver) -builddependencies = [('findlib', '1.5.2', versionsuffix)] dependencies = [ (ocaml, ocamlver), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb index 3ea3a84e5e..e9a5302250 100644 --- a/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb @@ -13,7 +13,6 @@ ocaml = 'OCaml' ocamlver = '4.01.0' versionsuffix = '-%s-%s' % (ocaml, ocamlver) -builddependencies = [('findlib', '1.5.2', versionsuffix)] dependencies = [ (ocaml, ocamlver), ('GSL', '1.16'), diff --git a/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb index 8ebdaa8e3c..c67373f3c9 100644 --- a/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb @@ -13,7 +13,6 @@ ocaml = 'OCaml' ocamlver = '4.01.0' versionsuffix = '-%s-%s' % (ocaml, ocamlver) -builddependencies = [('findlib', '1.5.2', versionsuffix)] dependencies = [ (ocaml, ocamlver), ('GSL', '1.16'), diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.2.eb new file mode 100644 index 0000000000..4658960398 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.2.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb index 87454947cb..5fa738e35a 100644 --- a/easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb @@ -13,7 +13,6 @@ sources = ['%(version)s.tar.gz'] ocaml = 'OCaml' ocamlver = '4.01.0' versionsuffix = '-%s-%s' % (ocaml, ocamlver) -builddependencies = [('findlib', '1.5.2', versionsuffix)] dependencies = [(ocaml, ocamlver)] preconfigopts = "ocaml setup.ml -configure --prefix %(installdir)s && " diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch deleted file mode 100644 index 595505634a..0000000000 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ocaml-4.01.0/configure.orig 2014-08-19 12:26:23.008974288 +0200 -+++ ocaml-4.01.0/configure 2014-08-19 12:27:15.800298562 +0200 -@@ -1015,7 +1015,7 @@ - fi - - has_select=no --if sh ./hasgot select && \ -+if cc="$cc -wd165" sh ./hasgot select && \ - sh ./hasgot -i sys/types.h $select_include -t fd_set ; then - echo "select() found." - echo "#define HAS_SELECT" >> s.h diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb similarity index 85% rename from easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb rename to easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb index 5c9d36e6b7..e9d2b5b537 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb @@ -6,8 +6,8 @@ # License:: MIT/GPL # $Id$ ## -name = "OCaml" -version = "4.01.0" +name = 'OCaml' +version = '4.02.3' homepage = 'http://ocaml.org/' description = """OCaml is a general purpose industrial-strength programming language @@ -15,7 +15,7 @@ description = """OCaml is a general purpose industrial-strength programming lang it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming.""" -toolchain = {'version': '1.4.10', 'name': 'goolf'} +toolchain = {'name': 'foss', 'version': '2015a'} ocaml_sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) opam_ver = '1.2.2' @@ -28,9 +28,9 @@ sources = [ 'opam-full-%s.tar.gz' % opam_ver, ] -patches = ['OCaml-%(version)s_icc-fixes.patch'] +patches = ['OCaml-4.01.0_icc-fixes.patch'] -builddependencies = [('Autoconf', '2.69')] +builddependencies = [('Autotools', '20150215', '', ('GCC', '4.9.2'))] dependencies = [('ncurses', '5.9')] # parallel build tends to break diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha17-foss-2015a-OCaml-4.02.3.eb similarity index 74% rename from easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb rename to easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha17-foss-2015a-OCaml-4.02.3.eb index 48464d06a1..69404fe220 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha17-foss-2015a-OCaml-4.02.3.eb @@ -1,34 +1,30 @@ easyblock = 'MakeCp' name = 'pplacer' -version = '1.1.alpha16' +version = '1.1.alpha17' homepage = 'http://matsen.fhcrc.org/pplacer/' description = """Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.""" -toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['https://github.com/matsen/pplacer/archive/'] sources = ['v%(version)s.tar.gz'] ocaml = 'OCaml' -ocamlver = '4.01.0' +ocamlver = '4.02.3' versionsuffix = '-%s-%s' % (ocaml, ocamlver) -builddependencies = [('findlib', '1.5.2', versionsuffix)] dependencies = [ (ocaml, ocamlver), - ('batteries', '2.2', versionsuffix), ('CamlZIP', '1.05', versionsuffix), ('GSL-OCaml', '0.6.3', versionsuffix), - ('csv', '1.3.3', versionsuffix), ('SQLite3-OCaml', '2.0.6', versionsuffix), - ('Xmlm', '1.2.0', versionsuffix), ('MCL', '12-068oasis4', versionsuffix), ] -prebuildopts = "echo 'let version = \"v1.1.alpha16-9-g78ea126\"\n' > common_src/version.ml && " +prebuildopts = "echo 'let version = \"v1.1.alpha17-9-g78ea126\"\n' > common_src/version.ml && " parallel = 1 files_to_copy = ['bin'] diff --git a/easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb index d08ea78903..991bbf5a9c 100644 --- a/easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb @@ -13,7 +13,6 @@ ocaml = 'OCaml' ocamlver = '4.01.0' versionsuffix = '-%s-%s' % (ocaml, ocamlver) -builddependencies = [('findlib', '1.5.2', versionsuffix)] dependencies = [ (ocaml, ocamlver), ('SQLite', '3.8.6'), -- GitLab From 2563bafe964b284017091c4688b1cc5d3cb5d469 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Oct 2015 13:44:40 +0200 Subject: [PATCH 0104/2133] remove use of faulty patch file --- ...-OCaml-4.01.0.eb => CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb} | 0 easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb | 2 -- 2 files changed, 2 deletions(-) rename easybuild/easyconfigs/c/CamlZIP/{CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb => CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb} (100%) diff --git a/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb similarity index 100% rename from easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-ictce-5.5.0-OCaml-4.01.0.eb rename to easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb index e9d2b5b537..91034014ce 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb @@ -28,8 +28,6 @@ sources = [ 'opam-full-%s.tar.gz' % opam_ver, ] -patches = ['OCaml-4.01.0_icc-fixes.patch'] - builddependencies = [('Autotools', '20150215', '', ('GCC', '4.9.2'))] dependencies = [('ncurses', '5.9')] -- GitLab From b37238968792f1982fecd3cdb9dd2de654991ed3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Oct 2015 13:44:53 +0200 Subject: [PATCH 0105/2133] fix easyconfig for CamlZIP --- .../CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb | 18 +++++------------- 1 file changed, 5 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb b/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb index 6a52cf9add..860031c69b 100644 --- a/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb +++ b/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb @@ -1,3 +1,5 @@ +easyblock = 'OCamlPackage' + name = 'CamlZIP' version = '1.05' @@ -6,27 +8,17 @@ description = """This OCaml library provides easy access to compressed files in and GZIP format, as well as to Java JAR files. It provides functions for reading from and writing to compressed files in these formats.""" -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ['https://forge.ocamlcore.org/frs/download.php/1037/'] -sources = [SOURCE_TAR_GZ] +toolchain = {'name': 'foss', 'version': '2015a'} ocaml = 'OCaml' -ocamlver = '4.01.0' +ocamlver = '4.02.3' versionsuffix = '-%s-%s' % (ocaml, ocamlver) dependencies = [ (ocaml, ocamlver), - ('zlib', '1.2.7'), + ('zlib', '1.2.8'), ] -skipsteps = ['configure', 'install'] - -prebuildopts = "mkdir -p %(installdir)s/site-lib && " -buildopts = 'all && make allopt && OCAMLFIND_DESTDIR=%(installdir)s/site-lib make install-findlib' - -modextrapaths = {'OCAMLPATH': 'site-lib'} - sanity_check_paths = { 'files': [], 'dirs': ['site-lib/zip'], -- GitLab From 4b040f6a85bdf133223f052d23f6bdec715ed401 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Oct 2015 16:30:21 +0200 Subject: [PATCH 0106/2133] add ocaml+twt and gsl extensions, drop csv and xmlm specialized extensions --- ...L-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb | 31 ------------------- .../o/OCaml/OCaml-4.02.3-foss-2015a.eb | 12 ++++--- 2 files changed, 8 insertions(+), 35 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb diff --git a/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb deleted file mode 100644 index c67373f3c9..0000000000 --- a/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-1.17.2-ictce-5.5.0-OCaml-4.01.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'GSL-OCaml' -version = '1.17.2' - -homepage = 'http://mmottl.github.io/gsl-ocaml/' -description = "OCaml bindings to the GSL (GNU Scientific Library)." - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ['https://github.com/mmottl/gsl-ocaml/archive/'] -sources = ['v%(version)s.tar.gz'] - -ocaml = 'OCaml' -ocamlver = '4.01.0' -versionsuffix = '-%s-%s' % (ocaml, ocamlver) - -dependencies = [ - (ocaml, ocamlver), - ('GSL', '1.16'), -] - -configopts = "--destdir=%(installdir)s" -preinstallopts = "mkdir -p %(installdir)s/site-lib && OCAMLFIND_DESTDIR=%(installdir)s/site-lib" - -modextrapaths = {'OCAMLPATH': 'site-lib'} - -sanity_check_paths = { - 'files': [], - 'dirs': ["site-lib/gsl"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb index 91034014ce..ecb933f867 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb @@ -28,8 +28,12 @@ sources = [ 'opam-full-%s.tar.gz' % opam_ver, ] -builddependencies = [('Autotools', '20150215', '', ('GCC', '4.9.2'))] -dependencies = [('ncurses', '5.9')] +builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +dependencies = [ + ('ncurses', '5.9'), + ('libreadline', '6.3'), + ('GSL', '1.16'), +] # parallel build tends to break parallel = 1 @@ -38,8 +42,8 @@ parallel = 1 exts_list = [ ('ocamlfind', '1.5.5'), ('batteries', '2.3.1'), - ('csv', '1.3.4'), - ('xmlm', '1.2.0'), + ('ocaml+twt', '0.94.0'), + ('gsl', '1.18.5'), ] moduleclass = 'lang' -- GitLab From 1bdbf8dfaf7f246d059eb5bbb98bdf5b83155727 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Oct 2015 16:43:24 +0200 Subject: [PATCH 0107/2133] fix Autotools version --- easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb index ecb933f867..9eee49210d 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb @@ -28,7 +28,7 @@ sources = [ 'opam-full-%s.tar.gz' % opam_ver, ] -builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +builddependencies = [('Autotools', '20150215', '', ('GCC', '4.9.2'))] dependencies = [ ('ncurses', '5.9'), ('libreadline', '6.3'), -- GitLab From 79ba11a9a26daff11e20a797ac6916e5e4efcfdd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Oct 2015 21:04:21 +0200 Subject: [PATCH 0108/2133] fix style isses, drop extensions from existing OCaml 4.01.0 easyconfig --- .../o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb index eef25b2450..25110fc6a9 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -6,8 +6,8 @@ # License:: MIT/GPL # $Id$ ## -name = "OCaml" -version = "4.01.0" +name = 'OCaml' +version = '4.01.0' homepage = 'http://ocaml.org/' description = """OCaml is a general purpose industrial-strength programming language @@ -15,7 +15,7 @@ description = """OCaml is a general purpose industrial-strength programming lang it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming.""" -toolchain = {'version': '1.4.10', 'name': 'goolf'} +toolchain = {'name': 'goolf', 'version': '1.4.10'} ocaml_sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) opam_ver = '1.2.2' @@ -34,12 +34,4 @@ dependencies = [('ncurses', '5.9')] # parallel build tends to break parallel = 1 -# handled by OPAM, order matters! -exts_list = [ - ('ocamlfind', '1.5.5'), - ('batteries', '2.3.1'), - ('csv', '1.3.4'), - ('xmlm', '1.2.0'), -] - moduleclass = 'lang' -- GitLab From 6af98e53eafac0f0bbc45d49271156f37d35e65b Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 2 Oct 2015 11:32:28 +0200 Subject: [PATCH 0109/2133] igv and igvtools easyconfigs --- .../i/IGV/IGV-2.3.60-Java-1.7.0_80.eb | 38 +++++++++++++++++++ .../IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb | 36 ++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb create mode 100644 easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb new file mode 100644 index 0000000000..c33a4578e1 --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'Tarball' + +name = 'IGV' +version = '2.3.60' + +homepage = 'http://www.broadinstitute.org/software/igv/' +description = """ The Integrative Genomics Viewer (IGV) is a high-performance visualization + tool for interactive exploration of large, integrated genomic datasets. It supports a wide + variety of data types, including array-based and next-generation sequence data, and genomic annotations. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] +sources = ['%(name)s_%(version)s.zip'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +# add the installation dir to PATH +modextrapaths = { + 'PATH': "", + } + +modloadmsg = """ To execute IGV run igv.sh """ + +sanity_check_paths = { + 'files': ["igv.sh"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb new file mode 100644 index 0000000000..1753b4227a --- /dev/null +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'Tarball' + +name = 'IGVTools' +version = '2.3.60' + +homepage = 'http://www.broadinstitute.org/software/igv/' +description = """ This package contains command line utilities for preprocessing, + computing feature count density (coverage), sorting, and indexing data files. + See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] +sources = ['%(namelower)s_%(version)s.zip'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +# add the installation dir to PATH +modextrapaths = { + 'PATH': "", + } + +sanity_check_paths = { + 'files': ["igvtools.jar", "igvtools"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From f91fcbe470777cc827184a5ade80ff40f00b1943 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Oct 2015 09:36:53 +0200 Subject: [PATCH 0110/2133] drop separate easyconfigs for OCaml packages, switch back to pplacer v1.1.alpha16 w/ ictce/5.5.0 and follow recommended build procedure for pplacer --- .../CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb | 27 ----------- ...SL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb | 34 ------------- ...L-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb | 30 ------------ .../o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 37 ++++++++++++++ ...er-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb | 48 +++++++++++++++++++ ...cer-1.1.alpha17-foss-2015a-OCaml-4.02.3.eb | 37 -------------- .../s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb | 16 ++++--- ...e3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb | 31 ------------ .../t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb | 6 +++ 9 files changed, 100 insertions(+), 166 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb delete mode 100644 easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb delete mode 100644 easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb create mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb delete mode 100644 easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha17-foss-2015a-OCaml-4.02.3.eb delete mode 100644 easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb diff --git a/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb b/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb deleted file mode 100644 index 860031c69b..0000000000 --- a/easybuild/easyconfigs/c/CamlZIP/CamlZIP-1.05-foss-2015a-OCaml-4.02.3.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'OCamlPackage' - -name = 'CamlZIP' -version = '1.05' - -homepage = 'https://forge.ocamlcore.org/projects/camlzip/' -description = """This OCaml library provides easy access to compressed files in ZIP - and GZIP format, as well as to Java JAR files. It provides functions - for reading from and writing to compressed files in these formats.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -ocaml = 'OCaml' -ocamlver = '4.02.3' -versionsuffix = '-%s-%s' % (ocaml, ocamlver) - -dependencies = [ - (ocaml, ocamlver), - ('zlib', '1.2.8'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['site-lib/zip'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb deleted file mode 100644 index e9a5302250..0000000000 --- a/easybuild/easyconfigs/g/GSL-OCaml/GSL-OCaml-0.6.3-ictce-5.5.0-OCaml-4.01.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'GSL-OCaml' -version = '0.6.3' - -homepage = 'http://mmottl.github.io/gsl-ocaml/' -description = "OCaml bindings to the GSL (GNU Scientific Library)." - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ['https://github.com/mmottl/gsl-ocaml/archive/'] -sources = ['v%(version)s.tar.gz'] - -ocaml = 'OCaml' -ocamlver = '4.01.0' -versionsuffix = '-%s-%s' % (ocaml, ocamlver) - -dependencies = [ - (ocaml, ocamlver), - ('GSL', '1.16'), -] - -skipsteps = ['configure'] -prebuildopts = "OCAML_BACKEND=gcc" -preinstallopts = "mkdir -p %(installdir)s/site-lib && OCAML_BACKEND=gcc OCAMLFIND_DESTDIR=%(installdir)s/site-lib" - -parallel = 1 - -modextrapaths = {'OCAMLPATH': 'site-lib'} - -sanity_check_paths = { - 'files': [], - 'dirs': ["site-lib/gsl"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb deleted file mode 100644 index 5fa738e35a..0000000000 --- a/easybuild/easyconfigs/m/MCL/MCL-12-068oasis4-ictce-5.5.0-OCaml-4.01.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -name = 'MCL' -version = '12-068oasis4' - -homepage = 'https://github.com/fhcrc/mcl' -description = """Graph clustering by flow simulation.""" - -toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/fhcrc/mcl/archive/'] -sources = ['%(version)s.tar.gz'] - -ocaml = 'OCaml' -ocamlver = '4.01.0' -versionsuffix = '-%s-%s' % (ocaml, ocamlver) -dependencies = [(ocaml, ocamlver)] - -preconfigopts = "ocaml setup.ml -configure --prefix %(installdir)s && " -buildopts = "&& ocaml setup.ml -build" -preinstallopts = "mkdir -p %(installdir)s/site-lib &&" -installopts = "&& OCAMLFIND_DESTDIR=%(installdir)s/site-lib ocaml setup.ml -install" - -modextrapaths = {'OCAMLPATH': 'site-lib'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb new file mode 100644 index 0000000000..00cc54b782 --- /dev/null +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## +name = 'OCaml' +version = '4.01.0' + +homepage = 'http://ocaml.org/' +description = """OCaml is a general purpose industrial-strength programming language + with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria + it benefits from one of the most advanced type systems and supports functional, + imperative and object-oriented styles of programming.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +ocaml_sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) +opam_ver = '1.2.2' +source_urls = [ + 'http://caml.inria.fr/pub/distrib/%s' % ocaml_sourcedir, + 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, +] +sources = [ + 'ocaml-%(version)s.tar.gz', + 'opam-full-%s.tar.gz' % opam_ver, +] + +builddependencies = [('Autoconf', '2.69')] +dependencies = [('ncurses', '5.9')] + +# parallel build tends to break +parallel = 1 + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb new file mode 100644 index 0000000000..f16f8b1dff --- /dev/null +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'pplacer' +version = '1.1.alpha16' + +homepage = 'http://matsen.fhcrc.org/pplacer/' +description = """Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic + likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give + useful information about uncertainty, and to offer advanced visualization and downstream analysis.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [ + 'https://github.com/matsen/pplacer/archive/', + 'https://github.com/matsen/pplacer-opam-repository/archive/', +] +sources = [ + 'v%(version)s.tar.gz', + 'ba5e766.tar.gz', # pplacer-opam-repository (20151002) +] + +ocaml = 'OCaml' +ocamlver = '4.01.0' +versionsuffix = '-%s-%s' % (ocaml, ocamlver) +dependencies = [ + (ocaml, ocamlver), + ('zlib', '1.2.7'), # for CamlZIP OCaml package + ('GSL', '1.16'), # for GSL-OCaml package + ('SQLite', '3.8.6'), # for SQLite3-OCaml package +] + +start_dir = '%(name)-%(version)s' + +# see http://matsen.github.io/pplacer/compiling.html#opam +prebuildopts = "export OPAMROOT=%(installdir)s && opam init && " +prebuildopts += "opam repo add pplacer-deps %(builddir)s/pplacer-opam-repository*/ && " +prebuildopts += "opam update pplacer-deps && eval `opam config env` && " +prebuildopts += "cat opam-requirements.txt | xargs opam install -y && " +parallel = 1 + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/guppy', 'bin/pplacer', 'bin/rppr'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha17-foss-2015a-OCaml-4.02.3.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha17-foss-2015a-OCaml-4.02.3.eb deleted file mode 100644 index 69404fe220..0000000000 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha17-foss-2015a-OCaml-4.02.3.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'MakeCp' - -name = 'pplacer' -version = '1.1.alpha17' - -homepage = 'http://matsen.fhcrc.org/pplacer/' -description = """Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic - likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give - useful information about uncertainty, and to offer advanced visualization and downstream analysis.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -source_urls = ['https://github.com/matsen/pplacer/archive/'] -sources = ['v%(version)s.tar.gz'] - -ocaml = 'OCaml' -ocamlver = '4.02.3' -versionsuffix = '-%s-%s' % (ocaml, ocamlver) -dependencies = [ - (ocaml, ocamlver), - ('CamlZIP', '1.05', versionsuffix), - ('GSL-OCaml', '0.6.3', versionsuffix), - ('SQLite3-OCaml', '2.0.6', versionsuffix), - ('MCL', '12-068oasis4', versionsuffix), -] - -prebuildopts = "echo 'let version = \"v1.1.alpha17-9-g78ea126\"\n' > common_src/version.ml && " -parallel = 1 - -files_to_copy = ['bin'] - -sanity_check_paths = { - 'files': ['bin/guppy', 'bin/pplacer', 'bin/rppr'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb index ab3d1ec5e2..68d585b3df 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ # @@ -10,18 +10,20 @@ # http://hpcbios.readthedocs.org/en/latest/ ## +easyblock = 'ConfigureMake' + name = 'SQLite' version = '3.8.6' -homepage = 'http://www.hwaci.com/sw/sqlite/' +homepage = 'http://www.sqlite.org/' description = "SQLite: SQL Database Engine in a C Library" -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - toolchain = {'name': 'ictce', 'version': '5.5.0'} +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2014/'] +sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + dependencies = [ ('libreadline', '6.2'), ('Tcl', '8.6.1'), diff --git a/easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb deleted file mode 100644 index 991bbf5a9c..0000000000 --- a/easybuild/easyconfigs/s/SQLite3-OCaml/SQLite3-OCaml-2.0.6-ictce-5.5.0-OCaml-4.01.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'SQLite3-OCaml' -version = '2.0.6' - -homepage = 'https://github.com/mmottl/sqlite3-ocaml' -description = "OCaml bindings to the SQLite3 database.""" - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ['https://github.com/mmottl/sqlite3-ocaml/archive/'] -sources = ['v%(version)s.tar.gz'] - -ocaml = 'OCaml' -ocamlver = '4.01.0' -versionsuffix = '-%s-%s' % (ocaml, ocamlver) - -dependencies = [ - (ocaml, ocamlver), - ('SQLite', '3.8.6'), -] - -configopts = "--destdir=%(installdir)s" -preinstallopts = "mkdir -p %(installdir)s/site-lib && OCAMLFIND_DESTDIR=%(installdir)s/site-lib" - -modextrapaths = {'OCAMLPATH': 'site-lib'} - -sanity_check_paths = { - 'files': [], - 'dirs': ["site-lib/sqlite3"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb index 19a137231e..335678c031 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'Tcl' version = '8.6.1' @@ -10,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' -- GitLab From f51f48edb7f71ed1c835e3ea124c013e460ee60a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Oct 2015 09:38:07 +0200 Subject: [PATCH 0111/2133] remove unused easyconfigs --- .../Autotools/Autotools-20150215-GCC-4.9.2.eb | 17 ------- .../l/libtool/libtool-2.4.6-GCC-4.9.2.eb | 17 ------- .../o/OCaml/OCaml-4.02.3-foss-2015a.eb | 49 ------------------- 3 files changed, 83 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb delete mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.2.eb delete mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb deleted file mode 100644 index 9fe586bfbb..0000000000 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb +++ /dev/null @@ -1,17 +0,0 @@ -easyblock = 'Bundle' - -name = 'Autotools' -version = '20150215' # date of the most recent change - -homepage = 'http://autotools.io' -description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" - -toolchain = {'name': 'GCC', 'version': '4.9.2'} - -dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 -] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.2.eb deleted file mode 100644 index 4658960398..0000000000 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.2.eb +++ /dev/null @@ -1,17 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libtool' -version = '2.4.6' - -homepage = 'http://www.gnu.org/software/libtool' -description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries - behind a consistent, portable interface.""" - -toolchain = {'name': 'GCC', 'version': '4.9.2'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -dependencies = [('M4', '1.4.17')] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb deleted file mode 100644 index 9eee49210d..0000000000 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb +++ /dev/null @@ -1,49 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -## -name = 'OCaml' -version = '4.02.3' - -homepage = 'http://ocaml.org/' -description = """OCaml is a general purpose industrial-strength programming language - with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria - it benefits from one of the most advanced type systems and supports functional, - imperative and object-oriented styles of programming.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -ocaml_sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) -opam_ver = '1.2.2' -source_urls = [ - 'http://caml.inria.fr/pub/distrib/%s' % ocaml_sourcedir, - 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, -] -sources = [ - 'ocaml-%(version)s.tar.gz', - 'opam-full-%s.tar.gz' % opam_ver, -] - -builddependencies = [('Autotools', '20150215', '', ('GCC', '4.9.2'))] -dependencies = [ - ('ncurses', '5.9'), - ('libreadline', '6.3'), - ('GSL', '1.16'), -] - -# parallel build tends to break -parallel = 1 - -# handled by OPAM, order matters! -exts_list = [ - ('ocamlfind', '1.5.5'), - ('batteries', '2.3.1'), - ('ocaml+twt', '0.94.0'), - ('gsl', '1.18.5'), -] - -moduleclass = 'lang' -- GitLab From a19fa08e929b1b6e54ca429439c883fd565ae431 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Oct 2015 10:27:38 +0200 Subject: [PATCH 0112/2133] add patch to make compilation of OCaml 4.01.0 with ictce/5.5.0 work --- .../easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 2 ++ .../easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch | 11 +++++++++++ 2 files changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb index 00cc54b782..51e6fb3d9d 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -28,6 +28,8 @@ sources = [ 'opam-full-%s.tar.gz' % opam_ver, ] +patches = ['OCaml-%(version)s_icc-fixes.patch'] + builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch new file mode 100644 index 0000000000..bbad224e68 --- /dev/null +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch @@ -0,0 +1,11 @@ +--- configure.orig 2015-10-06 10:19:12.763826416 +0200 ++++ configure 2015-10-06 10:19:56.005026703 +0200 +@@ -1084,7 +1084,7 @@ + fi + + has_gettimeofday=no +-if sh ./hasgot gettimeofday; then ++if sh ./hasgot cc="$cc -wd165" gettimeofday; then + echo "gettimeofday() found." + echo "#define HAS_GETTIMEOFDAY" >> s.h + has_gettimeofday="yes" -- GitLab From 89733709d862d84e04bbcadba1a839e63146cc3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Oct 2015 10:49:36 +0200 Subject: [PATCH 0113/2133] fix patch --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch index bbad224e68..6037d7e236 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch @@ -5,7 +5,7 @@ has_gettimeofday=no -if sh ./hasgot gettimeofday; then -+if sh ./hasgot cc="$cc -wd165" gettimeofday; then ++if sh cc="$cc -wd165" ./hasgot gettimeofday; then echo "gettimeofday() found." echo "#define HAS_GETTIMEOFDAY" >> s.h has_gettimeofday="yes" -- GitLab From 196677c005995eff4b5dc881d82e919c4d733329 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Oct 2015 12:54:26 +0200 Subject: [PATCH 0114/2133] really fix patch --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch index 6037d7e236..ab2cf73c3e 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch @@ -5,7 +5,7 @@ has_gettimeofday=no -if sh ./hasgot gettimeofday; then -+if sh cc="$cc -wd165" ./hasgot gettimeofday; then ++if cc="$cc -wd165" sh ./hasgot gettimeofday; then echo "gettimeofday() found." echo "#define HAS_GETTIMEOFDAY" >> s.h has_gettimeofday="yes" -- GitLab From 414eb8ad2bba443c5c1177c01e7d3fd8751efbd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Oct 2015 14:16:19 +0200 Subject: [PATCH 0115/2133] fix typo --- .../p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb index f16f8b1dff..fd414fb69a 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('SQLite', '3.8.6'), # for SQLite3-OCaml package ] -start_dir = '%(name)-%(version)s' +start_dir = '%(name)s-%(version)s' # see http://matsen.github.io/pplacer/compiling.html#opam prebuildopts = "export OPAMROOT=%(installdir)s && opam init && " -- GitLab From 2f7d0856b564dc0bf2a249e5f53ab14e7007fee4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Oct 2015 14:24:19 +0200 Subject: [PATCH 0116/2133] no need to specify start_dir --- .../p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb index fd414fb69a..020232dbc3 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb @@ -29,8 +29,6 @@ dependencies = [ ('SQLite', '3.8.6'), # for SQLite3-OCaml package ] -start_dir = '%(name)s-%(version)s' - # see http://matsen.github.io/pplacer/compiling.html#opam prebuildopts = "export OPAMROOT=%(installdir)s && opam init && " prebuildopts += "opam repo add pplacer-deps %(builddir)s/pplacer-opam-repository*/ && " -- GitLab From 79c87bad7b6658455c0c9577b6b1e76407cc36c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Oct 2015 20:05:24 +0200 Subject: [PATCH 0117/2133] extend patch for OCaml configure, add M4 as build dep for pplacer --- .../easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch | 9 +++++++++ .../pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb | 11 ++++++++--- .../pplacer-1.1.alpha16_fix-sqlite3-req-pkg.patch | 11 +++++++++++ 3 files changed, 28 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16_fix-sqlite3-req-pkg.patch diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch index ab2cf73c3e..1d8950ff29 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch @@ -1,5 +1,14 @@ --- configure.orig 2015-10-06 10:19:12.763826416 +0200 +++ configure 2015-10-06 10:19:56.005026703 +0200 +@@ -1015,7 +1015,7 @@ + fi + + has_select=no +-if sh ./hasgot select && \ ++if cc="$cc -wd165" sh ./hasgot select && \ + sh ./hasgot -i sys/types.h $select_include -t fd_set ; then + echo "select() found." + echo "#define HAS_SELECT" >> s.h @@ -1084,7 +1084,7 @@ fi diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb index 020232dbc3..8a7218977a 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb @@ -19,6 +19,8 @@ sources = [ 'ba5e766.tar.gz', # pplacer-opam-repository (20151002) ] +patches = ['pplacer-%(version)s_fix-sqlite3-req-pkg.patch'] + ocaml = 'OCaml' ocamlver = '4.01.0' versionsuffix = '-%s-%s' % (ocaml, ocamlver) @@ -28,12 +30,15 @@ dependencies = [ ('GSL', '1.16'), # for GSL-OCaml package ('SQLite', '3.8.6'), # for SQLite3-OCaml package ] +builddependencies = [ + ('M4', '1.4.17'), +] # see http://matsen.github.io/pplacer/compiling.html#opam -prebuildopts = "export OPAMROOT=%(installdir)s && opam init && " +prebuildopts = "rm -rf %(installdir)s && export OPAMROOT=%(installdir)s && opam init && " prebuildopts += "opam repo add pplacer-deps %(builddir)s/pplacer-opam-repository*/ && " -prebuildopts += "opam update pplacer-deps && eval `opam config env` && " -prebuildopts += "cat opam-requirements.txt | xargs opam install -y && " +prebuildopts += "echo 'OPAM UPDATE' && opam update pplacer-deps && echo 'OPAM CONFIG' && eval `opam config env` && " +prebuildopts += "echo 'OPAM INSTALL' && cat opam-requirements.txt | xargs opam install -y && " parallel = 1 files_to_copy = ['bin'] diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16_fix-sqlite3-req-pkg.patch b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16_fix-sqlite3-req-pkg.patch new file mode 100644 index 0000000000..6bb8c7268d --- /dev/null +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16_fix-sqlite3-req-pkg.patch @@ -0,0 +1,11 @@ +fix name of required sqlite3-ocaml package +see also https://github.com/matsen/pplacer/commit/4ae1c6803486a6460a776b6807657a3bcc4005da +--- opam-requirements.txt.orig 2015-10-06 16:38:42.246475661 +0200 ++++ opam-requirements.txt 2015-10-06 16:38:50.586708932 +0200 +@@ -4,5 +4,5 @@ + mcl.12-068oasis3 + batteries.2.1.0 + ocaml-gsl.0.6.3 +-sqlite3-ocaml.1.6.3 ++sqlite3.1.6.3 + camlzip.1.05 -- GitLab From 50eed51b8a23e4febfda9ac834e68d778cf545b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Oct 2015 20:51:29 +0200 Subject: [PATCH 0118/2133] set $OCAML_BACKEND to 'gcc' to fix issue with building gsl-ocaml --- .../p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb index 8a7218977a..b23402e2e0 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb @@ -37,8 +37,8 @@ builddependencies = [ # see http://matsen.github.io/pplacer/compiling.html#opam prebuildopts = "rm -rf %(installdir)s && export OPAMROOT=%(installdir)s && opam init && " prebuildopts += "opam repo add pplacer-deps %(builddir)s/pplacer-opam-repository*/ && " -prebuildopts += "echo 'OPAM UPDATE' && opam update pplacer-deps && echo 'OPAM CONFIG' && eval `opam config env` && " -prebuildopts += "echo 'OPAM INSTALL' && cat opam-requirements.txt | xargs opam install -y && " +prebuildopts += "opam update pplacer-deps && eval `opam config env` && " +prebuildopts += "export OCAML_BACKEND=gcc && cat opam-requirements.txt | xargs opam install -y && " parallel = 1 files_to_copy = ['bin'] -- GitLab From 494cc57bad11ad1669a241d34e95ce0b1e0bdb45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Oct 2015 11:01:28 +0100 Subject: [PATCH 0119/2133] {vis}[intel/2015b] p4vasp 0.3.29 --- .../p/p4vasp/p4vasp-0.3.29-intel-2015b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b.eb diff --git a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b.eb b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b.eb new file mode 100644 index 0000000000..1a98acb8a6 --- /dev/null +++ b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'p4vasp' +version = '0.3.29' + +homepage = 'http://www.p4vasp.at/' +description = """Visualization suite for VASP""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +# download via http://www.p4vasp.at/index.php/downloads +sources = [SOURCE_TGZ] + +skipsteps = ['configure', 'build'] + +# redefine $HOME to specify installation prefix O_o +preinstallopts = "HOME=%(installdir)s make local &&" + +sanity_check_paths = { + 'files': ['p4vasp/bin/p4v', 'p4vasp/lib/libODP.a', 'p4vasp/lib/libp4vasp.a'], + 'dirs': ['p4vasp/data', 'p4vasp/include/ODP', 'p4vasp/include/p4vasp', 'p4vasp/python-packages', 'p4vasp/utils'], +} + +modextrapaths = { + 'CPATH': ['p4vasp/include'], + 'LIBRARY_PATH': ['p4vasp/lib'], + 'PATH': ['p4vasp/bin'], + 'PYTHONPATH': ['p4vasp/python-packages'], +} + +moduleclass = 'vis' -- GitLab From 3dcf130206be4537076431d0d2e92e7ceeccd566 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Oct 2015 14:45:50 +0100 Subject: [PATCH 0120/2133] add PyGTK dep in p4vasp easyconfig --- .../g/GLib/GLib-2.47.1-intel-2015b.eb | 21 +++++++++++ ...Object-Introspection-1.46.0-intel-2015b.eb | 37 +++++++++++++++++++ ...ject-Introspection-1.46.0_env-python.patch | 8 ++++ ...Object-2.28.3-intel-2015b-Python-2.7.10.eb | 30 +++++++++++++++ .../PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb | 30 +++++++++++++++ ...4vasp-0.3.29-intel-2015b-Python-2.7.10.eb} | 5 +++ 6 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch create mode 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb rename easybuild/easyconfigs/p/p4vasp/{p4vasp-0.3.29-intel-2015b.eb => p4vasp-0.3.29-intel-2015b-Python-2.7.10.eb} (89%) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb new file mode 100644 index 0000000000..d5db1754d1 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.1' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.6'), +] +builddependencies = [('Python', '2.7.10')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b.eb new file mode 100644 index 0000000000..adb7b2d88a --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.46.0' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +patches = ['GObject-Introspection-%(version)s_env-python.patch'] + +dependencies = [ + ('Python', '2.7.10'), + ('GLib', '2.47.1'), + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch new file mode 100644 index 0000000000..a308f8a3ed --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch @@ -0,0 +1,8 @@ +--- gobject-introspection-1.46.0.orig/tools/g-ir-tool-template.in 2015-10-27 12:42:43.844025247 +0100 ++++ gobject-introspection-1.46.0/tools/g-ir-tool-template.in 2015-10-27 12:41:09.431855691 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env @PYTHON@ ++#!/usr/bin/env python + # -*- Mode: Python -*- + # GObject-Introspection - a framework for introspecting GObject libraries + # Copyright (C) 2008 Johan Dahlin diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..447454d5c1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'PyGObject' +version = '2.28.3' + +homepage = 'http://www.pygtk.org/' +description = """Python Bindings for GLib/GObject/GIO/GTK+""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +pyver_maj_min = '2.7' +pyver = '%s.10' % pyver_maj_min +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('GLib', '2.47.1'), + ('GObject-Introspection', '1.46.0'), + ('pycairo', '1.10.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pygtk' % pyver_maj_min], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..b4ce217801 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'PyGTK' +version = '2.24.0' + +homepage = 'http://www.pygtk.org/' +description = """PyGTK lets you to easily create programs with a graphical user interface + using the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +pyver_maj_min = '2.7' +pyver = '%s.10' % pyver_maj_min +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('GLib', '2.47.1'), + ('PyGObject', '2.28.3', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pygtk' % pyver_maj_min], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b.eb b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b-Python-2.7.10.eb similarity index 89% rename from easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b.eb rename to easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b-Python-2.7.10.eb index 1a98acb8a6..7fcc6c3b0b 100644 --- a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b.eb +++ b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b-Python-2.7.10.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'p4vasp' version = '0.3.29' +versionsuffix = '-Python-2.7.10' homepage = 'http://www.p4vasp.at/' description = """Visualization suite for VASP""" @@ -11,6 +12,10 @@ toolchain = {'name': 'intel', 'version': '2015b'} # download via http://www.p4vasp.at/index.php/downloads sources = [SOURCE_TGZ] +dependencies = [ + ('PyGTK', '2.24.0', versionsuffix), +] + skipsteps = ['configure', 'build'] # redefine $HOME to specify installation prefix O_o -- GitLab From 84d3505c022625c9693e88955f25f0768c5d37a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Oct 2015 16:44:17 +0100 Subject: [PATCH 0121/2133] add comment to patch for GObject-Introspection --- .../GObject-Introspection-1.46.0_env-python.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch index a308f8a3ed..10ef1bbb3f 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch @@ -1,3 +1,5 @@ +avoid that full path to bin/python is used in Python scripts +author: Kenneth Hoste (HPC-UGent) --- gobject-introspection-1.46.0.orig/tools/g-ir-tool-template.in 2015-10-27 12:42:43.844025247 +0100 +++ gobject-introspection-1.46.0/tools/g-ir-tool-template.in 2015-10-27 12:41:09.431855691 +0100 @@ -1,4 +1,4 @@ -- GitLab From a533eb7d3ecbc97ed4dc2e732b3da4d903366985 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Oct 2015 17:05:52 +0100 Subject: [PATCH 0122/2133] fix versionsuffix for GObject-Introspection --- ...Object-Introspection-1.46.0-intel-2015b-Python-2.7.10.eb} | 5 ++++- .../PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/GObject-Introspection/{GObject-Introspection-1.46.0-intel-2015b.eb => GObject-Introspection-1.46.0-intel-2015b-Python-2.7.10.eb} (93%) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b-Python-2.7.10.eb similarity index 93% rename from easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b.eb rename to easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b-Python-2.7.10.eb index adb7b2d88a..1cf131481f 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b-Python-2.7.10.eb @@ -17,8 +17,11 @@ sources = [SOURCELOWER_TAR_XZ] patches = ['GObject-Introspection-%(version)s_env-python.patch'] +pyver = '2.7.10' +versionsuffix = '-Python-%s' % pyver + dependencies = [ - ('Python', '2.7.10'), + ('Python', pyver), ('GLib', '2.47.1'), ('Bison', '3.0.4'), ] diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb index 447454d5c1..386119a809 100644 --- a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb @@ -18,7 +18,7 @@ versionsuffix = '-Python-%s' % pyver dependencies = [ ('Python', pyver), ('GLib', '2.47.1'), - ('GObject-Introspection', '1.46.0'), + ('GObject-Introspection', '1.46.0', versionsuffix), ('pycairo', '1.10.0', versionsuffix), ] -- GitLab From 668e7a21a2ec5781fd5288f20b78df181adf052d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Oct 2015 22:57:37 +0100 Subject: [PATCH 0123/2133] switch to GLib 2.29.92 and PyGObject 2.28.6 --- .../cairo-1.14.2-intel-2015b-GLib-2.29.92.eb | 46 +++++++++++++++++++ ...l-2015b.eb => GLib-2.29.92-intel-2015b.eb} | 5 +- ...ction-0.10.8-intel-2015b-Python-2.7.10.eb} | 8 ++-- ...ject-Introspection-1.46.0_env-python.patch | 10 ---- ...Object-2.28.3-intel-2015b-Python-2.7.10.eb | 30 ------------ ...Object-2.28.6-intel-2015b-Python-2.7.10.eb | 34 ++++++++++++++ .../PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb | 8 ++-- ...-intel-2015b-Python-2.7.10-GLib-2.29.92.eb | 30 ++++++++++++ 8 files changed, 120 insertions(+), 51 deletions(-) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015b-GLib-2.29.92.eb rename easybuild/easyconfigs/g/GLib/{GLib-2.47.1-intel-2015b.eb => GLib-2.29.92-intel-2015b.eb} (84%) rename easybuild/easyconfigs/g/GObject-Introspection/{GObject-Introspection-1.46.0-intel-2015b-Python-2.7.10.eb => GObject-Introspection-0.10.8-intel-2015b-Python-2.7.10.eb} (87%) delete mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch delete mode 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10-GLib-2.29.92.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015b-GLib-2.29.92.eb new file mode 100644 index 0000000000..75af067c33 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015b-GLib-2.29.92.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.2' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +glibver = '2.29.92' +versionsuffix = '-GLib-%s' % glibver + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.18'), + ('freetype', '2.6.1'), + ('pixman', '0.32.8'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), + ('GLib', glibver), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes" + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.29.92-intel-2015b.eb similarity index 84% rename from easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb rename to easybuild/easyconfigs/g/GLib/GLib-2.29.92-intel-2015b.eb index d5db1754d1..053d541683 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.29.92-intel-2015b.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GLib' -version = '2.47.1' +version = '2.29.92' homepage = 'http://www.gtk.org/' description = """GLib is one of the base libraries of the GTK+ project""" @@ -10,11 +10,12 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] -sources = [SOURCELOWER_TAR_XZ] +sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.10')] diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-0.10.8-intel-2015b-Python-2.7.10.eb similarity index 87% rename from easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-0.10.8-intel-2015b-Python-2.7.10.eb index 1cf131481f..669dcee41a 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-0.10.8-intel-2015b-Python-2.7.10.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GObject-Introspection' -version = '1.46.0' +version = '0.10.8' homepage = 'https://wiki.gnome.org/GObjectIntrospection/' description = """GObject introspection is a middleware layer between C libraries @@ -13,16 +13,14 @@ description = """GObject introspection is a middleware layer between C libraries toolchain = {'name': 'intel', 'version': '2015b'} source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] - -patches = ['GObject-Introspection-%(version)s_env-python.patch'] +sources = [SOURCELOWER_TAR_GZ] pyver = '2.7.10' versionsuffix = '-Python-%s' % pyver dependencies = [ ('Python', pyver), - ('GLib', '2.47.1'), + ('GLib', '2.29.92'), ('Bison', '3.0.4'), ] diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch deleted file mode 100644 index 10ef1bbb3f..0000000000 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.46.0_env-python.patch +++ /dev/null @@ -1,10 +0,0 @@ -avoid that full path to bin/python is used in Python scripts -author: Kenneth Hoste (HPC-UGent) ---- gobject-introspection-1.46.0.orig/tools/g-ir-tool-template.in 2015-10-27 12:42:43.844025247 +0100 -+++ gobject-introspection-1.46.0/tools/g-ir-tool-template.in 2015-10-27 12:41:09.431855691 +0100 -@@ -1,4 +1,4 @@ --#!/usr/bin/env @PYTHON@ -+#!/usr/bin/env python - # -*- Mode: Python -*- - # GObject-Introspection - a framework for introspecting GObject libraries - # Copyright (C) 2008 Johan Dahlin diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb deleted file mode 100644 index 386119a809..0000000000 --- a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.3-intel-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PyGObject' -version = '2.28.3' - -homepage = 'http://www.pygtk.org/' -description = """Python Bindings for GLib/GObject/GIO/GTK+""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_BZ2] - -pyver_maj_min = '2.7' -pyver = '%s.10' % pyver_maj_min -versionsuffix = '-Python-%s' % pyver - -dependencies = [ - ('Python', pyver), - ('GLib', '2.47.1'), - ('GObject-Introspection', '1.46.0', versionsuffix), - ('pycairo', '1.10.0', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/pygtk' % pyver_maj_min], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..3c627c6217 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'PyGObject' +version = '2.28.6' + +homepage = 'http://www.pygtk.org/' +description = """Python Bindings for GLib/GObject/GIO/GTK+""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +pyver_maj_min = '2.7' +pyver = '%s.10' % pyver_maj_min +versionsuffix = '-Python-%s' % pyver + +glibver = '2.29.92' +dependencies = [ + ('Python', pyver), + ('GLib', glibver), + ('GObject-Introspection', '0.10.8', versionsuffix), + ('pycairo', '1.10.0', versionsuffix + '-GLib-%s' % glibver), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/pygtk-%(version_major)s.0/pyglib.h', 'include/pygtk-%(version_major)s.0/pygobject.h', + 'lib/libpyglib-%(version_major)s.0-python.so'], + 'dirs': ['bin', 'lib/python%s/site-packages/' % pyver_maj_min], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb index b4ce217801..acfff835e3 100644 --- a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb @@ -18,13 +18,13 @@ versionsuffix = '-Python-%s' % pyver dependencies = [ ('Python', pyver), - ('GLib', '2.47.1'), - ('PyGObject', '2.28.3', versionsuffix), + ('GLib', '2.29.92'), + ('PyGObject', '2.28.6', versionsuffix), ] sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/pygtk' % pyver_maj_min], + 'files': ['lib/pkgconfig/pygtk-%(version_major)s.0.pc'], + 'dirs': ['lib/pygtk'], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10-GLib-2.29.92.eb b/easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10-GLib-2.29.92.eb new file mode 100644 index 0000000000..23337bffcc --- /dev/null +++ b/easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10-GLib-2.29.92.eb @@ -0,0 +1,30 @@ +easyblock = 'Waf' + +name = 'pycairo' +version = '1.10.0' + +homepage = 'http://cairographics.org/pycairo/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://cairographics.org/releases/'] +# py2cairo is the Python 2 compatible release +sources = ['py2cairo-%(version)s.tar.bz2'] + +pyver_maj_min = '2.7' +pyver = '%s.10' % pyver_maj_min +glibver = '2.29.92' +versionsuffix = '-Python-%s-GLib-%s' % (pyver, glibver) + +dependencies = [ + ('Python', pyver), + ('cairo', '1.14.2', '-GLib-%s' % glibver), +] + +sanity_check_paths = { + 'files': ['include/pycairo/pycairo.h', 'lib/pkgconfig/pycairo.pc'], + 'dirs': ['lib/python%s/site-packages/cairo' % pyver_maj_min], +} + +moduleclass = 'vis' -- GitLab From c929d00dbed60900915cfd079f8be663be842d04 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 28 Oct 2015 18:10:47 +0000 Subject: [PATCH 0124/2133] Add BEDTools 2.25.0 for FOSS 2015a --- .../b/BEDTools/BEDTools-2.25.0-foss-2015a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb new file mode 100644 index 0000000000..0b9e9a4fe5 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.25.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 306eacbedac40cda6710e8a68df8507f78c7efaa Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Thu, 29 Oct 2015 01:55:55 +0100 Subject: [PATCH 0125/2133] List M4 as a dependency for GMP 6 --- easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb | 4 ++++ easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb | 4 ++++ easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb | 4 ++++ easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb | 4 ++++ easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb | 4 ++++ easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb | 4 ++++ easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb | 4 ++++ 7 files changed, 28 insertions(+) diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb index df7b8848c5..b16a7b8c54 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] +builddependencies = [ + ('M4', '1.4.17', '', True), +] + # enable C++ interface configopts = '--enable-cxx' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb index fde2319360..76ac083034 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] +builddependencies = [ + ('M4', '1.4.17', '', True), +] + # enable C++ interface configopts = '--enable-cxx' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb index 86bd52156f..3e20c04d02 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] +builddependencies = [ + ('M4', '1.4.17', '', True), +] + # enable C++ interface configopts = '--enable-cxx' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb index a9855e2029..538e7d54e0 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] +builddependencies = [ + ('M4', '1.4.17', '', True), +] + # enable C++ interface configopts = '--enable-cxx' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb index 692f1fd842..5b737a7310 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] +builddependencies = [ + ('M4', '1.4.17', '', True), +] + # enable C++ interface configopts = '--enable-cxx' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb index 2b5b650040..9e8c8a4785 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] +builddependencies = [ + ('M4', '1.4.17', '', True), +] + # enable C++ interface configopts = '--enable-cxx' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb index 9195f21b77..8ed3dafbd2 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb @@ -13,6 +13,10 @@ toolchainopts = {'pic': True, 'precise': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = [GNU_SOURCE] +builddependencies = [ + ('M4', '1.4.17', '', True), +] + # enable C++ interface configopts = '--enable-cxx' -- GitLab From 4783dccea6e7aee7e482796ac97aedb1f3467270 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Thu, 29 Oct 2015 15:00:27 +0100 Subject: [PATCH 0126/2133] GMP: use `Autotools` dependency instead of `M4` --- .../a/Autotools/Autotools-20150215.eb | 17 +++++++++++++++++ .../easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb | 2 +- .../g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb | 2 +- 8 files changed, 24 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb new file mode 100644 index 0000000000..918da84b18 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb index b16a7b8c54..5ca82b023b 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb @@ -13,7 +13,7 @@ sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] builddependencies = [ - ('M4', '1.4.17', '', True), + ('Autotools', '20150215', '', True), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb index 76ac083034..9c006ffc82 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb @@ -13,7 +13,7 @@ sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] builddependencies = [ - ('M4', '1.4.17', '', True), + ('Autotools', '20150215', '', True), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb index 3e20c04d02..38da00d968 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb @@ -13,7 +13,7 @@ sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] builddependencies = [ - ('M4', '1.4.17', '', True), + ('Autotools', '20150215', '', True), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb index 538e7d54e0..4f6f5b5c3b 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb @@ -13,7 +13,7 @@ sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] builddependencies = [ - ('M4', '1.4.17', '', True), + ('Autotools', '20150215', '', True), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb index 5b737a7310..80d5264128 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb @@ -13,7 +13,7 @@ sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] builddependencies = [ - ('M4', '1.4.17', '', True), + ('Autotools', '20150215', '', True), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb index 9e8c8a4785..09a8825768 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] builddependencies = [ - ('M4', '1.4.17', '', True), + ('Autotools', '20150215', '', True), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb index 8ed3dafbd2..9c4dc8d9de 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = [GNU_SOURCE] builddependencies = [ - ('M4', '1.4.17', '', True), + ('Autotools', '20150215', '', True), ] # enable C++ interface -- GitLab From 71fe724c2ab74dc2bd27ad47b9d2329126ea6703 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Thu, 29 Oct 2015 15:33:42 +0100 Subject: [PATCH 0127/2133] Add dummy-toolchain versions of Autoconf, Automake, libtool --- .../easyconfigs/a/Autoconf/Autoconf-2.69.eb | 26 +++++++++++++++ .../easyconfigs/a/Automake/Automake-1.15.eb | 33 +++++++++++++++++++ .../easyconfigs/l/libtool/libtool-2.4.6.eb | 17 ++++++++++ 3 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb new file mode 100644 index 0000000000..eaaffaa618 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15.eb new file mode 100644 index 0000000000..6700ff348a --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb new file mode 100644 index 0000000000..8e3a3f64d4 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' -- GitLab From a523524465bd534fa98d36575ba90b38b465b807 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Thu, 29 Oct 2015 17:49:46 +0100 Subject: [PATCH 0128/2133] Use empty version with the "dummy" toolchain in Autotools-related build files. --- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb | 2 +- easybuild/easyconfigs/a/Automake/Automake-1.15.eb | 2 +- easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb | 2 +- easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb index eaaffaa618..88f6a855ea 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb @@ -10,7 +10,7 @@ description = """Autoconf is an extensible package of M4 macros that produce she creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15.eb index 6700ff348a..155ccd39aa 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15.eb @@ -18,7 +18,7 @@ version = "1.15" homepage = 'http://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb index 918da84b18..6763feae56 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb @@ -6,7 +6,7 @@ version = '20150215' # date of the most recent change homepage = 'http://autotools.io' description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} dependencies = [ ('Autoconf', '2.69'), # 20120424 diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb index 8e3a3f64d4..3533b0aa04 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -- GitLab From 9f185b43cf9bf44d3d34cc79627508acff8a92d3 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 30 Oct 2015 12:38:28 +1300 Subject: [PATCH 0129/2133] New easyconfig for DFT-D3 --- .../d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb new file mode 100644 index 0000000000..b28f706ce6 --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.1.1' + +homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] +sources = ['dftd3.tgz'] + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 339843c8214e538e3e4504fa272cf25d44f2db1f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 2 Nov 2015 11:22:04 +1300 Subject: [PATCH 0130/2133] Added MD5 checksum for tarball --- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index b28f706ce6..79b12d07a2 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] sources = ['dftd3.tgz'] +checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From b67dff1790779871c93a0dde2618d8ba18f2ebab Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 4 Nov 2015 11:06:45 +0100 Subject: [PATCH 0131/2133] 1 --- .../e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb | 37 + .../f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb | 43 + .../easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch | 871 ++++++++++++++++++ .../o/Octopus/Octopus-5.0.0-intel-2015b.eb | 51 + .../p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb | 27 + 5 files changed, 1029 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch create mode 100644 easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb create mode 100644 easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb new file mode 100644 index 0000000000..1e01d1ca9a --- /dev/null +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ETSF_IO' +version = '1.0.4' + +homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' +description = """A library of F90 routines to read/write the ETSF file +format has been written. It is called ETSF_IO and available under LGPL. """ + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://www.etsf.eu/system/files'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-netcdf-prefix=$EBROOTNETCDF " +configopts += "--with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' " +configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include'" + +dependencies = [ + ('netCDF', '4.3.3.1'), + ('netCDF-Fortran', '4.4.2'), +] + +sanity_check_paths = { + 'files': ["bin/etsf_io"], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb new file mode 100644 index 0000000000..05f0826bb5 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4-p2' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%s-%s.tar.gz' % (name.lower(), version.split("-")[0])] +source_urls = [homepage] + +patches = ['%(name)s_%(version)s.patch'] + +builddependencies = [ + ('Autotools', '20150215', '', ('GNU', '4.9.3-2.25')), +] + +# the patch changed a Makefile.am, so we need to call autoreconf +preconfigopts = "autoreconf --verbose --symlink --force && " + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +# no quad precision, requires GCC v4.6 or higher +# see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch b/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch new file mode 100644 index 0000000000..981d2feb46 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch @@ -0,0 +1,871 @@ +#https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en#scripts +#Within these scripts we apply the following patches that have been submitted to FFTW but are not yet included in FFTW-3.3.4: +#We add two more global transposition algorithms to the planner. +#We patch file mpi/transpose-pairwise.c in order to fix a double free bug. +diff -rupN fftw-3.3.4/mpi/conf.c fftw-3.3.4-patched/mpi/conf.c +--- fftw-3.3.4/mpi/conf.c 2014-03-04 19:41:03.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/conf.c 2015-09-05 05:53:19.085516467 +0200 +@@ -29,6 +29,8 @@ static const solvtab s = + SOLVTAB(XM(transpose_pairwise_register)), + SOLVTAB(XM(transpose_alltoall_register)), + SOLVTAB(XM(transpose_recurse_register)), ++ SOLVTAB(XM(transpose_pairwise_transposed_register)), ++ SOLVTAB(XM(transpose_alltoall_transposed_register)), + SOLVTAB(XM(dft_rank_geq2_register)), + SOLVTAB(XM(dft_rank_geq2_transposed_register)), + SOLVTAB(XM(dft_serial_register)), +diff -rupN fftw-3.3.4/mpi/Makefile.am fftw-3.3.4-patched/mpi/Makefile.am +--- fftw-3.3.4/mpi/Makefile.am 2013-03-18 13:10:45.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/Makefile.am 2015-09-05 05:53:19.084516437 +0200 +@@ -16,6 +16,7 @@ BUILT_SOURCES = fftw3-mpi.f03.in fftw3-m + CLEANFILES = fftw3-mpi.f03 fftw3l-mpi.f03 + + TRANSPOSE_SRC = transpose-alltoall.c transpose-pairwise.c transpose-recurse.c transpose-problem.c transpose-solve.c mpi-transpose.h ++TRANSPOSE_SRC += transpose-alltoall-transposed.c transpose-pairwise-transposed.c + DFT_SRC = dft-serial.c dft-rank-geq2.c dft-rank-geq2-transposed.c dft-rank1.c dft-rank1-bigvec.c dft-problem.c dft-solve.c mpi-dft.h + RDFT_SRC = rdft-serial.c rdft-rank-geq2.c rdft-rank-geq2-transposed.c rdft-rank1-bigvec.c rdft-problem.c rdft-solve.c mpi-rdft.h + RDFT2_SRC = rdft2-serial.c rdft2-rank-geq2.c rdft2-rank-geq2-transposed.c rdft2-problem.c rdft2-solve.c mpi-rdft2.h +diff -rupN fftw-3.3.4/mpi/mpi-transpose.h fftw-3.3.4-patched/mpi/mpi-transpose.h +--- fftw-3.3.4/mpi/mpi-transpose.h 2014-03-04 19:41:03.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/mpi-transpose.h 2015-09-05 05:53:19.085516467 +0200 +@@ -59,3 +59,5 @@ int XM(mkplans_posttranspose)(const prob + void XM(transpose_pairwise_register)(planner *p); + void XM(transpose_alltoall_register)(planner *p); + void XM(transpose_recurse_register)(planner *p); ++void XM(transpose_pairwise_transposed_register)(planner *p); ++void XM(transpose_alltoall_transposed_register)(planner *p); +diff -rupN fftw-3.3.4/mpi/transpose-alltoall-transposed.c fftw-3.3.4-patched/mpi/transpose-alltoall-transposed.c +--- fftw-3.3.4/mpi/transpose-alltoall-transposed.c 1970-01-01 01:00:00.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/transpose-alltoall-transposed.c 2015-09-05 05:53:19.085516467 +0200 +@@ -0,0 +1,280 @@ ++/* ++ * Copyright (c) 2003, 2007-11 Matteo Frigo ++ * Copyright (c) 2003, 2007-11 Massachusetts Institute of Technology ++ * Copyright (c) 2012 Michael Pippig ++ * ++ * This program is free software; you can redistribute it and/or modify ++ * it under the terms of the GNU General Public License as published by ++ * the Free Software Foundation; either version 2 of the License, or ++ * (at your option) any later version. ++ * ++ * This program is distributed in the hope that it will be useful, ++ * but WITHOUT ANY WARRANTY; without even the implied warranty of ++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++ * GNU General Public License for more details. ++ * ++ * You should have received a copy of the GNU General Public License ++ * along with this program; if not, write to the Free Software ++ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA ++ * ++ */ ++ ++/* plans for distributed out-of-place transpose using MPI_Alltoall, ++ and which destroy the input array (also if TRANSPOSED_IN is used) */ ++ ++#include "mpi-transpose.h" ++#include ++ ++typedef struct { ++ solver super; ++ int copy_transposed_out; /* whether to copy the output for TRANSPOSED_OUT, ++ which makes the first transpose out-of-place ++ but costs an extra copy and requires us ++ to destroy the input */ ++} S; ++ ++typedef struct { ++ plan_mpi_transpose super; ++ ++ plan *cld1, *cld2, *cld2rest, *cld3; ++ ++ MPI_Comm comm; ++ int *send_block_sizes, *send_block_offsets; ++ int *recv_block_sizes, *recv_block_offsets; ++ ++ INT rest_Ioff, rest_Ooff; ++ ++ int equal_blocks; ++} P; ++ ++/* transpose locally to get contiguous chunks ++ this may take two transposes if the block sizes are unequal ++ (3 subplans, two of which operate on disjoint data) */ ++static void apply_pretranspose( ++ const P *ego, R *I, R *O ++ ) ++{ ++ plan_rdft *cld2, *cld2rest, *cld3; ++ ++ cld3 = (plan_rdft *) ego->cld3; ++ if (cld3) ++ cld3->apply(ego->cld3, O, O); ++ /* else TRANSPOSED_IN is true and user wants I transposed */ ++ ++ cld2 = (plan_rdft *) ego->cld2; ++ cld2->apply(ego->cld2, I, O); ++ cld2rest = (plan_rdft *) ego->cld2rest; ++ if (cld2rest) { ++ cld2rest->apply(ego->cld2rest, ++ I + ego->rest_Ioff, O + ego->rest_Ooff); ++ } ++} ++ ++static void apply(const plan *ego_, R *I, R *O) ++{ ++ const P *ego = (const P *) ego_; ++ plan_rdft *cld1 = (plan_rdft *) ego->cld1; ++ ++ if (cld1) { ++ /* transpose locally to get contiguous chunks */ ++ apply_pretranspose(ego, I, O); ++ ++ /* transpose chunks globally */ ++ if (ego->equal_blocks) ++ MPI_Alltoall(O, ego->send_block_sizes[0], FFTW_MPI_TYPE, ++ I, ego->recv_block_sizes[0], FFTW_MPI_TYPE, ++ ego->comm); ++ else ++ MPI_Alltoallv(O, ego->send_block_sizes, ego->send_block_offsets, ++ FFTW_MPI_TYPE, ++ I, ego->recv_block_sizes, ego->recv_block_offsets, ++ FFTW_MPI_TYPE, ++ ego->comm); ++ ++ /* transpose locally to get non-transposed output */ ++ cld1->apply(ego->cld1, I, O); ++ } /* else TRANSPOSED_OUT is true and user wants O transposed */ ++ else { ++ /* transpose locally to get contiguous chunks */ ++ apply_pretranspose(ego, I, I); ++ ++ /* transpose chunks globally */ ++ if (ego->equal_blocks) ++ MPI_Alltoall(I, ego->send_block_sizes[0], FFTW_MPI_TYPE, ++ O, ego->recv_block_sizes[0], FFTW_MPI_TYPE, ++ ego->comm); ++ else ++ MPI_Alltoallv(I, ego->send_block_sizes, ego->send_block_offsets, ++ FFTW_MPI_TYPE, ++ O, ego->recv_block_sizes, ego->recv_block_offsets, ++ FFTW_MPI_TYPE, ++ ego->comm); ++ } ++} ++ ++static int applicable(const S *ego, const problem *p_, ++ const planner *plnr) ++{ ++ /* in contrast to transpose-alltoall this algorithm can not preserve the input, ++ * since we need at least one transpose before the (out-of-place) Alltoall */ ++ const problem_mpi_transpose *p = (const problem_mpi_transpose *) p_; ++ return (1 ++ && p->I != p->O ++ && (!NO_DESTROY_INPUTP(plnr)) ++ && ((p->flags & TRANSPOSED_OUT) || !ego->copy_transposed_out) ++ && ONLY_TRANSPOSEDP(p->flags) ++ ); ++} ++ ++static void awake(plan *ego_, enum wakefulness wakefulness) ++{ ++ P *ego = (P *) ego_; ++ X(plan_awake)(ego->cld1, wakefulness); ++ X(plan_awake)(ego->cld2, wakefulness); ++ X(plan_awake)(ego->cld2rest, wakefulness); ++ X(plan_awake)(ego->cld3, wakefulness); ++} ++ ++static void destroy(plan *ego_) ++{ ++ P *ego = (P *) ego_; ++ X(ifree0)(ego->send_block_sizes); ++ MPI_Comm_free(&ego->comm); ++ X(plan_destroy_internal)(ego->cld3); ++ X(plan_destroy_internal)(ego->cld2rest); ++ X(plan_destroy_internal)(ego->cld2); ++ X(plan_destroy_internal)(ego->cld1); ++} ++ ++static void print(const plan *ego_, printer *p) ++{ ++ const P *ego = (const P *) ego_; ++ p->print(p, "(mpi-transpose-alltoall-transposed%s%(%p%)%(%p%)%(%p%)%(%p%))", ++ ego->equal_blocks ? "/e" : "", ++ ego->cld1, ego->cld2, ego->cld2rest, ego->cld3); ++} ++ ++static plan *mkplan(const solver *ego_, const problem *p_, planner *plnr) ++{ ++ const S *ego = (const S *) ego_; ++ const problem_mpi_transpose *p; ++ P *pln; ++ plan *cld1 = 0, *cld2 = 0, *cld2rest = 0, *cld3 = 0; ++ INT b, bt, vn, rest_Ioff, rest_Ooff; ++ R *O; ++ int *sbs, *sbo, *rbs, *rbo; ++ int pe, my_pe, n_pes; ++ int equal_blocks = 1; ++ static const plan_adt padt = { ++ XM(transpose_solve), awake, print, destroy ++ }; ++ ++ if (!applicable(ego, p_, plnr)) ++ return (plan *) 0; ++ ++ p = (const problem_mpi_transpose *) p_; ++ vn = p->vn; ++ ++ MPI_Comm_rank(p->comm, &my_pe); ++ MPI_Comm_size(p->comm, &n_pes); ++ ++ bt = XM(block)(p->ny, p->tblock, my_pe); ++ ++ if (p->flags & TRANSPOSED_OUT) { /* O stays transposed */ ++ if (ego->copy_transposed_out) { ++ cld1 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)(X(mktensor_1d) ++ (bt * p->nx * vn, 1, 1), ++ p->I, O = p->O), ++ 0, 0, NO_SLOW); ++ if (XM(any_true)(!cld1, p->comm)) goto nada; ++ } ++ else /* first transpose is in-place */ ++ O = p->I; ++ } ++ else { /* transpose nx x bt x vn -> bt x nx x vn */ ++ cld1 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)(X(mktensor_3d) ++ (bt, vn, p->nx * vn, ++ p->nx, bt * vn, vn, ++ vn, 1, 1), ++ p->I, O = p->O), ++ 0, 0, NO_SLOW); ++ if (XM(any_true)(!cld1, p->comm)) goto nada; ++ } ++ ++ if (XM(any_true)(!XM(mkplans_pretranspose)(p, plnr, p->I, O, my_pe, ++ &cld2, &cld2rest, &cld3, ++ &rest_Ioff, &rest_Ooff), ++ p->comm)) goto nada; ++ ++ ++ pln = MKPLAN_MPI_TRANSPOSE(P, &padt, apply); ++ ++ pln->cld1 = cld1; ++ pln->cld2 = cld2; ++ pln->cld2rest = cld2rest; ++ pln->rest_Ioff = rest_Ioff; ++ pln->rest_Ooff = rest_Ooff; ++ pln->cld3 = cld3; ++ ++ MPI_Comm_dup(p->comm, &pln->comm); ++ ++ /* Compute sizes/offsets of blocks to send for all-to-all command. */ ++ sbs = (int *) MALLOC(4 * n_pes * sizeof(int), PLANS); ++ sbo = sbs + n_pes; ++ rbs = sbo + n_pes; ++ rbo = rbs + n_pes; ++ b = XM(block)(p->nx, p->block, my_pe); ++ bt = XM(block)(p->ny, p->tblock, my_pe); ++ for (pe = 0; pe < n_pes; ++pe) { ++ INT db, dbt; /* destination block sizes */ ++ db = XM(block)(p->nx, p->block, pe); ++ dbt = XM(block)(p->ny, p->tblock, pe); ++ if (db != p->block || dbt != p->tblock) ++ equal_blocks = 0; ++ ++ /* MPI requires type "int" here; apparently it ++ has no 64-bit API? Grrr. */ ++ sbs[pe] = (int) (b * dbt * vn); ++ sbo[pe] = (int) (pe * (b * p->tblock) * vn); ++ rbs[pe] = (int) (db * bt * vn); ++ rbo[pe] = (int) (pe * (p->block * bt) * vn); ++ } ++ pln->send_block_sizes = sbs; ++ pln->send_block_offsets = sbo; ++ pln->recv_block_sizes = rbs; ++ pln->recv_block_offsets = rbo; ++ pln->equal_blocks = equal_blocks; ++ ++ X(ops_zero)(&pln->super.super.ops); ++ if (cld1) X(ops_add2)(&cld1->ops, &pln->super.super.ops); ++ if (cld2) X(ops_add2)(&cld2->ops, &pln->super.super.ops); ++ if (cld2rest) X(ops_add2)(&cld2rest->ops, &pln->super.super.ops); ++ if (cld3) X(ops_add2)(&cld3->ops, &pln->super.super.ops); ++ /* FIXME: should MPI operations be counted in "other" somehow? */ ++ ++ return &(pln->super.super); ++ ++ nada: ++ X(plan_destroy_internal)(cld3); ++ X(plan_destroy_internal)(cld2rest); ++ X(plan_destroy_internal)(cld2); ++ X(plan_destroy_internal)(cld1); ++ return (plan *) 0; ++} ++ ++static solver *mksolver(int copy_transposed_out) ++{ ++ static const solver_adt sadt = { PROBLEM_MPI_TRANSPOSE, mkplan, 0 }; ++ S *slv = MKSOLVER(S, &sadt); ++ slv->copy_transposed_out = copy_transposed_out; ++ return &(slv->super); ++} ++ ++void XM(transpose_alltoall_transposed_register)(planner *p) ++{ ++ int cto; ++ for (cto = 0; cto <= 1; ++cto) ++ REGISTER_SOLVER(p, mksolver(cto)); ++} +diff -rupN fftw-3.3.4/mpi/transpose-pairwise.c fftw-3.3.4-patched/mpi/transpose-pairwise.c +--- fftw-3.3.4/mpi/transpose-pairwise.c 2014-03-04 19:41:03.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/transpose-pairwise.c 2015-09-05 06:00:05.715433709 +0200 +@@ -53,7 +53,6 @@ static void transpose_chunks(int *sched, + { + if (sched) { + int i; +- MPI_Status status; + + /* TODO: explore non-synchronous send/recv? */ + +@@ -74,7 +73,7 @@ static void transpose_chunks(int *sched, + O + rbo[pe], (int) (rbs[pe]), + FFTW_MPI_TYPE, + pe, (pe * n_pes + my_pe) & 0xffff, +- comm, &status); ++ comm, MPI_STATUS_IGNORE); + } + } + +@@ -92,7 +91,7 @@ static void transpose_chunks(int *sched, + O + rbo[pe], (int) (rbs[pe]), + FFTW_MPI_TYPE, + pe, (pe * n_pes + my_pe) & 0xffff, +- comm, &status); ++ comm, MPI_STATUS_IGNORE); + } + } + } +@@ -350,6 +349,7 @@ nada: + X(plan_destroy_internal)(*cld3); + X(plan_destroy_internal)(*cld2rest); + X(plan_destroy_internal)(*cld2); ++ *cld2 = *cld2rest = *cld3 = NULL; + return 0; + } + +diff -rupN fftw-3.3.4/mpi/transpose-pairwise-transposed.c fftw-3.3.4-patched/mpi/transpose-pairwise-transposed.c +--- fftw-3.3.4/mpi/transpose-pairwise-transposed.c 1970-01-01 01:00:00.000000000 +0100 ++++ fftw-3.3.4-patched/mpi/transpose-pairwise-transposed.c 2015-09-05 06:00:07.280481042 +0200 +@@ -0,0 +1,510 @@ ++/* ++ * Copyright (c) 2003, 2007-11 Matteo Frigo ++ * Copyright (c) 2003, 2007-11 Massachusetts Institute of Technology ++ * Copyright (c) 2012 Michael Pippig ++ * ++ * This program is free software; you can redistribute it and/or modify ++ * it under the terms of the GNU General Public License as published by ++ * the Free Software Foundation; either version 2 of the License, or ++ * (at your option) any later version. ++ * ++ * This program is distributed in the hope that it will be useful, ++ * but WITHOUT ANY WARRANTY; without even the implied warranty of ++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++ * GNU General Public License for more details. ++ * ++ * You should have received a copy of the GNU General Public License ++ * along with this program; if not, write to the Free Software ++ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA ++ * ++ */ ++ ++/* Distributed transposes using a sequence of carefully scheduled ++ pairwise exchanges. This has the advantage that it can be done ++ in-place, or out-of-place while preserving the input, using buffer ++ space proportional to the local size divided by the number of ++ processes (i.e. to the total array size divided by the number of ++ processes squared). */ ++ ++#include "mpi-transpose.h" ++#include ++ ++typedef struct { ++ solver super; ++ int preserve_input; /* preserve input even if DESTROY_INPUT was passed */ ++} S; ++ ++typedef struct { ++ plan_mpi_transpose super; ++ ++ plan *cld1, *cld2, *cld2rest, *cld3; ++ INT rest_Ioff, rest_Ooff; ++ ++ int n_pes, my_pe, *sched; ++ INT *send_block_sizes, *send_block_offsets; ++ INT *recv_block_sizes, *recv_block_offsets; ++ MPI_Comm comm; ++ int preserve_input; ++} P; ++ ++static void transpose_chunks(int *sched, int n_pes, int my_pe, ++ INT *sbs, INT *sbo, INT *rbs, INT *rbo, ++ MPI_Comm comm, ++ R *I, R *O) ++{ ++ if (sched) { ++ int i; ++ ++ /* TODO: explore non-synchronous send/recv? */ ++ ++ if (I == O) { ++ R *buf = (R*) MALLOC(sizeof(R) * sbs[0], BUFFERS); ++ ++ for (i = 0; i < n_pes; ++i) { ++ int pe = sched[i]; ++ if (my_pe == pe) { ++ if (rbo[pe] != sbo[pe]) ++ memmove(O + rbo[pe], O + sbo[pe], ++ sbs[pe] * sizeof(R)); ++ } ++ else { ++ memcpy(buf, O + sbo[pe], sbs[pe] * sizeof(R)); ++ MPI_Sendrecv(buf, (int) (sbs[pe]), FFTW_MPI_TYPE, ++ pe, (my_pe * n_pes + pe) & 0xffff, ++ O + rbo[pe], (int) (rbs[pe]), ++ FFTW_MPI_TYPE, ++ pe, (pe * n_pes + my_pe) & 0xffff, ++ comm, MPI_STATUS_IGNORE); ++ } ++ } ++ ++ X(ifree)(buf); ++ } ++ else { /* I != O */ ++ for (i = 0; i < n_pes; ++i) { ++ int pe = sched[i]; ++ if (my_pe == pe) ++ memcpy(O + rbo[pe], I + sbo[pe], sbs[pe] * sizeof(R)); ++ else ++ MPI_Sendrecv(I + sbo[pe], (int) (sbs[pe]), ++ FFTW_MPI_TYPE, ++ pe, (my_pe * n_pes + pe) & 0xffff, ++ O + rbo[pe], (int) (rbs[pe]), ++ FFTW_MPI_TYPE, ++ pe, (pe * n_pes + my_pe) & 0xffff, ++ comm, MPI_STATUS_IGNORE); ++ } ++ } ++ } ++} ++ ++/* transpose locally to get contiguous chunks ++ this may take two transposes if the block sizes are unequal ++ (3 subplans, two of which operate on disjoint data) */ ++static void apply_pretranspose( ++ const P *ego, R *I, R *O ++ ) ++{ ++ plan_rdft *cld2, *cld2rest, *cld3; ++ ++ cld3 = (plan_rdft *) ego->cld3; ++ if (cld3) ++ cld3->apply(ego->cld3, O, O); ++ /* else TRANSPOSED_IN is true and user wants I transposed */ ++ ++ cld2 = (plan_rdft *) ego->cld2; ++ cld2->apply(ego->cld2, I, O); ++ cld2rest = (plan_rdft *) ego->cld2rest; ++ if (cld2rest) { ++ cld2rest->apply(ego->cld2rest, ++ I + ego->rest_Ioff, O + ego->rest_Ooff); ++ } ++} ++ ++static void apply(const plan *ego_, R *I, R *O) ++{ ++ const P *ego = (const P *) ego_; ++ plan_rdft *cld1 = (plan_rdft *) ego->cld1; ++ ++ if (cld1) { ++ /* transpose locally to get contiguous chunks */ ++ apply_pretranspose(ego, I, O); ++ ++ if(ego->preserve_input) I = O; ++ ++ /* transpose chunks globally */ ++ transpose_chunks(ego->sched, ego->n_pes, ego->my_pe, ++ ego->send_block_sizes, ego->send_block_offsets, ++ ego->recv_block_sizes, ego->recv_block_offsets, ++ ego->comm, O, I); ++ ++ /* transpose locally to get non-transposed output */ ++ cld1->apply(ego->cld1, I, O); ++ } /* else TRANSPOSED_OUT is true and user wants O transposed */ ++ else if (ego->preserve_input) { ++ /* transpose locally to get contiguous chunks */ ++ apply_pretranspose(ego, I, O); ++ ++ /* transpose chunks globally */ ++ transpose_chunks(ego->sched, ego->n_pes, ego->my_pe, ++ ego->send_block_sizes, ego->send_block_offsets, ++ ego->recv_block_sizes, ego->recv_block_offsets, ++ ego->comm, O, O); ++ } ++ else { ++ /* transpose locally to get contiguous chunks */ ++ apply_pretranspose(ego, I, I); ++ ++ /* transpose chunks globally */ ++ transpose_chunks(ego->sched, ego->n_pes, ego->my_pe, ++ ego->send_block_sizes, ego->send_block_offsets, ++ ego->recv_block_sizes, ego->recv_block_offsets, ++ ego->comm, I, O); ++ } ++} ++ ++static int applicable(const S *ego, const problem *p_, ++ const planner *plnr) ++{ ++ const problem_mpi_transpose *p = (const problem_mpi_transpose *) p_; ++ /* Note: this is *not* UGLY for out-of-place, destroy-input plans; ++ the planner often prefers transpose-pairwise to transpose-alltoall, ++ at least with LAM MPI on my machine. */ ++ return (1 ++ && (!ego->preserve_input || (!NO_DESTROY_INPUTP(plnr) ++ && p->I != p->O)) ++ && ONLY_TRANSPOSEDP(p->flags)); ++} ++ ++static void awake(plan *ego_, enum wakefulness wakefulness) ++{ ++ P *ego = (P *) ego_; ++ X(plan_awake)(ego->cld1, wakefulness); ++ X(plan_awake)(ego->cld2, wakefulness); ++ X(plan_awake)(ego->cld2rest, wakefulness); ++ X(plan_awake)(ego->cld3, wakefulness); ++} ++ ++static void destroy(plan *ego_) ++{ ++ P *ego = (P *) ego_; ++ X(ifree0)(ego->sched); ++ X(ifree0)(ego->send_block_sizes); ++ MPI_Comm_free(&ego->comm); ++ X(plan_destroy_internal)(ego->cld3); ++ X(plan_destroy_internal)(ego->cld2rest); ++ X(plan_destroy_internal)(ego->cld2); ++ X(plan_destroy_internal)(ego->cld1); ++} ++ ++static void print(const plan *ego_, printer *p) ++{ ++ const P *ego = (const P *) ego_; ++ p->print(p, "(mpi-transpose-pairwise-transposed%s%(%p%)%(%p%)%(%p%)%(%p%))", ++ ego->preserve_input==2 ?"/p":"", ++ ego->cld1, ego->cld2, ego->cld2rest, ego->cld3); ++} ++ ++/* Given a process which_pe and a number of processes npes, fills ++ the array sched[npes] with a sequence of processes to communicate ++ with for a deadlock-free, optimum-overlap all-to-all communication. ++ (All processes must call this routine to get their own schedules.) ++ The schedule can be re-ordered arbitrarily as long as all processes ++ apply the same permutation to their schedules. ++ ++ The algorithm here is based upon the one described in: ++ J. A. M. Schreuder, "Constructing timetables for sport ++ competitions," Mathematical Programming Study 13, pp. 58-67 (1980). ++ In a sport competition, you have N teams and want every team to ++ play every other team in as short a time as possible (maximum overlap ++ between games). This timetabling problem is therefore identical ++ to that of an all-to-all communications problem. In our case, there ++ is one wrinkle: as part of the schedule, the process must do ++ some data transfer with itself (local data movement), analogous ++ to a requirement that each team "play itself" in addition to other ++ teams. With this wrinkle, it turns out that an optimal timetable ++ (N parallel games) can be constructed for any N, not just for even ++ N as in the original problem described by Schreuder. ++*/ ++static void fill1_comm_sched(int *sched, int which_pe, int npes) ++{ ++ int pe, i, n, s = 0; ++ A(which_pe >= 0 && which_pe < npes); ++ if (npes % 2 == 0) { ++ n = npes; ++ sched[s++] = which_pe; ++ } ++ else ++ n = npes + 1; ++ for (pe = 0; pe < n - 1; ++pe) { ++ if (npes % 2 == 0) { ++ if (pe == which_pe) sched[s++] = npes - 1; ++ else if (npes - 1 == which_pe) sched[s++] = pe; ++ } ++ else if (pe == which_pe) sched[s++] = pe; ++ ++ if (pe != which_pe && which_pe < n - 1) { ++ i = (pe - which_pe + (n - 1)) % (n - 1); ++ if (i < n/2) ++ sched[s++] = (pe + i) % (n - 1); ++ ++ i = (which_pe - pe + (n - 1)) % (n - 1); ++ if (i < n/2) ++ sched[s++] = (pe - i + (n - 1)) % (n - 1); ++ } ++ } ++ A(s == npes); ++} ++ ++/* Sort the communication schedule sched for npes so that the schedule ++ on process sortpe is ascending or descending (!ascending). This is ++ necessary to allow in-place transposes when the problem does not ++ divide equally among the processes. In this case there is one ++ process where the incoming blocks are bigger/smaller than the ++ outgoing blocks and thus have to be received in ++ descending/ascending order, respectively, to avoid overwriting data ++ before it is sent. */ ++static void sort1_comm_sched(int *sched, int npes, int sortpe, int ascending) ++{ ++ int *sortsched, i; ++ sortsched = (int *) MALLOC(npes * sizeof(int) * 2, OTHER); ++ fill1_comm_sched(sortsched, sortpe, npes); ++ if (ascending) ++ for (i = 0; i < npes; ++i) ++ sortsched[npes + sortsched[i]] = sched[i]; ++ else ++ for (i = 0; i < npes; ++i) ++ sortsched[2*npes - 1 - sortsched[i]] = sched[i]; ++ for (i = 0; i < npes; ++i) ++ sched[i] = sortsched[npes + i]; ++ X(ifree)(sortsched); ++} ++ ++/* make the plans to do the pre-MPI transpositions (shared with ++ transpose-alltoall-transposed) */ ++int XM(mkplans_pretranspose)(const problem_mpi_transpose *p, planner *plnr, ++ R *I, R *O, int my_pe, ++ plan **cld2, plan **cld2rest, plan **cld3, ++ INT *rest_Ioff, INT *rest_Ooff) ++{ ++ INT vn = p->vn; ++ INT b = XM(block)(p->nx, p->block, my_pe); ++ INT bt = p->tblock; ++ INT nyb = p->ny / bt; /* number of equal-sized blocks */ ++ INT nyr = p->ny - nyb * bt; /* leftover rows after equal blocks */ ++ ++ *cld2 = *cld2rest = *cld3 = NULL; ++ *rest_Ioff = *rest_Ooff = 0; ++ ++ if (!(p->flags & TRANSPOSED_IN) && (nyr == 0 || I != O)) { ++ INT ny = p->ny * vn; ++ bt *= vn; ++ *cld2 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)(X(mktensor_3d) ++ (nyb, bt, b * bt, ++ b, ny, bt, ++ bt, 1, 1), ++ I, O), ++ 0, 0, NO_SLOW); ++ if (!*cld2) goto nada; ++ ++ if (nyr > 0) { ++ *rest_Ioff = nyb * bt; ++ *rest_Ooff = nyb * b * bt; ++ bt = nyr * vn; ++ *cld2rest = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)(X(mktensor_2d) ++ (b, ny, bt, ++ bt, 1, 1), ++ I + *rest_Ioff, ++ O + *rest_Ooff), ++ 0, 0, NO_SLOW); ++ if (!*cld2rest) goto nada; ++ } ++ } ++ else { ++ *cld2 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)( ++ X(mktensor_4d) ++ (nyb, b * bt * vn, b * bt * vn, ++ b, vn, bt * vn, ++ bt, b * vn, vn, ++ vn, 1, 1), ++ I, O), ++ 0, 0, NO_SLOW); ++ if (!*cld2) goto nada; ++ ++ *rest_Ioff = *rest_Ooff = nyb * bt * b * vn; ++ *cld2rest = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)( ++ X(mktensor_3d) ++ (b, vn, nyr * vn, ++ nyr, b * vn, vn, ++ vn, 1, 1), ++ I + *rest_Ioff, O + *rest_Ooff), ++ 0, 0, NO_SLOW); ++ if (!*cld2rest) goto nada; ++ ++ if (!(p->flags & TRANSPOSED_IN)) { ++ *cld3 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)( ++ X(mktensor_3d) ++ (p->ny, vn, b * vn, ++ b, p->ny * vn, vn, ++ vn, 1, 1), ++ I, I), ++ 0, 0, NO_SLOW); ++ if (!*cld3) goto nada; ++ } ++ } ++ ++ return 1; ++ ++nada: ++ X(plan_destroy_internal)(*cld3); ++ X(plan_destroy_internal)(*cld2rest); ++ X(plan_destroy_internal)(*cld2); ++ *cld2 = *cld2rest = *cld3 = NULL; ++ return 0; ++} ++ ++static plan *mkplan(const solver *ego_, const problem *p_, planner *plnr) ++{ ++ const S *ego = (const S *) ego_; ++ const problem_mpi_transpose *p; ++ P *pln; ++ plan *cld1 = 0, *cld2 = 0, *cld2rest = 0, *cld3 = 0; ++ INT b, bt, vn, rest_Ioff, rest_Ooff; ++ INT *sbs, *sbo, *rbs, *rbo; ++ int pe, my_pe, n_pes, sort_pe = -1, ascending = 1; ++ R *I, *O; ++ static const plan_adt padt = { ++ XM(transpose_solve), awake, print, destroy ++ }; ++ ++ UNUSED(ego); ++ ++ if (!applicable(ego, p_, plnr)) ++ return (plan *) 0; ++ ++ p = (const problem_mpi_transpose *) p_; ++ vn = p->vn; ++ I = p->I; O = p->O; ++ ++ MPI_Comm_rank(p->comm, &my_pe); ++ MPI_Comm_size(p->comm, &n_pes); ++ ++ bt = XM(block)(p->ny, p->tblock, my_pe); ++ ++ ++ if (ego->preserve_input || NO_DESTROY_INPUTP(plnr)) I = p->O; ++ ++ if (!(p->flags & TRANSPOSED_OUT)) { /* nx x bt x vn -> bt x nx x vn */ ++ cld1 = X(mkplan_f_d)(plnr, ++ X(mkproblem_rdft_0_d)(X(mktensor_3d) ++ (bt, vn, p->nx * vn, ++ p->nx, bt * vn, vn, ++ vn, 1, 1), ++ I, O = p->O), ++ 0, 0, NO_SLOW); ++ if (XM(any_true)(!cld1, p->comm)) goto nada; ++ ++ } ++ else { ++ if (ego->preserve_input || NO_DESTROY_INPUTP(plnr)) ++ O = p->O; ++ else ++ O = p->I; ++ } ++ ++ if (XM(any_true)(!XM(mkplans_pretranspose)(p, plnr, p->I, O, my_pe, ++ &cld2, &cld2rest, &cld3, ++ &rest_Ioff, &rest_Ooff), ++ p->comm)) goto nada; ++ ++ pln = MKPLAN_MPI_TRANSPOSE(P, &padt, apply); ++ ++ pln->cld1 = cld1; ++ pln->cld2 = cld2; ++ pln->cld2rest = cld2rest; ++ pln->rest_Ioff = rest_Ioff; ++ pln->rest_Ooff = rest_Ooff; ++ pln->cld3 = cld3; ++ pln->preserve_input = ego->preserve_input ? 2 : NO_DESTROY_INPUTP(plnr); ++ ++ MPI_Comm_dup(p->comm, &pln->comm); ++ ++ n_pes = (int) X(imax)(XM(num_blocks)(p->nx, p->block), ++ XM(num_blocks)(p->ny, p->tblock)); ++ ++ /* Compute sizes/offsets of blocks to exchange between processors */ ++ sbs = (INT *) MALLOC(4 * n_pes * sizeof(INT), PLANS); ++ sbo = sbs + n_pes; ++ rbs = sbo + n_pes; ++ rbo = rbs + n_pes; ++ b = XM(block)(p->nx, p->block, my_pe); ++ bt = XM(block)(p->ny, p->tblock, my_pe); ++ for (pe = 0; pe < n_pes; ++pe) { ++ INT db, dbt; /* destination block sizes */ ++ db = XM(block)(p->nx, p->block, pe); ++ dbt = XM(block)(p->ny, p->tblock, pe); ++ ++ sbs[pe] = b * dbt * vn; ++ sbo[pe] = pe * (b * p->tblock) * vn; ++ rbs[pe] = db * bt * vn; ++ rbo[pe] = pe * (p->block * bt) * vn; ++ ++ if (db * dbt > 0 && db * p->tblock != p->block * dbt) { ++ A(sort_pe == -1); /* only one process should need sorting */ ++ sort_pe = pe; ++ ascending = db * p->tblock > p->block * dbt; ++ } ++ } ++ pln->n_pes = n_pes; ++ pln->my_pe = my_pe; ++ pln->send_block_sizes = sbs; ++ pln->send_block_offsets = sbo; ++ pln->recv_block_sizes = rbs; ++ pln->recv_block_offsets = rbo; ++ ++ if (my_pe >= n_pes) { ++ pln->sched = 0; /* this process is not doing anything */ ++ } ++ else { ++ pln->sched = (int *) MALLOC(n_pes * sizeof(int), PLANS); ++ fill1_comm_sched(pln->sched, my_pe, n_pes); ++ if (sort_pe >= 0) ++ sort1_comm_sched(pln->sched, n_pes, sort_pe, ascending); ++ } ++ ++ X(ops_zero)(&pln->super.super.ops); ++ if (cld1) X(ops_add2)(&cld1->ops, &pln->super.super.ops); ++ if (cld2) X(ops_add2)(&cld2->ops, &pln->super.super.ops); ++ if (cld2rest) X(ops_add2)(&cld2rest->ops, &pln->super.super.ops); ++ if (cld3) X(ops_add2)(&cld3->ops, &pln->super.super.ops); ++ /* FIXME: should MPI operations be counted in "other" somehow? */ ++ ++ return &(pln->super.super); ++ ++ nada: ++ X(plan_destroy_internal)(cld3); ++ X(plan_destroy_internal)(cld2rest); ++ X(plan_destroy_internal)(cld2); ++ X(plan_destroy_internal)(cld1); ++ return (plan *) 0; ++} ++ ++static solver *mksolver(int preserve_input) ++{ ++ static const solver_adt sadt = { PROBLEM_MPI_TRANSPOSE, mkplan, 0 }; ++ S *slv = MKSOLVER(S, &sadt); ++ slv->preserve_input = preserve_input; ++ return &(slv->super); ++} ++ ++void XM(transpose_pairwise_transposed_register)(planner *p) ++{ ++ int preserve_input; ++ for (preserve_input = 0; preserve_input <= 1; ++preserve_input) ++ REGISTER_SOLVER(p, mksolver(preserve_input)); ++} diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb new file mode 100644 index 0000000000..7750dafbb8 --- /dev/null +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'Octopus' +version = '5.0.0' +versionsuffix = '-mpi' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page' +description = """Octopus is a scientific program aimed at the ab initio virtual experimentation +on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically +within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations +in time. Nuclei are described classically as point particles. +Electron-nucleus interaction is described within the pseudopotential approximation.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': True, 'opt': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=%(version)s/' ] + +builddependencies = [ + ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), +# ('Perl', '5.20.3'), +] + +dependencies = [ + ('libxc', '2.2.2'), + ('netCDF', '4.3.3.1'), + ('netCDF-Fortran', '4.4.2'), + ('FFTW', '3.3.4-p2'), + ('PFFT', '1.0.8-alpha'), + ('ETSF_IO', '1.0.4'), + ('GSL', '1.16'), +] + +configopts = '--disable-openmp --enable-mpi --enable-newuoa --disable-python --disable-gdlib ' +configopts += '--with-libxc-prefix=$EBROOTLIBXC --with-gsl-prefix=$EBROOTGSL ' +configopts += '--with-blas="-L$MKLROOT/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" ' +configopts += '--with-blacs="$MKLROOT/lib/intel64/libmkl_blacs_intelmpi_lp64.a" ' +configopts += '--with-scalapack="$MKLROOT/lib/intel64/libmkl_scalapack_lp64.a" ' +configopts += '--with-netcdf-prefix=$EBROOTNETCDFMINFORTRAN ' +configopts += '--with-etsf-io-prefix=$EBROOTETSF_IO ' +configopts += '--with-pfft-prefix=$EBROOTPFFT --with-mpifftw-prefix=$EBROOTFFTW ' + +sanity_check_paths = { + 'files': ["bin/octopus_mpi"], + 'dirs': [] +} + +#runtest = 'MPIEXEC=`which mpirun` check' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb b/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb new file mode 100644 index 0000000000..4ee4858b6d --- /dev/null +++ b/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'PFFT' +version = '1.0.8-alpha' + +homepage = 'https://www-user.tu-chemnitz.de/~mpip/software.php?lang=en' +description = """PFFT is a software library for computing massively parallel, fast Fourier +transformations on distributed memory architectures. PFFT can be understood as a generalization +of FFTW-MPI to multidimensional data decomposition.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tu-chemnitz.de/~potts/workgroup/pippig/software/'] + +dependencies = [ + ('FFTW', '3.3.4-p2'), + ('Autotools', '20150215', '', ('GNU', '4.9.3-2.25')), +] + +sanity_check_paths = { + 'files': ['lib/libpfft.so.0.0.0', 'lib/libpfft.a'], + 'dirs': [], +} + +moduleclass = 'numlib' -- GitLab From 679c30c70d08293daf73c4c1a2569e5c1d749bd0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 10 Nov 2015 08:24:09 +0100 Subject: [PATCH 0132/2133] 2 --- easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb index 7750dafbb8..932a21ffc2 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb @@ -19,7 +19,7 @@ source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=%(version)s/ builddependencies = [ ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), -# ('Perl', '5.20.3'), + ('Perl', '5.20.3'), ] dependencies = [ @@ -46,6 +46,6 @@ sanity_check_paths = { 'dirs': [] } -#runtest = 'MPIEXEC=`which mpirun` check' +runtest = 'MPIEXEC=`which mpirun` check' moduleclass = 'chem' -- GitLab From 7bc76b9140a480e3e34c5bec9f3aa2187e24b8f4 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 27 Nov 2015 08:38:19 +1300 Subject: [PATCH 0133/2133] Add easy_install to setup.cfg --- setup.cfg | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 setup.cfg diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000000..700c19b72c --- /dev/null +++ b/setup.cfg @@ -0,0 +1,2 @@ +[easy_install] + -- GitLab From 9cc16dd62a592aab16ef33ed9e95c2b1fca7f120 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Nov 2015 09:13:27 +0100 Subject: [PATCH 0134/2133] {tools}[intel/2015b] vsc-base 2.4.16 w/ Python 2.7.10 --- ...c-base-2.4.16-intel-2015b-Python-2.7.10.eb | 30 ++++++++++++++++ ...nstall-0.9.12-intel-2015b-Python-2.7.10.eb | 29 ++++++++++++++++ ...tel-2015b-Python-2.7.10-vsc-base-2.4.16.eb | 34 +++++++++++++++++++ 3 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2015b-Python-2.7.10.eb create mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.10-vsc-base-2.4.16.eb diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..e9057b41f7 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'vsc-base' +version = '2.4.16' + +homepage = 'https://pypi.python.org/pypi/vsc-base' +description = """Base library for Python tools developed by UGent's HPC group, including generaloption (option parser) +and fancylogger (logging functionality).""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +pyver = '2.7.10' +versionsuffix = '-Python-%s' % pyver +dependencies = [ + ('Python', pyver), + ('vsc-install', '0.9.12', versionsuffix), +] + +options = {'modulename': 'vsc.utils.fancylogger'} + +shortpyver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % shortpyver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..27d473bb9f --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'vsc-install' +version = '0.9.12' + +homepage = 'https://pypi.python.org/pypi/vsc-install' +description = """vsc-install provides shared setuptools functions and classes for Python libraries + developed by UGent's HPC group""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +pyver = '2.7.10' +versionsuffix = '-Python-%s' % pyver +dependencies = [ + ('Python', pyver), +] + +options = {'modulename': 'vsc.install'} + +shortpyver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % shortpyver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.10-vsc-base-2.4.16.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.10-vsc-base-2.4.16.eb new file mode 100755 index 0000000000..9f4a65aee3 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.10-vsc-base-2.4.16.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'vsc-mympirun' +version = '3.4.2' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] + +pyver = '2.7.10' +vsc_base_ver = '2.4.16' +versionsuffix = '-Python-%s-vsc-base-%s' % (pyver, vsc_base_ver) + +dependencies = [ + ('Python', pyver), + ('vsc-base', vsc_base_ver, '-Python-%s' % pyver), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +options = {'modulename': 'vsc.mympirun'} + +shortpyver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/mympirun'], + 'dirs': ['lib/python%(pyver)s/site-packages/vsc_mympirun-%%(version)s-py%(pyver)s.egg' % {'pyver': shortpyver}], +} + +moduleclass = 'tools' -- GitLab From ac13f4062019f59b9f70870c5005b240ea5f919d Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Wed, 2 Dec 2015 16:52:49 +0100 Subject: [PATCH 0135/2133] Modified CUDA easyconfig to support wrapper creation (to enable easier use of icpc as a host compiler). Requires a modified CUDA easyblock. --- ...5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..66010feb7a --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -0,0 +1,20 @@ +name = 'CUDA' +version = '7.5.18' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} + +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux.run'] +checksums = [('md5', '4b3bcecf0dfc35928a0898793cf3e4c6')] + +moduleclass = 'system' + +generate_wrapper = True +default_host_compiler = 'icpc' -- GitLab From 72e0b2cdf87f0a4c7a6c911d79537db34bb0d347 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Wed, 2 Dec 2015 17:13:29 +0100 Subject: [PATCH 0136/2133] Modified CUDA easyconfig to support wrapper creation (to enable easier use of icpc as a host compiler). Requires a modified CUDA easyblock. --- ...5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 28 ++++++++++++++++--- 1 file changed, 24 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 66010feb7a..91b0d98477 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -1,3 +1,17 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html +## + +#easyblock = 'ConfigureMake' + name = 'CUDA' version = '7.5.18' @@ -7,14 +21,20 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} +toolchain = {'name': 'iccifort', 'version': '2015.3.187-GCC-bare-4.9.3'} -source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] +# eg. http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run +#source_urls = ['http://developer.download.nvidia.com/compute/cuda/7_5/rel/installers/'] +source_urls = ['http://developer.download.nvidia.com/compute/cuda/7.5/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_linux.run'] checksums = [('md5', '4b3bcecf0dfc35928a0898793cf3e4c6')] +installopts = '-override compiler' + moduleclass = 'system' -generate_wrapper = True -default_host_compiler = 'icpc' +generate_intel_wrapper = True + +# Be careful and have a message consistent with the wrappers present +modloadmsg = """nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use invcc, or nvcc -ccbin=icpc""" -- GitLab From 91da9d18e08a6d453e77b543a8d440efebf2714b Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 3 Dec 2015 15:47:06 +0100 Subject: [PATCH 0137/2133] Small changes to better respect EB coding standards --- ...5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 91b0d98477..dcd435b3cb 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -1,8 +1,10 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University, +# Forschungszentrum Juelich # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste +# Damian Alvarez # License:: MIT/GPL # $Id$ # @@ -21,20 +23,22 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'iccifort', 'version': '2015.3.187-GCC-bare-4.9.3'} +toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} -# eg. http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run -#source_urls = ['http://developer.download.nvidia.com/compute/cuda/7_5/rel/installers/'] source_urls = ['http://developer.download.nvidia.com/compute/cuda/7.5/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_linux.run'] -checksums = [('md5', '4b3bcecf0dfc35928a0898793cf3e4c6')] +checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] +# Necessary to allow to use a GCC 4.9.3 toolchain, as CUDA by default just supports up to 4.9.2. +# Tested, but not throughly, so it is not guaranteed to don't cause problems installopts = '-override compiler' -moduleclass = 'system' - generate_intel_wrapper = True # Be careful and have a message consistent with the wrappers present -modloadmsg = """nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use invcc, or nvcc -ccbin=icpc""" +modloadmsg = """nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" ++" invcc, or nvcc -ccbin=icpc""" + +moduleclass = 'system' + -- GitLab From 4a7c5a0d234733ce577675706436fd3e8d9d2742 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Fri, 4 Dec 2015 18:02:06 +0100 Subject: [PATCH 0138/2133] Updated easyblock with support for generic wrappers --- .../CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index dcd435b3cb..be0effa8e8 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -34,11 +34,12 @@ checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] # Tested, but not throughly, so it is not guaranteed to don't cause problems installopts = '-override compiler' -generate_intel_wrapper = True +generate_wrapper = True +host_compiler = "icpc" # Be careful and have a message consistent with the wrappers present -modloadmsg = """nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" -+" invcc, or nvcc -ccbin=icpc""" +modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" +modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc" moduleclass = 'system' -- GitLab From c5e37e8ce40ab0005f2b50b149ca694a0750660e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 9 Dec 2015 13:56:39 +0100 Subject: [PATCH 0139/2133] Add deps for shift --- .../b/bbFTP/bbFTP-3.2.1-foss-2015b.eb | 42 + .../p/Perl/Perl-5.22.0-foss-2015b.eb | 909 ++++++++++++++++++ 2 files changed, 951 insertions(+) create mode 100644 easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-foss-2015b.eb new file mode 100644 index 0000000000..ec80570d1a --- /dev/null +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-foss-2015b.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'bbFTP' +version = '3.2.1' + +homepage = 'http://doc.in2p3.fr/bbftp/' +description = """bbFTP is a file transfer software. It implements its own transfer protocol, + which is optimized for large files (larger than 2GB) and secure as it does not read the + password in a file and encrypts the connection information. bbFTP main features are: + * Encoded username and password at connection * SSH and Certificate authentication modules + * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression + * Automatic retry * Customizable time-outs * Transfer simulation + * AFS authentication integration * RFIO interface""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +# fi. http://doc.in2p3.fr/bbftp/dist/bbftp-client-3.2.0.tar.gz +sources = ['%s-client-%s.tar.gz' % (name.lower(), version)] +source_urls = [homepage + 'dist'] + +start_dir = 'bbftpc' + +buildopts = "CC=$CC" + +dependencies = [('zlib', '1.2.8')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/bbftp'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b.eb new file mode 100644 index 0000000000..37c67413c1 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b.eb @@ -0,0 +1,909 @@ +name = 'Perl' +version = '5.22.0' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.58', { + 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('TAP::Harness::Env', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.021', { + 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '0.46', { + 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.93', { + 'source_tmpl': 'DateTime-TimeZone-1.93.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.22', { + 'source_tmpl': 'Try-Tiny-0.22.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Params::Validate', '1.21', { + 'source_tmpl': 'Params-Validate-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.20', { + 'source_tmpl': 'DateTime-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Module::Build', '0.4214', { + 'source_tmpl': 'Module-Build-0.4214.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Readonly', '2.00', { + 'source_tmpl': 'Readonly-2.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.27', { + 'source_tmpl': 'Tree-DAG_Node-1.27.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.48', { + 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.72', { + 'source_tmpl': 'Shell-0.72.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.47', { + 'source_tmpl': 'PathTools-3.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::WrapTie', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.40', { + 'source_tmpl': 'Test-Exception-0.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.11', { + 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.69', { + 'source_tmpl': 'URI-1.69.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.00', { + 'source_tmpl': 'Pod-POM-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.43', { + 'source_tmpl': 'Text-Diff-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.020', { + 'source_tmpl': 'IO-Socket-SSL-2.020.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Getopt::Long', '2.47', { + 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '0.117', { + 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.000002', { + 'source_tmpl': 'Moo-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.05', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.63', { + 'source_tmpl': 'Test-Differences-0.63.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.14', { + 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9912', { + 'source_tmpl': 'version-0.9912.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + # fails: uses 'gcc' + #('XML::Bare', '0.53', { + # 'source_tmpl': 'XML-Bare-0.53.tar.gz', + # 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + #}), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.30', { + 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.11', { + 'source_tmpl': 'AnyEvent-7.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0609', { + 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::Tester', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967012', { + 'source_tmpl': 'Parse-RecDescent-1.967012.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.36', { + 'source_tmpl': 'Carp-1.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.13', { + 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT'], + }), + ('Capture::Tiny', '0.30', { + 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('LWP', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000001', { + 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.19', { + 'source_tmpl': 'File-Which-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.39', { + 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.42', { + 'source_tmpl': 'Scalar-List-Utils-1.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('IO::Scalar', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.87', { + 'source_tmpl': 'Log-Handler-0.87.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Devel::StackTrace', '2.00', { + 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1603', { + 'source_tmpl': 'Moose-2.1603.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.33', { + 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9154', { + 'source_tmpl': 'CPANPLUS-0.9154.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Harness', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.04', { + 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.14', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' -- GitLab From 26c49f89043ad588f34d00698478ec7643e27424 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 9 Dec 2015 13:57:37 +0100 Subject: [PATCH 0140/2133] Added shift/4.0 for foss/2015b --- .../s/shift/shift-4.0-foss-2015b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/shift/shift-4.0-foss-2015b.eb diff --git a/easybuild/easyconfigs/s/shift/shift-4.0-foss-2015b.eb b/easybuild/easyconfigs/s/shift/shift-4.0-foss-2015b.eb new file mode 100644 index 0000000000..7adef50aac --- /dev/null +++ b/easybuild/easyconfigs/s/shift/shift-4.0-foss-2015b.eb @@ -0,0 +1,30 @@ +easyblock = 'CmdCp' + +name = 'shift' +version = '4.0' + +homepage = 'http://people.nas.nasa.gov/~kolano/projects/shift.html' +description = """ +Shift is a framework for Self-Healing Independent File Transfer that provides high +performance and resilience for local and remote transfers through a variety of techniques. +""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TGZ] +source_urls = [('http://sourceforge.net/projects/shiftc/files', 'download')] + +dependencies = [ + ('Perl', '5.22.0'), + ('bbFTP', '3.2.1'), +] + +files_to_copy = [(['perl/shiftc', 'perl/shift-mgr', 'perl/shift-aux'], 'bin'), 'etc', (['doc/shiftc.1'], 'man/man1')] +cmds_map = [] + +sanity_check_paths = { + 'files': ['bin/shiftc'], + 'dirs': ['etc'] +} + +moduleclass = 'tools' -- GitLab From 88057a2fdbd91c578c8e81abf5df8c23a85a850d Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 14 Dec 2015 13:38:09 +0100 Subject: [PATCH 0141/2133] added new toolchain version with dependency pinning --- .../c/CrayGNU/CrayGNU-2015.06-XC.eb | 20 +++++++++++++++++++ .../c/CrayGNU/CrayGNU-2015.11-XC.eb | 20 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..f804d0e859 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb @@ -0,0 +1,20 @@ +easyblock = 'CrayToolchain' + +name = 'CrayGNU' +version = '2015.06-XC' + +homepage = 'http://docs.cray.com/books/S-9407-1506' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2015).\n""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-gnu/5.2.40', EXTERNAL_MODULE), + ('gcc/4.8.2', EXTERNAL_MODULE), + ('craype/2.4.0', EXTERNAL_MODULE), + ('cray-libsci/13.0.4', EXTERNAL_MODULE), + ('cray-mpich/7.2.2', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..15eb5087e5 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb @@ -0,0 +1,20 @@ +easyblock = 'CrayToolchain' + +name = 'CrayGNU' +version = '2015.11-XC' + +homepage = 'http://docs.cray.com/books/S-9407-1511' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-gnu/5.2.82', EXTERNAL_MODULE), + ('gcc/4.9.3', EXTERNAL_MODULE), + ('craype/2.4.2', EXTERNAL_MODULE), + ('cray-libsci/13.2.0', EXTERNAL_MODULE), + ('cray-mpich/7.2.6', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' -- GitLab From 7ec4aad741fdace1bb58192fabb608239ad4789a Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 14 Dec 2015 13:57:12 +0100 Subject: [PATCH 0142/2133] added sample easyconfig files for new CrayGNU XC toolchain --- .../h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb | 18 ++++++++++++++++++ .../h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..fe0de8812c --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..ecd5998b8d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From f2af2a8166064f60f06746f0a9c34179e87e3561 Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 18 Dec 2015 11:34:10 +0100 Subject: [PATCH 0143/2133] added new ebs for CrayCCE, CrayIntel TCs and HPL --- .../c/CrayCCE/CrayCCE-2015.06-XC.eb | 20 +++++++++++++++++ .../c/CrayCCE/CrayCCE-2015.11-XC.eb | 20 +++++++++++++++++ .../c/CrayIntel/CrayIntel-2015.06-XC.eb | 19 ++++++++++++++++ .../c/CrayIntel/CrayIntel-2015.11-XC.eb | 19 ++++++++++++++++ .../h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb | 22 +++++++++++++++++++ .../h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb | 22 +++++++++++++++++++ .../h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb | 18 +++++++++++++++ 8 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb new file mode 100644 index 0000000000..c35ce0b32e --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb @@ -0,0 +1,20 @@ +easyblock = 'CrayToolchain' + +name = 'CrayCCE' +version = '2015.06-XC' + +homepage = 'http://docs.cray.com/books/S-9407-1511' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-cray/5.2.40', EXTERNAL_MODULE), + ('cce/8.3.12', EXTERNAL_MODULE), + ('craype/2.4.0', EXTERNAL_MODULE), + ('cray-libsci/13.0.4', EXTERNAL_MODULE), + ('cray-mpich/7.2.2', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb new file mode 100644 index 0000000000..3433ca305d --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb @@ -0,0 +1,20 @@ +easyblock = 'CrayToolchain' + +name = 'CrayCCE' +version = '2015.11-XC' + +homepage = 'http://docs.cray.com/books/S-9407-1511' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-cray/5.2.82', EXTERNAL_MODULE), + ('cce/8.4.1', EXTERNAL_MODULE), + ('craype/2.4.2', EXTERNAL_MODULE), + ('cray-libsci/13.2.0', EXTERNAL_MODULE), + ('cray-mpich/7.2.6', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb new file mode 100644 index 0000000000..eb0449a963 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb @@ -0,0 +1,19 @@ +easyblock = 'CrayToolchain' + +name = 'CrayIntel' +version = '2015.06-XC' + +homepage = 'http://docs.cray.com/books/S-9407-1511' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-intel/5.2.82', EXTERNAL_MODULE), + ('craype/2.4.0', EXTERNAL_MODULE), + ('cray-libsci/13.0.4', EXTERNAL_MODULE), + ('cray-mpich/7.2.2', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb new file mode 100644 index 0000000000..1ae0fb83c7 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb @@ -0,0 +1,19 @@ +easyblock = 'CrayToolchain' + +name = 'CrayIntel' +version = '2015.11-XC' + +homepage = 'http://docs.cray.com/books/S-9407-1511' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-intel/5.2.82', EXTERNAL_MODULE), + ('craype/2.4.2', EXTERNAL_MODULE), + ('cray-libsci/13.2.0', EXTERNAL_MODULE), + ('cray-mpich/7.2.6', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb new file mode 100644 index 0000000000..845802b504 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '2015.06-XC'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb new file mode 100644 index 0000000000..f4a0256f79 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '2015.11-XC'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb new file mode 100644 index 0000000000..32e943a8d6 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.06-XC'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb new file mode 100644 index 0000000000..370ce49b4c --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 3ead2449def8a10bc0ade4635f5461b634b49356 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 5 Jan 2016 11:07:13 +1030 Subject: [PATCH 0144/2133] Easyconfig for installing picard-2.0.1-Java-1.8.0_66 --- .../p/picard/picard-2.0.1-Java-1.8.0_66.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb diff --git a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb new file mode 100644 index 0000000000..2035d823b9 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb @@ -0,0 +1,14 @@ +name = 'picard' +version = '2.0.1' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = ['picard-tools-%(version)s.zip'] + +dependencies = [('Java', '1.8.0_66')] + +moduleclass = 'bio' -- GitLab From 79b88251817abe85c465f6679cd06d591321e490 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 5 Jan 2016 13:19:53 +1030 Subject: [PATCH 0145/2133] Follow easyconfig style of most recent picard-1.119-Java-1.7.0_80 --- .../p/picard/picard-2.0.1-Java-1.8.0_66.eb | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb index 2035d823b9..2c0ba3aaf4 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb @@ -1,14 +1,18 @@ name = 'picard' version = '2.0.1' -homepage = 'http://sourceforge.net/projects/picard' -description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" +homepage = 'http://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM + (http://samtools.github.io/hts-specs) format.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] -sources = ['picard-tools-%(version)s.zip'] +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] +sources = ['%(name)s-tools-%(version)s.zip'] -dependencies = [('Java', '1.8.0_66')] +java = 'Java' +javaver = '1.8.0_66' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] moduleclass = 'bio' -- GitLab From 83eee361133707fc007e69986f1973c8f68ea30c Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 5 Jan 2016 13:36:25 +1030 Subject: [PATCH 0146/2133] Added picard-1.120-Java-1.8.0_66\n\nThis identifies the version which transitioned from sourceforge to GitHub. --- .../p/picard/picard-1.120-Java-1.8.0_66.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb diff --git a/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb new file mode 100644 index 0000000000..0d15ad9204 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb @@ -0,0 +1,18 @@ +name = 'picard' +version = '1.120' + +homepage = 'http://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM + (http://samtools.github.io/hts-specs) format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] +sources = ['%(name)s-tools-%(version)s.zip'] + +java = 'Java' +javaver = '1.8.0_66' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +moduleclass = 'bio' -- GitLab From 57f73ac1adc543a5a4e1e378bf2c6703eefa2728 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 6 Jan 2016 13:25:32 +1300 Subject: [PATCH 0147/2133] Comment out checksum, rename source file and add an explanatory comment --- .../easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 79b12d07a2..54c92da4c6 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -9,8 +9,13 @@ description = """DFT-D3 implements a dispersion correction for density functiona toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] -sources = ['dftd3.tgz'] -checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] +# Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version +# numbering. Also, the authors are prone (alas) to stealth upgrades, so that two +# tarballs with the same version number can have different checksums. For this +# reason, it is suggested to manually download and rename the tarball, and the +# checksum input has been disabled. +sources = ['dftd3-%(version)s.tgz'] +#checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From 4d5fc2d330eee5dead6ffbe303c00ff066116cb5 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 6 Jan 2016 13:56:45 +1030 Subject: [PATCH 0148/2133] Dummy/placeholder easyconfig file --- easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb new file mode 100644 index 0000000000..e69de29bb2 -- GitLab From 04244b1223e8db6a1e132cd4881c8e6bfea27b6a Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 6 Jan 2016 14:22:38 +1030 Subject: [PATCH 0149/2133] Added easyconfig for libffi-3.2.1-foss-2015b Changed source_url order to try http before ftp - my organisations filewall rules cause timeout issues with ftp sites. --- .../l/libffi/libffi-3.2.1-foss-2015b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015b.eb new file mode 100644 index 0000000000..d516d79d6d --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [ + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', + 'ftp://sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 81778dcb0bab10a38110361fe50f5b8d7468599b Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 6 Jan 2016 14:38:05 +1030 Subject: [PATCH 0150/2133] Added easyconfig for gettext-0.19.7-foss-2015b --- .../g/gettext/gettext-0.19.7-foss-2015b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb new file mode 100644 index 0000000000..26649681d7 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' -- GitLab From e03ea02dd30cbdaa0838875d61deea9cf51d7255 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 6 Jan 2016 15:17:02 +1030 Subject: [PATCH 0151/2133] Easyconfig for installing Exonerate-2.4.0-foss-2015b --- .../e/Exonerate/Exonerate-2.4.0-foss-2015b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb index e69de29bb2..524d427c0e 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'http://www.ebi.ac.uk/~guy/exonerate/' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/nathanweeks/exonerate/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GLib', '2.46.2')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' -- GitLab From f9f30a2a03acdf83081310b27f6a385ba1944530 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 6 Jan 2016 15:35:07 +1030 Subject: [PATCH 0152/2133] Dummy/placeholder easyconfig file --- easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-foss-2015b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-foss-2015b.eb diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-foss-2015b.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-foss-2015b.eb new file mode 100644 index 0000000000..e69de29bb2 -- GitLab From 95d826c0cb5ad83e398ebbe3615c4d718583660f Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 6 Jan 2016 16:08:36 +1030 Subject: [PATCH 0153/2133] FastQC doesn't need a toolchain --- .../f/fastqc/{fastqc-0.11.4-foss-2015b.eb => fastqc-0.11.4.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/fastqc/{fastqc-0.11.4-foss-2015b.eb => fastqc-0.11.4.eb} (100%) diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-foss-2015b.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb similarity index 100% rename from easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-foss-2015b.eb rename to easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb -- GitLab From 3bcb41468dd84744810c719da3ee2898fdedabdd Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 6 Jan 2016 16:11:06 +1030 Subject: [PATCH 0154/2133] Include Java version in filename --- .../f/fastqc/{fastqc-0.11.4.eb => fastqc-0.11.4-Java-1.8.0_66.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/fastqc/{fastqc-0.11.4.eb => fastqc-0.11.4-Java-1.8.0_66.eb} (100%) diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-Java-1.8.0_66.eb similarity index 100% rename from easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb rename to easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-Java-1.8.0_66.eb -- GitLab From ee4bb1f44ecaea8e3eaf639ebcbde181decc92e3 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 6 Jan 2016 16:15:03 +1030 Subject: [PATCH 0155/2133] Easyconfig for installing fastqc-0.11.4-Java-1.8.0_66 --- .../f/fastqc/fastqc-0.11.4-Java-1.8.0_66.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-Java-1.8.0_66.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-Java-1.8.0_66.eb index e69de29bb2..091fd04f7d 100644 --- a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-Java-1.8.0_66.eb @@ -0,0 +1,28 @@ +easyblock = 'EB_Java' + +name = 'fastqc' +version = '0.11.4' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] +sources = ['%(name)s_v%(version)s.zip'] + +java = 'Java' +javaver = '1.8.0_66' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' -- GitLab From 8eb70c2e968b456b35c4ac189478961a1c02caac Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 6 Jan 2016 16:20:10 +1030 Subject: [PATCH 0156/2133] Added modloadmsg so users know how to run picard properly --- easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb index 2c0ba3aaf4..2d067163eb 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb @@ -15,4 +15,6 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] +modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" + moduleclass = 'bio' -- GitLab From 8ddc8adda57134077b0b2266e0fd109f7239a9b2 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 7 Jan 2016 15:06:45 +1030 Subject: [PATCH 0157/2133] Added GLib-2.46.2-foss-2015b dependency --- .../g/GLib/GLib-2.46.2-foss-2015b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb new file mode 100644 index 0000000000..c1a803f76a --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.46.2' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), +] +#builddependencies = [('Python', '2.7.9')] + +moduleclass = 'vis' -- GitLab From 27e326f7d3da848d7fe13ec2c28498bfdb0ada0f Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 7 Jan 2016 15:31:38 +1030 Subject: [PATCH 0158/2133] Corrected capitalisation of fastqc to FastQC --- .../f/{fastqc/fastqc-0.11.2.eb => FastQC/FastQC-0.11.2.eb} | 0 .../f/{fastqc/fastqc-0.11.3.eb => FastQC/FastQC-0.11.3.eb} | 0 .../FastQC-0.11.4-Java-1.8.0_66.eb} | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/{fastqc/fastqc-0.11.2.eb => FastQC/FastQC-0.11.2.eb} (100%) rename easybuild/easyconfigs/f/{fastqc/fastqc-0.11.3.eb => FastQC/FastQC-0.11.3.eb} (100%) rename easybuild/easyconfigs/f/{fastqc/fastqc-0.11.4-Java-1.8.0_66.eb => FastQC/FastQC-0.11.4-Java-1.8.0_66.eb} (100%) diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb similarity index 100% rename from easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb rename to easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb similarity index 100% rename from easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb rename to easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-Java-1.8.0_66.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb similarity index 100% rename from easybuild/easyconfigs/f/fastqc/fastqc-0.11.4-Java-1.8.0_66.eb rename to easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb -- GitLab From 9a3b218782568032ce513a7f6021b0bcac23b35c Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 7 Jan 2016 15:32:04 +1030 Subject: [PATCH 0159/2133] Corrected capitalisation of fastqc to FastQC --- easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb | 2 +- easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb | 2 +- easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb index 9ff730ebed..9d17537446 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb @@ -1,6 +1,6 @@ easyblock = 'EB_Java' -name = 'fastqc' +name = 'FastQC' version = '0.11.2' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb index c5f20b9165..4523d751de 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb @@ -1,6 +1,6 @@ easyblock = 'EB_Java' -name = 'fastqc' +name = 'FastQC' version = '0.11.3' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb index 091fd04f7d..b235fb563b 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb @@ -1,6 +1,6 @@ easyblock = 'EB_Java' -name = 'fastqc' +name = 'FastQC' version = '0.11.4' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' -- GitLab From b8cc7ccf74b59a8f3a7bb53067ebcf1f9f5548e2 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 7 Jan 2016 17:35:53 +1030 Subject: [PATCH 0160/2133] Covert from using EB_Java easyblock to PackedBinary --- .../easyconfigs/f/FastQC/FastQC-0.11.2.eb | 20 +++++++++++-------- .../easyconfigs/f/FastQC/FastQC-0.11.3.eb | 20 +++++++++++-------- .../f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb | 13 +++++++----- 3 files changed, 32 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb index 9d17537446..7f918037ff 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb @@ -1,21 +1,25 @@ -easyblock = 'EB_Java' +easyblock = 'PackedBinary' name = 'FastQC' version = '0.11.2' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' -description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] -sources = ['%(name)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] -dependencies = [('Java', '1.7.0_60')] +java = 'Java' +javaver = '1.7.0_60' +#versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] -postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] - -modextrapaths = {'PATH': ['']} +postinstallcmds = ['chmod +x %(installdir)s/fastqc'] sanity_check_paths = { 'files': ['fastqc'], diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb index 4523d751de..9847842efa 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb @@ -1,21 +1,25 @@ -easyblock = 'EB_Java' +easyblock = 'PackedBinary' name = 'FastQC' version = '0.11.3' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' -description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] -sources = ['%(name)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] -dependencies = [('Java', '1.7.0_80')] +java = 'Java' +javaver = '1.7.0_80' +#versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] -postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] - -modextrapaths = {'PATH': ['']} +postinstallcmds = ['chmod +x %(installdir)s/fastqc'] sanity_check_paths = { 'files': ['fastqc'], diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb index b235fb563b..301434b905 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb @@ -1,22 +1,25 @@ -easyblock = 'EB_Java' +easyblock = 'PackedBinary' name = 'FastQC' version = '0.11.4' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' -description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] -sources = ['%(name)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] java = 'Java' javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] +postinstallcmds = ['chmod +x %(installdir)s/fastqc'] sanity_check_paths = { 'files': ['fastqc'], -- GitLab From 3fe8c6646c75870a7050add588f13b84a0b0bbdc Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 7 Jan 2016 21:40:16 +1030 Subject: [PATCH 0161/2133] Cleaned up older FastQC easyconfig files. The versionsuffix is now set to the Java version specified as the dependency. --- ...f-1.4.10.eb => FastQC-0.10.1-Java-1.7.0_80.eb} | 15 ++++++++------- ...C-0.11.2.eb => FastQC-0.11.2-Java-1.7.0_60.eb} | 2 +- ...C-0.11.3.eb => FastQC-0.11.3-Java-1.7.0_80.eb} | 2 +- 3 files changed, 10 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/f/FastQC/{FastQC-0.10.1-goolf-1.4.10.eb => FastQC-0.10.1-Java-1.7.0_80.eb} (69%) rename easybuild/easyconfigs/f/FastQC/{FastQC-0.11.2.eb => FastQC-0.11.2-Java-1.7.0_60.eb} (95%) rename easybuild/easyconfigs/f/FastQC/{FastQC-0.11.3.eb => FastQC-0.11.3-Java-1.7.0_80.eb} (95%) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb similarity index 69% rename from easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb index 41209b695a..505f4f2807 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb @@ -17,22 +17,23 @@ description = """FastQC is a quality control application for high throughput seq application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%(namelower)s_v%(version)s.zip'] source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] java = 'Java' javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] -dependencies = [('Java', '1.7.0_80', '', True)] - -install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc" +postinstallcmds = ['chmod +x %(installdir)s/fastqc'] sanity_check_paths = { - 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.32.jar"], - 'dirs': ["Contaminants", "Help", "Templates", "uk"], + 'files': ['fastqc'], + 'dirs': [], } +sanity_check_commands = [('fastqc', '-v')] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb similarity index 95% rename from easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb rename to easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb index 7f918037ff..c8f4df417f 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb @@ -16,7 +16,7 @@ sources = ['%(namelower)s_v%(version)s.zip'] java = 'Java' javaver = '1.7.0_60' -#versionsuffix = '-%s-%s' % (java, javaver) +versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] postinstallcmds = ['chmod +x %(installdir)s/fastqc'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb similarity index 95% rename from easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb rename to easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb index 9847842efa..5b66419773 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb @@ -16,7 +16,7 @@ sources = ['%(namelower)s_v%(version)s.zip'] java = 'Java' javaver = '1.7.0_80' -#versionsuffix = '-%s-%s' % (java, javaver) +versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] postinstallcmds = ['chmod +x %(installdir)s/fastqc'] -- GitLab From 63ff88d71fd08e9083f5b96273936602856ffcd8 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Mon, 11 Jan 2016 06:14:38 +1030 Subject: [PATCH 0162/2133] Use modified FastQC with dummy toolchain --- .../easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index 53e79949f3..8087d1607f 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.10.1'), + ('FastQC', '0.10.1', '', True), ('cutadapt', '1.5', '-Python-2.7.10'), ] -- GitLab From 1e6fb7a9d2d54c6d76c3b78e9537998291adc84d Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Mon, 11 Jan 2016 07:40:13 +1030 Subject: [PATCH 0163/2133] Include Java version suffix for FastQC dependency --- .../easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index 8087d1607f..dacf5b481c 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.10.1', '', True), + ('FastQC', '0.10.1', '-Java-1.7.0_80', True), ('cutadapt', '1.5', '-Python-2.7.10'), ] -- GitLab From 17034187bba746893c393312f3dfa928f8b7d421 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Mon, 11 Jan 2016 12:53:00 +1030 Subject: [PATCH 0164/2133] Enabled Python 2.7.9 as a build dependency --- .../g/GLib/GLib-2.46.2-foss-2015b.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015b.eb | 116 ++++++++++++++++++ 2 files changed, 117 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb index c1a803f76a..55b64d46c2 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb @@ -16,6 +16,6 @@ dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.7'), ] -#builddependencies = [('Python', '2.7.9')] +builddependencies = [('Python', '2.7.9')] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb new file mode 100644 index 0000000000..81bfd4da01 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb @@ -0,0 +1,116 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' -- GitLab From 25b0f43a3e8940197505d12a11a30bb8a535aceb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Jan 2016 21:34:16 +0100 Subject: [PATCH 0165/2133] {dummy}[toolchain] foss/2016a (WIP) --- easybuild/easyconfigs/f/foss/foss-2016a.eb | 39 ++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/foss/foss-2016a.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2016a.eb b/easybuild/easyconfigs/f/foss/foss-2016a.eb new file mode 100644 index 0000000000..cce53461f2 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.3' # 20150626 +#gccver = '5.3.0' # 20151204 +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.10.1', '', ('GCC', '%s-%s' % (gccver, binutilsver))), + (blaslib, blasver, blassuff, ('GCC', '%s-%s' % (gccver, binutilsver))), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' -- GitLab From 42b52c8f4f2cef6b3289330c6f50b1d3896df98a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Jan 2016 21:34:52 +0100 Subject: [PATCH 0166/2133] {dummy}[toolchain] intel/2016a (WIP) --- easybuild/easyconfigs/i/intel/intel-2016a.eb | 23 ++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel/intel-2016a.eb diff --git a/easybuild/easyconfigs/i/intel/intel-2016a.eb b/easybuild/easyconfigs/i/intel/intel-2016a.eb new file mode 100644 index 0000000000..367a775846 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016a' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +#compver = '2015.5.223' +compver = '2016.1.150' +gccsuff = '-GCC-4.9.3-2.25' +#gccsuff = '-GCC-5.3.0-2.25' + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.2.150', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.1.150', '', ('iimpi', '8.4.5%s' % gccsuff)), +] + +moduleclass = 'toolchain' -- GitLab From 50346e29f8a3f80364294d97283728bc5602b45f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Jan 2016 23:12:30 +0100 Subject: [PATCH 0167/2133] {compiler}[dummy] GCC 5.3.0 --- easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb | 49 + .../GCC/mpfr-3.1.3-allpatches-20151029.patch | 1830 +++++++++++++++++ 2 files changed, 1879 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20151029.patch diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb new file mode 100644 index 0000000000..83ebb4cb78 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb @@ -0,0 +1,49 @@ +name = 'GCC' +version = '5.3.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.3' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.1.0.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.15.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20151029.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [('M4', '1.4.17')] + +checksums = [ + 'c9616fd448f980259c31de613e575719', # gcc-5.3.0.tar.bz2 + '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 + '7b650781f0a7c4a62e9bc8bdaaa0018b', # mpfr-3.1.3.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + '8428efbbc6f6e2810ce5c1ba73ecf98c', # isl-0.15.tar.bz2 + '6476b450c3db177b2250f3549362380e', # mpfr-3.1.3-allpatches-20151029.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20151029.patch b/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20151029.patch new file mode 100644 index 0000000000..891831f521 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20151029.patch @@ -0,0 +1,1830 @@ +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:49:23.950112879 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:49:24.042113845 +0000 +@@ -0,0 +1 @@ ++lngamma-and-doc +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-06-19 19:55:09.000000000 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:49:24.042113845 +0000 +@@ -1 +1 @@ +-3.1.3 ++3.1.3-p1 +diff -Naurd mpfr-3.1.3-a/doc/mpfr.texi mpfr-3.1.3-b/doc/mpfr.texi +--- mpfr-3.1.3-a/doc/mpfr.texi 2015-06-19 19:55:11.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.texi 2015-07-02 10:49:24.018113593 +0000 +@@ -810,13 +810,17 @@ + When the input point is in the closure of the domain of the mathematical + function and an input argument is +0 (resp.@: @minus{}0), one considers + the limit when the corresponding argument approaches 0 from above +-(resp.@: below). If the limit is not defined (e.g., @code{mpfr_log} on +-@minus{}0), the behavior is specified in the description of the MPFR function. ++(resp.@: below), if possible. If the limit is not defined (e.g., ++@code{mpfr_sqrt} and @code{mpfr_log} on @minus{}0), the behavior is ++specified in the description of the MPFR function, but must be consistent ++with the rule from the above paragraph (e.g., @code{mpfr_log} on @pom{}0 ++gives @minus{}Inf). + + When the result is equal to 0, its sign is determined by considering the + limit as if the input point were not in the domain: If one approaches 0 + from above (resp.@: below), the result is +0 (resp.@: @minus{}0); +-for example, @code{mpfr_sin} on +0 gives +0. ++for example, @code{mpfr_sin} on @minus{}0 gives @minus{}0 and ++@code{mpfr_acos} on 1 gives +0 (in all rounding modes). + In the other cases, the sign is specified in the description of the MPFR + function; for example @code{mpfr_max} on @minus{}0 and +0 gives +0. + +@@ -832,8 +836,8 @@ + @c that advantages in practice), like for any bug fix. + Example: @code{mpfr_hypot} on (NaN,0) gives NaN, but @code{mpfr_hypot} + on (NaN,+Inf) gives +Inf (as specified in @ref{Special Functions}), +-since for any finite input @var{x}, @code{mpfr_hypot} on (@var{x},+Inf) +-gives +Inf. ++since for any finite or infinite input @var{x}, @code{mpfr_hypot} on ++(@var{x},+Inf) gives +Inf. + + @node Exceptions, Memory Handling, Floating-Point Values on Special Numbers, MPFR Basics + @comment node-name, next, previous, up +@@ -1581,7 +1585,8 @@ + @deftypefunx int mpfr_add_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_add_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} + @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) + 0 = (+0) and (@minus{}0) + 0 = (@minus{}0)). + The @code{mpfr_add_d} function assumes that the radix of the @code{double} type + is a power of 2, with a precision at most that declared by the C implementation +@@ -1599,7 +1604,8 @@ + @deftypefunx int mpfr_sub_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sub_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} - @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) @minus{} 0 = (+0), (@minus{}0) @minus{} 0 = (@minus{}0), + 0 @minus{} (+0) = (@minus{}0) and 0 @minus{} (@minus{}0) = (+0)). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_sub} +@@ -1615,7 +1621,7 @@ + Set @var{rop} to @math{@var{op1} @GMPtimes{} @var{op2}} rounded in the + direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_mul_d}. + @end deftypefun + +@@ -1635,7 +1641,7 @@ + @deftypefunx int mpfr_div_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1}/@var{op2}} rounded in the direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_div} + and @code{mpfr_div_d}. + @end deftypefun +@@ -1643,15 +1649,18 @@ + @deftypefun int mpfr_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sqrt_ui (mpfr_t @var{rop}, unsigned long int @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{\sqrt{@var{op}}, the square root of @var{op}} +-rounded in the direction @var{rnd} (set @var{rop} to @minus{}0 if @var{op} is +-@minus{}0, to be consistent with the IEEE 754 standard). ++rounded in the direction @var{rnd}. Set @var{rop} to @minus{}0 if ++@var{op} is @minus{}0, to be consistent with the IEEE 754 standard. + Set @var{rop} to NaN if @var{op} is negative. + @end deftypefun + + @deftypefun int mpfr_rec_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{1/\sqrt{@var{op}}, the reciprocal square root of @var{op}} +-rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is +-@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. ++rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is ++@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. Warning! ++Therefore the result on @minus{}0 is different from the one of the rSqrt ++function recommended by the IEEE 754-2008 standard (Section 9.2.1), which ++is @minus{}Inf instead of +Inf. + @end deftypefun + + @deftypefun int mpfr_cbrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -1832,7 +1841,9 @@ + @m{\log_2 @var{op}, log2(@var{op})} or + @m{\log_{10} @var{op}, log10(@var{op})}, respectively, + rounded in the direction @var{rnd}. +-Set @var{rop} to @minus{}Inf if @var{op} is @minus{}0 ++Set @var{rop} to +0 if @var{op} is 1 (in all rounding modes), ++for consistency with the ISO C99 and IEEE 754-2008 standards. ++Set @var{rop} to @minus{}Inf if @var{op} is @pom{}0 + (i.e., the sign of the zero has no influence on the result). + @end deftypefun + +@@ -2003,8 +2014,11 @@ + @deftypefun int mpfr_lngamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to the value of the logarithm of the Gamma function on @var{op}, + rounded in the direction @var{rnd}. +-When @math{@minus{}2@var{k}@minus{}1 @le{} @var{op} @le{} @minus{}2@var{k}}, +-@var{k} being a non-negative integer, @var{rop} is set to NaN. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf, ++following the general rules on special values. ++When @math{@minus{}2@var{k}@minus{}1 < @var{op} < @minus{}2@var{k}}, ++@var{k} being a nonnegative integer, set @var{rop} to NaN@. + See also @code{mpfr_lgamma}. + @end deftypefun + +@@ -2012,10 +2026,11 @@ + Set @var{rop} to the value of the logarithm of the absolute value of the + Gamma function on @var{op}, rounded in the direction @var{rnd}. The sign + (1 or @minus{}1) of Gamma(@var{op}) is returned in the object pointed to +-by @var{signp}. When @var{op} is an infinity or a non-positive integer, set +-@var{rop} to +Inf. When @var{op} is NaN, @minus{}Inf or a negative integer, +-*@var{signp} is undefined, and when @var{op} is @pom{}0, *@var{signp} is +-the sign of the zero. ++by @var{signp}. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf. ++When @var{op} is NaN, @minus{}Inf or a negative integer, *@var{signp} is ++undefined, and when @var{op} is @pom{}0, *@var{signp} is the sign of the zero. + @end deftypefun + + @deftypefun int mpfr_digamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -2064,7 +2079,10 @@ + @deftypefunx int mpfr_fms (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_t @var{op3}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{(@var{op1} @GMPtimes{} @var{op2}) + @var{op3}} + (resp.@: @math{(@var{op1} @GMPtimes{} @var{op2}) - @var{op3}}) +-rounded in the direction @var{rnd}. ++rounded in the direction @var{rnd}. Concerning special values (signed zeros, ++infinities, NaN), these functions behave like a multiplication followed by a ++separate addition or subtraction. That is, the fused operation matters only ++for rounding. + @end deftypefun + + @deftypefun int mpfr_agm (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_rnd_t @var{rnd}) +@@ -2089,8 +2107,8 @@ + i.e., $\sqrt{x^2+y^2}$, + @end tex + rounded in the direction @var{rnd}. +-Special values are handled as described in Section F.9.4.3 of +-the ISO C99 and IEEE 754-2008 standards: ++Special values are handled as described in the ISO C99 (Section F.9.4.3) ++and IEEE 754-2008 (Section 9.2.1) standards: + If @var{x} or @var{y} is an infinity, then +Inf is returned in @var{rop}, + even if the other number is NaN. + @end deftypefun +diff -Naurd mpfr-3.1.3-a/doc/mpfr.info mpfr-3.1.3-b/doc/mpfr.info +--- mpfr-3.1.3-a/doc/mpfr.info 2015-06-19 19:55:53.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.info 2015-07-02 10:49:38.718267817 +0000 +@@ -1,4 +1,4 @@ +-This is mpfr.info, produced by makeinfo version 5.2 from mpfr.texi. ++This is mpfr.info, produced by makeinfo version 6.0 from mpfr.texi. + + This manual documents how to install and use the Multiple Precision + Floating-Point Reliable Library, version 3.1.3. +@@ -55,7 +55,7 @@ + MPFR Copying Conditions + *********************** + +-The GNU MPFR library (or MPFR for short) is "free"; this means that ++The GNU MPFR library (or MPFR for short) is “free”; this means that + everyone is free to use it and free to redistribute it on a free basis. + The library is not in the public domain; it is copyrighted and there are + restrictions on its distribution, but these restrictions are designed to +@@ -418,7 +418,7 @@ + 4.2 Nomenclature and Types + ========================== + +-A "floating-point number", or "float" for short, is an arbitrary ++A “floating-point number”, or “float” for short, is an arbitrary + precision significand (also called mantissa) with a limited precision + exponent. The C data type for such objects is ‘mpfr_t’ (internally + defined as a one-element array of a structure, and ‘mpfr_ptr’ is the C +@@ -432,7 +432,7 @@ + to the other functions supported by MPFR. Unless documented otherwise, + the sign bit of a NaN is unspecified. + +-The "precision" is the number of bits used to represent the significand ++The “precision” is the number of bits used to represent the significand + of a floating-point number; the corresponding C data type is + ‘mpfr_prec_t’. The precision can be any integer between ‘MPFR_PREC_MIN’ + and ‘MPFR_PREC_MAX’. In the current implementation, ‘MPFR_PREC_MIN’ is +@@ -446,7 +446,7 @@ + may abort, crash or have undefined behavior (depending on your C + implementation). + +-The "rounding mode" specifies the way to round the result of a ++The “rounding mode” specifies the way to round the result of a + floating-point operation, in case the exact result can not be + represented exactly in the destination significand; the corresponding C + data type is ‘mpfr_rnd_t’. +@@ -499,14 +499,14 @@ + representable numbers, it is rounded to the one with the least + significant bit set to zero. For example, the number 2.5, which is + represented by (10.1) in binary, is rounded to (10.0)=2 with a precision +-of two bits, and not to (11.0)=3. This rule avoids the "drift" ++of two bits, and not to (11.0)=3. This rule avoids the “drift” + phenomenon mentioned by Knuth in volume 2 of The Art of Computer + Programming (Section 4.2.2). + + Most MPFR functions take as first argument the destination variable, + as second and following arguments the input variables, as last argument + a rounding mode, and have a return value of type ‘int’, called the +-"ternary value". The value stored in the destination variable is ++“ternary value”. The value stored in the destination variable is + correctly rounded, i.e., MPFR behaves as if it computed the result with + an infinite precision, then rounded it to the precision of this + variable. The input variables are regarded as exact (in particular, +@@ -572,15 +572,18 @@ + When the input point is in the closure of the domain of the + mathematical function and an input argument is +0 (resp. −0), one + considers the limit when the corresponding argument approaches 0 from +-above (resp. below). If the limit is not defined (e.g., ‘mpfr_log’ on +-−0), the behavior is specified in the description of the MPFR function. ++above (resp. below), if possible. If the limit is not defined (e.g., ++‘mpfr_sqrt’ and ‘mpfr_log’ on −0), the behavior is specified in the ++description of the MPFR function, but must be consistent with the rule ++from the above paragraph (e.g., ‘mpfr_log’ on ±0 gives −Inf). + + When the result is equal to 0, its sign is determined by considering + the limit as if the input point were not in the domain: If one + approaches 0 from above (resp. below), the result is +0 (resp. −0); for +-example, ‘mpfr_sin’ on +0 gives +0. In the other cases, the sign is +-specified in the description of the MPFR function; for example +-‘mpfr_max’ on −0 and +0 gives +0. ++example, ‘mpfr_sin’ on −0 gives −0 and ‘mpfr_acos’ on 1 gives +0 (in all ++rounding modes). In the other cases, the sign is specified in the ++description of the MPFR function; for example ‘mpfr_max’ on −0 and +0 ++gives +0. + + When the input point is not in the closure of the domain of the + function, the result is NaN. Example: ‘mpfr_sqrt’ on −17 gives NaN. +@@ -590,8 +593,8 @@ + numbers; such a case is always explicitly specified in *note MPFR + Interface::. Example: ‘mpfr_hypot’ on (NaN,0) gives NaN, but + ‘mpfr_hypot’ on (NaN,+Inf) gives +Inf (as specified in *note Special +-Functions::), since for any finite input X, ‘mpfr_hypot’ on (X,+Inf) +-gives +Inf. ++Functions::), since for any finite or infinite input X, ‘mpfr_hypot’ on ++(X,+Inf) gives +Inf. + +  + File: mpfr.info, Node: Exceptions, Next: Memory Handling, Prev: Floating-Point Values on Special Numbers, Up: MPFR Basics +@@ -1253,8 +1256,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_add_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 + OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) + 0 = ++ Set ROP to OP1 + OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) + 0 = + (+0) and (−0) + 0 = (−0)). The ‘mpfr_add_d’ function assumes that + the radix of the ‘double’ type is a power of 2, with a precision at + most that declared by the C implementation (macro +@@ -1280,8 +1284,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_sub_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 - OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) − 0 = ++ Set ROP to OP1 - OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) − 0 = + (+0), (−0) − 0 = (−0), 0 − (+0) = (−0) and 0 − (−0) = (+0)). The + same restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_sub’ and + ‘mpfr_sub_d’. +@@ -1300,7 +1305,7 @@ + mpfr_rnd_t RND) + Set ROP to OP1 times OP2 rounded in the direction RND. When a + result is zero, its sign is the product of the signs of the +- operands (for types having no signed zero, it is considered ++ operands (for types having no signed zeros, 0 is considered + positive). The same restrictions than for ‘mpfr_add_d’ apply to + ‘mpfr_mul_d’. + +@@ -1327,21 +1332,24 @@ + mpfr_rnd_t RND) + Set ROP to OP1/OP2 rounded in the direction RND. When a result is + zero, its sign is the product of the signs of the operands (for +- types having no signed zero, it is considered positive). The same ++ types having no signed zeros, 0 is considered positive). The same + restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_div’ and + ‘mpfr_div_d’. + + -- Function: int mpfr_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_sqrt_ui (mpfr_t ROP, unsigned long int OP, + mpfr_rnd_t RND) +- Set ROP to the square root of OP rounded in the direction RND (set +- ROP to −0 if OP is −0, to be consistent with the IEEE 754 +- standard). Set ROP to NaN if OP is negative. ++ Set ROP to the square root of OP rounded in the direction RND. Set ++ ROP to −0 if OP is −0, to be consistent with the IEEE 754 standard. ++ Set ROP to NaN if OP is negative. + + -- Function: int mpfr_rec_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the reciprocal square root of OP rounded in the + direction RND. Set ROP to +Inf if OP is ±0, +0 if OP is +Inf, and +- NaN if OP is negative. ++ NaN if OP is negative. Warning! Therefore the result on −0 is ++ different from the one of the rSqrt function recommended by the ++ IEEE 754-2008 standard (Section 9.2.1), which is −Inf instead of ++ +Inf. + + -- Function: int mpfr_cbrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_root (mpfr_t ROP, mpfr_t OP, unsigned long int K, +@@ -1515,8 +1523,10 @@ + -- Function: int mpfr_log2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_log10 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the natural logarithm of OP, log2(OP) or log10(OP), +- respectively, rounded in the direction RND. Set ROP to −Inf if OP +- is −0 (i.e., the sign of the zero has no influence on the result). ++ respectively, rounded in the direction RND. Set ROP to +0 if OP is ++ 1 (in all rounding modes), for consistency with the ISO C99 and ++ IEEE 754-2008 standards. Set ROP to −Inf if OP is ±0 (i.e., the ++ sign of the zero has no influence on the result). + + -- Function: int mpfr_exp (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_exp2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) +@@ -1649,17 +1659,21 @@ + + -- Function: int mpfr_lngamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the Gamma function on OP, +- rounded in the direction RND. When −2K−1 <= OP <= −2K, K being a +- non-negative integer, ROP is set to NaN. See also ‘mpfr_lgamma’. ++ rounded in the direction RND. When OP is 1 or 2, set ROP to +0 (in ++ all rounding modes). When OP is an infinity or a nonpositive ++ integer, set ROP to +Inf, following the general rules on special ++ values. When −2K−1 < OP < −2K, K being a nonnegative integer, set ++ ROP to NaN. See also ‘mpfr_lgamma’. + + -- Function: int mpfr_lgamma (mpfr_t ROP, int *SIGNP, mpfr_t OP, + mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the absolute value of the + Gamma function on OP, rounded in the direction RND. The sign (1 or + −1) of Gamma(OP) is returned in the object pointed to by SIGNP. +- When OP is an infinity or a non-positive integer, set ROP to +Inf. +- When OP is NaN, −Inf or a negative integer, *SIGNP is undefined, +- and when OP is ±0, *SIGNP is the sign of the zero. ++ When OP is 1 or 2, set ROP to +0 (in all rounding modes). When OP ++ is an infinity or a nonpositive integer, set ROP to +Inf. When OP ++ is NaN, −Inf or a negative integer, *SIGNP is undefined, and when ++ OP is ±0, *SIGNP is the sign of the zero. + + -- Function: int mpfr_digamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the Digamma (sometimes also called Psi) +@@ -1703,7 +1717,10 @@ + -- Function: int mpfr_fms (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, mpfr_t + OP3, mpfr_rnd_t RND) + Set ROP to (OP1 times OP2) + OP3 (resp. (OP1 times OP2) - OP3) +- rounded in the direction RND. ++ rounded in the direction RND. Concerning special values (signed ++ zeros, infinities, NaN), these functions behave like a ++ multiplication followed by a separate addition or subtraction. ++ That is, the fused operation matters only for rounding. + + -- Function: int mpfr_agm (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, + mpfr_rnd_t RND) +@@ -1717,9 +1734,10 @@ + RND) + Set ROP to the Euclidean norm of X and Y, i.e., the square root of + the sum of the squares of X and Y, rounded in the direction RND. +- Special values are handled as described in Section F.9.4.3 of the +- ISO C99 and IEEE 754-2008 standards: If X or Y is an infinity, then +- +Inf is returned in ROP, even if the other number is NaN. ++ Special values are handled as described in the ISO C99 (Section ++ F.9.4.3) and IEEE 754-2008 (Section 9.2.1) standards: If X or Y is ++ an infinity, then +Inf is returned in ROP, even if the other number ++ is NaN. + + -- Function: int mpfr_ai (mpfr_t ROP, mpfr_t X, mpfr_rnd_t RND) + Set ROP to the value of the Airy function Ai on X, rounded in the +@@ -2670,7 +2688,7 @@ + 5.16 Internals + ============== + +-A "limb" means the part of a multi-precision number that fits in a ++A “limb” means the part of a multi-precision number that fits in a + single word. Usually a limb contains 32 or 64 bits. The C data type + for a limb is ‘mp_limb_t’. + +@@ -3140,7 +3158,7 @@ + 0. PREAMBLE + + The purpose of this License is to make a manual, textbook, or other +- functional and useful document "free" in the sense of freedom: to ++ functional and useful document “free” in the sense of freedom: to + assure everyone the effective freedom to copy and redistribute it, + with or without modifying it, either commercially or + noncommercially. Secondarily, this License preserves for the +@@ -3655,9 +3673,9 @@ + * Menu: + + * mpfr_abs: Basic Arithmetic Functions. +- (line 160) +-* mpfr_acos: Special Functions. (line 51) +-* mpfr_acosh: Special Functions. (line 115) ++ (line 165) ++* mpfr_acos: Special Functions. (line 53) ++* mpfr_acosh: Special Functions. (line 117) + * mpfr_add: Basic Arithmetic Functions. + (line 6) + * mpfr_add_d: Basic Arithmetic Functions. +@@ -3670,15 +3688,15 @@ + (line 8) + * mpfr_add_z: Basic Arithmetic Functions. + (line 14) +-* mpfr_agm: Special Functions. (line 210) +-* mpfr_ai: Special Functions. (line 226) +-* mpfr_asin: Special Functions. (line 52) +-* mpfr_asinh: Special Functions. (line 116) ++* mpfr_agm: Special Functions. (line 219) ++* mpfr_ai: Special Functions. (line 236) ++* mpfr_asin: Special Functions. (line 54) ++* mpfr_asinh: Special Functions. (line 118) + * mpfr_asprintf: Formatted Output Functions. + (line 193) +-* mpfr_atan: Special Functions. (line 53) +-* mpfr_atan2: Special Functions. (line 63) +-* mpfr_atanh: Special Functions. (line 117) ++* mpfr_atan: Special Functions. (line 55) ++* mpfr_atan2: Special Functions. (line 65) ++* mpfr_atanh: Special Functions. (line 119) + * mpfr_buildopt_decimal_p: Miscellaneous Functions. + (line 162) + * mpfr_buildopt_gmpinternals_p: Miscellaneous Functions. +@@ -3690,7 +3708,7 @@ + * mpfr_can_round: Rounding Related Functions. + (line 39) + * mpfr_cbrt: Basic Arithmetic Functions. +- (line 108) ++ (line 113) + * mpfr_ceil: Integer Related Functions. + (line 7) + * mpfr_check_range: Exception Related Functions. +@@ -3735,18 +3753,18 @@ + (line 27) + * mpfr_cmp_z: Comparison Functions. + (line 11) +-* mpfr_const_catalan: Special Functions. (line 237) +-* mpfr_const_euler: Special Functions. (line 236) +-* mpfr_const_log2: Special Functions. (line 234) +-* mpfr_const_pi: Special Functions. (line 235) ++* mpfr_const_catalan: Special Functions. (line 247) ++* mpfr_const_euler: Special Functions. (line 246) ++* mpfr_const_log2: Special Functions. (line 244) ++* mpfr_const_pi: Special Functions. (line 245) + * mpfr_copysign: Miscellaneous Functions. + (line 109) +-* mpfr_cos: Special Functions. (line 29) +-* mpfr_cosh: Special Functions. (line 95) +-* mpfr_cot: Special Functions. (line 47) +-* mpfr_coth: Special Functions. (line 111) +-* mpfr_csc: Special Functions. (line 46) +-* mpfr_csch: Special Functions. (line 110) ++* mpfr_cos: Special Functions. (line 31) ++* mpfr_cosh: Special Functions. (line 97) ++* mpfr_cot: Special Functions. (line 49) ++* mpfr_coth: Special Functions. (line 113) ++* mpfr_csc: Special Functions. (line 48) ++* mpfr_csch: Special Functions. (line 112) + * mpfr_custom_get_exp: Custom Interface. (line 75) + * mpfr_custom_get_kind: Custom Interface. (line 65) + * mpfr_custom_get_significand: Custom Interface. (line 70) +@@ -3756,47 +3774,47 @@ + * mpfr_custom_move: Custom Interface. (line 82) + * MPFR_DECL_INIT: Initialization Functions. + (line 74) +-* mpfr_digamma: Special Functions. (line 166) ++* mpfr_digamma: Special Functions. (line 172) + * mpfr_dim: Basic Arithmetic Functions. +- (line 166) ++ (line 171) + * mpfr_div: Basic Arithmetic Functions. +- (line 72) ++ (line 74) + * mpfr_divby0_p: Exception Related Functions. + (line 134) + * mpfr_div_2exp: Compatibility with MPF. + (line 49) + * mpfr_div_2si: Basic Arithmetic Functions. +- (line 181) ++ (line 186) + * mpfr_div_2ui: Basic Arithmetic Functions. +- (line 179) ++ (line 184) + * mpfr_div_d: Basic Arithmetic Functions. +- (line 84) ++ (line 86) + * mpfr_div_q: Basic Arithmetic Functions. +- (line 88) ++ (line 90) + * mpfr_div_si: Basic Arithmetic Functions. +- (line 80) ++ (line 82) + * mpfr_div_ui: Basic Arithmetic Functions. +- (line 76) ++ (line 78) + * mpfr_div_z: Basic Arithmetic Functions. +- (line 86) ++ (line 88) + * mpfr_d_div: Basic Arithmetic Functions. +- (line 82) ++ (line 84) + * mpfr_d_sub: Basic Arithmetic Functions. +- (line 35) +-* mpfr_eint: Special Functions. (line 133) ++ (line 36) ++* mpfr_eint: Special Functions. (line 135) + * mpfr_eq: Compatibility with MPF. + (line 28) + * mpfr_equal_p: Comparison Functions. + (line 59) + * mpfr_erangeflag_p: Exception Related Functions. + (line 137) +-* mpfr_erf: Special Functions. (line 177) +-* mpfr_erfc: Special Functions. (line 178) +-* mpfr_exp: Special Functions. (line 23) +-* mpfr_exp10: Special Functions. (line 25) +-* mpfr_exp2: Special Functions. (line 24) +-* mpfr_expm1: Special Functions. (line 129) +-* mpfr_fac_ui: Special Functions. (line 121) ++* mpfr_erf: Special Functions. (line 183) ++* mpfr_erfc: Special Functions. (line 184) ++* mpfr_exp: Special Functions. (line 25) ++* mpfr_exp10: Special Functions. (line 27) ++* mpfr_exp2: Special Functions. (line 26) ++* mpfr_expm1: Special Functions. (line 131) ++* mpfr_fac_ui: Special Functions. (line 123) + * mpfr_fits_intmax_p: Conversion Functions. + (line 150) + * mpfr_fits_sint_p: Conversion Functions. +@@ -3815,20 +3833,20 @@ + (line 147) + * mpfr_floor: Integer Related Functions. + (line 8) +-* mpfr_fma: Special Functions. (line 203) ++* mpfr_fma: Special Functions. (line 209) + * mpfr_fmod: Integer Related Functions. + (line 92) +-* mpfr_fms: Special Functions. (line 205) ++* mpfr_fms: Special Functions. (line 211) + * mpfr_fprintf: Formatted Output Functions. + (line 157) + * mpfr_frac: Integer Related Functions. + (line 76) +-* mpfr_free_cache: Special Functions. (line 244) ++* mpfr_free_cache: Special Functions. (line 254) + * mpfr_free_str: Conversion Functions. + (line 137) + * mpfr_frexp: Conversion Functions. + (line 45) +-* mpfr_gamma: Special Functions. (line 148) ++* mpfr_gamma: Special Functions. (line 150) + * mpfr_get_d: Conversion Functions. + (line 7) + * mpfr_get_decimal64: Conversion Functions. +@@ -3887,7 +3905,7 @@ + (line 56) + * mpfr_greater_p: Comparison Functions. + (line 55) +-* mpfr_hypot: Special Functions. (line 218) ++* mpfr_hypot: Special Functions. (line 227) + * mpfr_inexflag_p: Exception Related Functions. + (line 136) + * mpfr_inf_p: Comparison Functions. +@@ -3922,21 +3940,21 @@ + (line 31) + * mpfr_integer_p: Integer Related Functions. + (line 119) +-* mpfr_j0: Special Functions. (line 182) +-* mpfr_j1: Special Functions. (line 183) +-* mpfr_jn: Special Functions. (line 184) ++* mpfr_j0: Special Functions. (line 188) ++* mpfr_j1: Special Functions. (line 189) ++* mpfr_jn: Special Functions. (line 190) + * mpfr_lessequal_p: Comparison Functions. + (line 58) + * mpfr_lessgreater_p: Comparison Functions. + (line 64) + * mpfr_less_p: Comparison Functions. + (line 57) +-* mpfr_lgamma: Special Functions. (line 157) +-* mpfr_li2: Special Functions. (line 143) +-* mpfr_lngamma: Special Functions. (line 152) ++* mpfr_lgamma: Special Functions. (line 162) ++* mpfr_li2: Special Functions. (line 145) ++* mpfr_lngamma: Special Functions. (line 154) + * mpfr_log: Special Functions. (line 16) + * mpfr_log10: Special Functions. (line 18) +-* mpfr_log1p: Special Functions. (line 125) ++* mpfr_log1p: Special Functions. (line 127) + * mpfr_log2: Special Functions. (line 17) + * mpfr_max: Miscellaneous Functions. + (line 22) +@@ -3947,29 +3965,29 @@ + * mpfr_modf: Integer Related Functions. + (line 82) + * mpfr_mul: Basic Arithmetic Functions. +- (line 51) ++ (line 53) + * mpfr_mul_2exp: Compatibility with MPF. + (line 47) + * mpfr_mul_2si: Basic Arithmetic Functions. +- (line 174) ++ (line 179) + * mpfr_mul_2ui: Basic Arithmetic Functions. +- (line 172) ++ (line 177) + * mpfr_mul_d: Basic Arithmetic Functions. +- (line 57) ++ (line 59) + * mpfr_mul_q: Basic Arithmetic Functions. +- (line 61) ++ (line 63) + * mpfr_mul_si: Basic Arithmetic Functions. +- (line 55) ++ (line 57) + * mpfr_mul_ui: Basic Arithmetic Functions. +- (line 53) ++ (line 55) + * mpfr_mul_z: Basic Arithmetic Functions. +- (line 59) ++ (line 61) + * mpfr_nanflag_p: Exception Related Functions. + (line 135) + * mpfr_nan_p: Comparison Functions. + (line 39) + * mpfr_neg: Basic Arithmetic Functions. +- (line 159) ++ (line 164) + * mpfr_nextabove: Miscellaneous Functions. + (line 15) + * mpfr_nextbelow: Miscellaneous Functions. +@@ -3983,13 +4001,13 @@ + * mpfr_overflow_p: Exception Related Functions. + (line 133) + * mpfr_pow: Basic Arithmetic Functions. +- (line 116) ++ (line 121) + * mpfr_pow_si: Basic Arithmetic Functions. +- (line 120) ++ (line 125) + * mpfr_pow_ui: Basic Arithmetic Functions. +- (line 118) ++ (line 123) + * mpfr_pow_z: Basic Arithmetic Functions. +- (line 122) ++ (line 127) + * mpfr_prec_round: Rounding Related Functions. + (line 13) + * ‘mpfr_prec_t’: Nomenclature and Types. +@@ -3999,7 +4017,7 @@ + * mpfr_print_rnd_mode: Rounding Related Functions. + (line 71) + * mpfr_rec_sqrt: Basic Arithmetic Functions. +- (line 103) ++ (line 105) + * mpfr_regular_p: Comparison Functions. + (line 43) + * mpfr_reldiff: Compatibility with MPF. +@@ -4021,11 +4039,11 @@ + * ‘mpfr_rnd_t’: Nomenclature and Types. + (line 34) + * mpfr_root: Basic Arithmetic Functions. +- (line 109) ++ (line 114) + * mpfr_round: Integer Related Functions. + (line 9) +-* mpfr_sec: Special Functions. (line 45) +-* mpfr_sech: Special Functions. (line 109) ++* mpfr_sec: Special Functions. (line 47) ++* mpfr_sech: Special Functions. (line 111) + * mpfr_set: Assignment Functions. + (line 9) + * mpfr_setsign: Miscellaneous Functions. +@@ -4100,57 +4118,57 @@ + (line 49) + * mpfr_signbit: Miscellaneous Functions. + (line 99) +-* mpfr_sin: Special Functions. (line 30) +-* mpfr_sinh: Special Functions. (line 96) +-* mpfr_sinh_cosh: Special Functions. (line 101) +-* mpfr_sin_cos: Special Functions. (line 35) ++* mpfr_sin: Special Functions. (line 32) ++* mpfr_sinh: Special Functions. (line 98) ++* mpfr_sinh_cosh: Special Functions. (line 103) ++* mpfr_sin_cos: Special Functions. (line 37) + * mpfr_si_div: Basic Arithmetic Functions. +- (line 78) ++ (line 80) + * mpfr_si_sub: Basic Arithmetic Functions. +- (line 31) ++ (line 32) + * mpfr_snprintf: Formatted Output Functions. + (line 180) + * mpfr_sprintf: Formatted Output Functions. + (line 170) + * mpfr_sqr: Basic Arithmetic Functions. +- (line 69) ++ (line 71) + * mpfr_sqrt: Basic Arithmetic Functions. +- (line 96) ++ (line 98) + * mpfr_sqrt_ui: Basic Arithmetic Functions. +- (line 97) ++ (line 99) + * mpfr_strtofr: Assignment Functions. + (line 80) + * mpfr_sub: Basic Arithmetic Functions. +- (line 25) ++ (line 26) + * mpfr_subnormalize: Exception Related Functions. + (line 60) + * mpfr_sub_d: Basic Arithmetic Functions. +- (line 37) ++ (line 38) + * mpfr_sub_q: Basic Arithmetic Functions. +- (line 43) ++ (line 44) + * mpfr_sub_si: Basic Arithmetic Functions. +- (line 33) ++ (line 34) + * mpfr_sub_ui: Basic Arithmetic Functions. +- (line 29) ++ (line 30) + * mpfr_sub_z: Basic Arithmetic Functions. +- (line 41) +-* mpfr_sum: Special Functions. (line 252) ++ (line 42) ++* mpfr_sum: Special Functions. (line 262) + * mpfr_swap: Assignment Functions. + (line 150) + * ‘mpfr_t’: Nomenclature and Types. + (line 6) +-* mpfr_tan: Special Functions. (line 31) +-* mpfr_tanh: Special Functions. (line 97) ++* mpfr_tan: Special Functions. (line 33) ++* mpfr_tanh: Special Functions. (line 99) + * mpfr_trunc: Integer Related Functions. + (line 10) + * mpfr_ui_div: Basic Arithmetic Functions. +- (line 74) ++ (line 76) + * mpfr_ui_pow: Basic Arithmetic Functions. +- (line 126) ++ (line 131) + * mpfr_ui_pow_ui: Basic Arithmetic Functions. +- (line 124) ++ (line 129) + * mpfr_ui_sub: Basic Arithmetic Functions. +- (line 27) ++ (line 28) + * mpfr_underflow_p: Exception Related Functions. + (line 132) + * mpfr_unordered_p: Comparison Functions. +@@ -4181,61 +4199,61 @@ + (line 182) + * mpfr_vsprintf: Formatted Output Functions. + (line 171) +-* mpfr_y0: Special Functions. (line 193) +-* mpfr_y1: Special Functions. (line 194) +-* mpfr_yn: Special Functions. (line 195) ++* mpfr_y0: Special Functions. (line 199) ++* mpfr_y1: Special Functions. (line 200) ++* mpfr_yn: Special Functions. (line 201) + * mpfr_zero_p: Comparison Functions. + (line 42) +-* mpfr_zeta: Special Functions. (line 171) +-* mpfr_zeta_ui: Special Functions. (line 172) ++* mpfr_zeta: Special Functions. (line 177) ++* mpfr_zeta_ui: Special Functions. (line 178) + * mpfr_z_sub: Basic Arithmetic Functions. +- (line 39) ++ (line 40) + + +  + Tag Table: + Node: Top775 + Node: Copying2007 +-Node: Introduction to MPFR3766 +-Node: Installing MPFR5880 +-Node: Reporting Bugs11323 +-Node: MPFR Basics13353 +-Node: Headers and Libraries13669 +-Node: Nomenclature and Types16828 +-Node: MPFR Variable Conventions18874 +-Node: Rounding Modes20418 +-Ref: ternary value21544 +-Node: Floating-Point Values on Special Numbers23526 +-Node: Exceptions26572 +-Node: Memory Handling29749 +-Node: MPFR Interface30894 +-Node: Initialization Functions33008 +-Node: Assignment Functions40318 +-Node: Combined Initialization and Assignment Functions49673 +-Node: Conversion Functions50974 +-Node: Basic Arithmetic Functions60035 +-Node: Comparison Functions69200 +-Node: Special Functions72687 +-Node: Input and Output Functions86672 +-Node: Formatted Output Functions88644 +-Node: Integer Related Functions98431 +-Node: Rounding Related Functions105051 +-Node: Miscellaneous Functions108888 +-Node: Exception Related Functions117568 +-Node: Compatibility with MPF124386 +-Node: Custom Interface127127 +-Node: Internals131526 +-Node: API Compatibility133066 +-Node: Type and Macro Changes134995 +-Node: Added Functions137844 +-Node: Changed Functions141132 +-Node: Removed Functions145545 +-Node: Other Changes145973 +-Node: Contributors147576 +-Node: References150219 +-Node: GNU Free Documentation License151973 +-Node: Concept Index174562 +-Node: Function and Type Index180659 ++Node: Introduction to MPFR3770 ++Node: Installing MPFR5884 ++Node: Reporting Bugs11327 ++Node: MPFR Basics13357 ++Node: Headers and Libraries13673 ++Node: Nomenclature and Types16832 ++Node: MPFR Variable Conventions18894 ++Node: Rounding Modes20438 ++Ref: ternary value21568 ++Node: Floating-Point Values on Special Numbers23554 ++Node: Exceptions26813 ++Node: Memory Handling29990 ++Node: MPFR Interface31135 ++Node: Initialization Functions33249 ++Node: Assignment Functions40559 ++Node: Combined Initialization and Assignment Functions49914 ++Node: Conversion Functions51215 ++Node: Basic Arithmetic Functions60276 ++Node: Comparison Functions69777 ++Node: Special Functions73264 ++Node: Input and Output Functions87862 ++Node: Formatted Output Functions89834 ++Node: Integer Related Functions99621 ++Node: Rounding Related Functions106241 ++Node: Miscellaneous Functions110078 ++Node: Exception Related Functions118758 ++Node: Compatibility with MPF125576 ++Node: Custom Interface128317 ++Node: Internals132716 ++Node: API Compatibility134260 ++Node: Type and Macro Changes136189 ++Node: Added Functions139038 ++Node: Changed Functions142326 ++Node: Removed Functions146739 ++Node: Other Changes147167 ++Node: Contributors148770 ++Node: References151413 ++Node: GNU Free Documentation License153167 ++Node: Concept Index175760 ++Node: Function and Type Index181857 +  + End Tag Table + +diff -Naurd mpfr-3.1.3-a/src/lngamma.c mpfr-3.1.3-b/src/lngamma.c +--- mpfr-3.1.3-a/src/lngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/lngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -603,16 +603,17 @@ + mpfr_get_prec (y), mpfr_log_prec, y, inex)); + + /* special cases */ +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x) || ++ (MPFR_IS_NEG (x) && mpfr_integer_p (x)))) + { +- if (MPFR_IS_NAN (x) || MPFR_IS_NEG (x)) ++ if (MPFR_IS_NAN (x)) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; + } +- else /* lngamma(+Inf) = lngamma(+0) = +Inf */ ++ else /* lngamma(+/-Inf) = lngamma(nonpositive integer) = +Inf */ + { +- if (MPFR_IS_ZERO (x)) ++ if (!MPFR_IS_INF (x)) + mpfr_set_divby0 (); + MPFR_SET_INF (y); + MPFR_SET_POS (y); +@@ -620,8 +621,8 @@ + } + } + +- /* if x < 0 and -2k-1 <= x <= -2k, then lngamma(x) = NaN */ +- if (MPFR_IS_NEG (x) && (unit_bit (x) == 0 || mpfr_integer_p (x))) ++ /* if -2k-1 < x < -2k <= 0, then lngamma(x) = NaN */ ++ if (MPFR_IS_NEG (x) && unit_bit (x) == 0) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3" ++#define MPFR_VERSION_STRING "3.1.3-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:49:24.042113845 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3"; ++ return "3.1.3-p1"; + } +diff -Naurd mpfr-3.1.3-a/tests/tlngamma.c mpfr-3.1.3-b/tests/tlngamma.c +--- mpfr-3.1.3-a/tests/tlngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tlngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -33,7 +33,7 @@ + special (void) + { + mpfr_t x, y; +- int inex; ++ int i, inex; + + mpfr_init (x); + mpfr_init (y); +@@ -46,25 +46,29 @@ + exit (1); + } + +- mpfr_set_inf (x, -1); ++ mpfr_set_inf (x, 1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(-Inf)\n"); ++ printf ("Error for lngamma(+Inf)\n"); + exit (1); + } + +- mpfr_set_inf (x, 1); ++ mpfr_set_inf (x, -1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(+Inf)\n"); ++ printf ("Error for lngamma(-Inf)\n"); + exit (1); + } + + mpfr_set_ui (x, 0, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(+0)\n"); + exit (1); +@@ -72,32 +76,58 @@ + + mpfr_set_ui (x, 0, MPFR_RNDN); + mpfr_neg (x, x, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(-0)\n"); + exit (1); + } + + mpfr_set_ui (x, 1, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(1)\n"); + exit (1); + } + +- mpfr_set_si (x, -1, MPFR_RNDN); +- mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ for (i = 1; i <= 5; i++) + { +- printf ("Error for lngamma(-1)\n"); +- exit (1); ++ int c; ++ ++ mpfr_set_si (x, -i, MPFR_RNDN); ++ mpfr_clear_flags (); ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) ++ { ++ printf ("Error for lngamma(-%d)\n", i); ++ exit (1); ++ } ++ if (i & 1) ++ { ++ mpfr_nextabove (x); ++ c = '+'; ++ } ++ else ++ { ++ mpfr_nextbelow (x); ++ c = '-'; ++ } ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_nan_p (y)) ++ { ++ printf ("Error for lngamma(-%d%cepsilon)\n", i, c); ++ exit (1); ++ } + } + + mpfr_set_ui (x, 2, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(2)\n"); + exit (1); +@@ -127,7 +157,7 @@ + mpfr_set_str (x, CHECK_X2, 10, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str (x, CHECK_Y2, 10, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp (y, x)) ++ if (mpfr_cmp0 (y, x)) + { + printf ("mpfr_lngamma("CHECK_X2") is wrong:\n" + "expected "); +@@ -143,7 +173,7 @@ + mpfr_lngamma (y, x, MPFR_RNDU); + mpfr_set_prec (x, 175); + mpfr_set_str_binary (x, "0.1010001100011101101011001101110010100001000001000001110011000001101100001111001001000101011011100100010101011110100111110101010100010011010010000101010111001100011000101111E7"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (1)\n"); + exit (1); +@@ -155,7 +185,7 @@ + mpfr_lngamma (x, y, MPFR_RNDZ); + mpfr_set_prec (y, 21); + mpfr_set_str_binary (y, "0.111000101000001100101E9"); +- if (MPFR_IS_NAN (x) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (120)\n"); + printf ("Expected "); mpfr_print_binary (y); puts (""); +@@ -169,7 +199,7 @@ + inex = mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 206); + mpfr_set_str_binary (x, "0.10000111011000000011100010101001100110001110000111100011000100100110110010001011011110101001111011110110000001010100111011010000000011100110110101100111000111010011110010000100010111101010001101000110101001E13"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (768)\n"); + exit (1); +@@ -185,7 +215,7 @@ + mpfr_set_str_binary (x, "0.1100E-66"); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str_binary (x, "0.1100E6"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(0.1100E-66)\n"); + exit (1); +@@ -199,7 +229,7 @@ + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 32); + mpfr_set_str_binary (x, "-0.10001000111011111011000010100010E207"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(-2^199+0.5)\n"); + printf ("Got "); +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:50:08.046573308 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:50:08.126574142 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-overflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:50:08.126574142 +0000 +@@ -1 +1 @@ +-3.1.3-p1 ++3.1.3-p2 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -49,7 +49,7 @@ + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +- else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || ++ else if (MPFR_UNLIKELY(n <= 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || + exp > __gmpfr_emax + n)) ) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 +@@ -32,7 +32,7 @@ + rnd_mode), + ("y[%Pu]=%.*Rg inexact=%d", mpfr_get_prec(y), mpfr_log_prec, y, inexact)); + +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (n == 0 || MPFR_IS_SINGULAR (x))) + return mpfr_set (y, x, rnd_mode); + else + { +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p1" ++#define MPFR_VERSION_STRING "3.1.3-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -39,7 +39,7 @@ + { + mpfr_exp_t exp = MPFR_GET_EXP (x); + MPFR_SETRAW (inexact, y, x, exp, rnd_mode); +- if (MPFR_UNLIKELY( n > 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || ++ if (MPFR_UNLIKELY(n >= 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || + exp > __gmpfr_emax - n))) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emin > MPFR_EMAX_MAX + n || +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:50:08.126574142 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p1"; ++ return "3.1.3-p2"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 +@@ -242,6 +242,76 @@ + large (MPFR_EMAX_MAX); + } + ++/* Cases where the function overflows on n = 0 when rounding is like ++ away from zero. */ ++static void ++overflow0 (mpfr_exp_t emax) ++{ ++ mpfr_exp_t old_emax; ++ mpfr_t x, y1, y2; ++ int neg, r, op; ++ static char *sop[4] = { "mul_2ui", "mul_2si", "div_2ui", "div_2si" }; ++ ++ old_emax = mpfr_get_emax (); ++ set_emax (emax); ++ ++ mpfr_init2 (x, 8); ++ mpfr_inits2 (6, y1, y2, (mpfr_ptr) 0); ++ ++ mpfr_set_inf (x, 1); ++ mpfr_nextbelow (x); ++ ++ for (neg = 0; neg <= 1; neg++) ++ { ++ RND_LOOP (r) ++ { ++ int inex1, inex2; ++ unsigned int flags1, flags2; ++ ++ /* Even if there isn't an overflow (rounding ~ toward zero), ++ the result is the same as the one of an overflow. */ ++ inex1 = mpfr_overflow (y1, (mpfr_rnd_t) r, neg ? -1 : 1); ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (mpfr_inf_p (y1)) ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ for (op = 0; op < 4; op++) ++ { ++ mpfr_clear_flags (); ++ inex2 = ++ op == 0 ? mpfr_mul_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 1 ? mpfr_mul_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 2 ? mpfr_div_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 3 ? mpfr_div_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ (MPFR_ASSERTN (0), 0); ++ flags2 = __gmpfr_flags; ++ if (!(mpfr_equal_p (y1, y2) && ++ SAME_SIGN (inex1, inex2) && ++ flags1 == flags2)) ++ { ++ printf ("Error in overflow0 for %s, mpfr_%s, emax = %" ++ MPFR_EXP_FSPEC "d,\nx = ", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r), sop[op], ++ (mpfr_eexp_t) emax); ++ mpfr_dump (x); ++ printf ("Expected "); ++ mpfr_dump (y1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (y2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } ++ mpfr_neg (x, x, MPFR_RNDN); ++ } ++ ++ mpfr_clears (x, y1, y2, (mpfr_ptr) 0); ++ set_emax (old_emax); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -334,6 +404,11 @@ + underflow0 (); + large0 (); + ++ if (mpfr_get_emax () != MPFR_EMAX_MAX) ++ overflow0 (mpfr_get_emax ()); ++ overflow0 (MPFR_EMAX_MAX); ++ overflow0 (-1); ++ + tests_end_mpfr (); + return 0; + } +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-17 08:54:48.592799981 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-17 08:54:48.616811495 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-underflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-17 08:54:48.616811495 +0000 +@@ -1 +1 @@ +-3.1.3-p2 ++3.1.3-p3 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -45,7 +45,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX - (n - 1) || + exp < __gmpfr_emin + (n - 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-17 08:54:48.608807656 +0000 +@@ -44,7 +44,9 @@ + if (MPFR_UNLIKELY (n >= diffexp)) /* exp - n <= emin - 1 */ + { + if (rnd_mode == MPFR_RNDN && +- (n > diffexp || (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ (n > diffexp || ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN (y)); + } +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-17 08:54:48.616811495 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p2" ++#define MPFR_VERSION_STRING "3.1.3-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -48,7 +48,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX + (n + 1) || + exp < __gmpfr_emin - (n + 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-17 08:54:48.616811495 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p2"; ++ return "3.1.3-p3"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-17 08:54:48.608807656 +0000 +@@ -50,77 +50,82 @@ + { + mpfr_t x, y, z1, z2; + mpfr_exp_t emin; +- int i, k; ++ int i, k, s; + int prec; + int rnd; + int div; + int inex1, inex2; + unsigned int flags1, flags2; + +- /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) +- * with emin = e, x = 1 + i/16, i in { -1, 0, 1 }, and k = 1 to 4, +- * by comparing the result with the one of a simple division. ++ /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) with ++ * emin = e, x = s * (1 + i/16), i in { -1, 0, 1 }, s in { -1, 1 }, and ++ * k = 1 to 4, by comparing the result with the one of a simple division. + */ + emin = mpfr_get_emin (); + set_emin (e); + mpfr_inits2 (8, x, y, (mpfr_ptr) 0); + for (i = 15; i <= 17; i++) +- { +- inex1 = mpfr_set_ui_2exp (x, i, -4, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- for (prec = 6; prec >= 3; prec -= 3) +- { +- mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); +- RND_LOOP (rnd) +- for (k = 1; k <= 4; k++) +- { +- /* The following one is assumed to be correct. */ +- inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- mpfr_clear_flags (); +- /* Do not use mpfr_div_ui to avoid the optimization +- by mpfr_div_2si. */ +- inex1 = mpfr_div (z1, y, z1, (mpfr_rnd_t) rnd); +- flags1 = __gmpfr_flags; +- +- for (div = 0; div <= 2; div++) ++ for (s = 1; s >= -1; s -= 2) ++ { ++ inex1 = mpfr_set_si_2exp (x, s * i, -4, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ for (prec = 6; prec >= 3; prec -= 3) ++ { ++ mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); ++ RND_LOOP (rnd) ++ for (k = 1; k <= 4; k++) + { ++ /* The following one is assumed to be correct. */ ++ inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); + mpfr_clear_flags (); +- inex2 = div == 0 ? +- mpfr_mul_2si (z2, x, e - k, (mpfr_rnd_t) rnd) : div == 1 ? +- mpfr_div_2si (z2, x, k - e, (mpfr_rnd_t) rnd) : +- mpfr_div_2ui (z2, x, k - e, (mpfr_rnd_t) rnd); +- flags2 = __gmpfr_flags; +- if (flags1 == flags2 && SAME_SIGN (inex1, inex2) && +- mpfr_equal_p (z1, z2)) +- continue; +- printf ("Error in underflow("); +- if (e == MPFR_EMIN_MIN) +- printf ("MPFR_EMIN_MIN"); +- else if (e == emin) +- printf ("default emin"); +- else if (e >= LONG_MIN) +- printf ("%ld", (long) e); +- else +- printf ("= LONG_MIN) ++ printf ("%ld", (long) e); ++ else ++ printf ("d1 or (np[n-1]=d1 and np[n-2]>=d0) here, ++ since we truncate the divisor at each step, but since {np,n} < D ++ originally, the largest possible partial quotient is B-1. */ ++ if (MPFR_UNLIKELY(np[n-1] > d1 || (np[n-1] == d1 && np[n-2] >= d0))) + q2 = ~ (mp_limb_t) 0; + else + udiv_qr_3by2 (q2, q1, q0, np[n - 1], np[n - 2], np[n - 3], +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-17 08:58:21.118986898 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-10-29 13:47:46.763900609 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p4"; ++ return "3.1.3-p5"; + } +diff -Naurd mpfr-3.1.3-a/tests/tdiv.c mpfr-3.1.3-b/tests/tdiv.c +--- mpfr-3.1.3-a/tests/tdiv.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tdiv.c 2015-10-29 13:47:46.751900855 +0000 +@@ -1099,6 +1099,69 @@ + mpfr_set_emax (old_emax); + } + ++/* Bug in mpfr_divhigh_n_basecase when all limbs of q (except the most ++ significant one) are B-1 where B=2^GMP_NUMB_BITS. Since we truncate ++ the divisor at each step, it might happen at some point that ++ (np[n-1],np[n-2]) > (d1,d0), and not only the equality. ++ Reported by Ricky Farr ++ ++ To get a failure, a MPFR_DIVHIGH_TAB entry below the MPFR_DIV_THRESHOLD ++ limit must have a value 0. With most mparam.h files, this cannot occur. */ ++static void ++test_20151023 (void) ++{ ++ mpfr_prec_t p; ++ mpfr_t n, d, q, q0; ++ int inex, i; ++ ++ for (p = GMP_NUMB_BITS; p <= 2000; p++) ++ { ++ mpfr_init2 (n, 2*p); ++ mpfr_init2 (d, p); ++ mpfr_init2 (q, p); ++ mpfr_init2 (q0, GMP_NUMB_BITS); ++ ++ /* generate a random divisor of p bits */ ++ mpfr_urandomb (d, RANDS); ++ /* generate a random quotient of GMP_NUMB_BITS bits */ ++ mpfr_urandomb (q0, RANDS); ++ /* zero-pad the quotient to p bits */ ++ inex = mpfr_prec_round (q0, p, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ ++ for (i = 0; i < 3; i++) ++ { ++ /* i=0: try with the original quotient xxx000...000 ++ i=1: try with the original quotient minus one ulp ++ i=2: try with the original quotient plus one ulp */ ++ if (i == 1) ++ mpfr_nextbelow (q0); ++ else if (i == 2) ++ { ++ mpfr_nextabove (q0); ++ mpfr_nextabove (q0); ++ } ++ ++ inex = mpfr_mul (n, d, q0, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_nextabove (n); ++ mpfr_div (q, n, d, MPFR_RNDN); ++ MPFR_ASSERTN(mpfr_cmp (q, q0) == 0); ++ ++ inex = mpfr_mul (n, d, q0, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_nextbelow (n); ++ mpfr_div (q, n, d, MPFR_RNDN); ++ MPFR_ASSERTN(mpfr_cmp (q, q0) == 0); ++ } ++ ++ mpfr_clear (n); ++ mpfr_clear (d); ++ mpfr_clear (q); ++ mpfr_clear (q0); ++ } ++} ++ + #define TEST_FUNCTION test_div + #define TWO_ARGS + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) +@@ -1219,6 +1282,7 @@ + consistency (); + test_20070603 (); + test_20070628 (); ++ test_20151023 (); + test_generic (2, 800, 50); + test_extreme (); + -- GitLab From 90427ca99116eb944d585b3e41cf26b47de181ae Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 12 Jan 2016 17:07:12 +1030 Subject: [PATCH 0168/2133] Added easyconfig for GMAP-GSNAP-2015-12-31.v2-foss-2015b --- .../GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb new file mode 100644 index 0000000000..01cd80052a --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = "2015-12-31.v2" + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +# with these deps you can use standard compressed files +# to support files in gobby format take a look at README for extra dependencies +# http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] + +# you can change the MAX_READLENGTH for GSNAP with something like this. +# details in the README http://research-pub.gene.com/gmap/src/README +#configopts = 'MAX_READLENGTH=250' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From 4c185363dd81f57c8e41ffcfa096d67076e374a3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 12 Jan 2016 08:52:59 +0100 Subject: [PATCH 0169/2133] {bio}[GNU/4.9.3-2.25] RSEM 1.2.26 (REVIEW) --- .../r/RSEM/RSEM-1.2.26-GNU-4.9.3-2.25.eb | 57 +++++++++++++++ .../r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch | 73 +++++++++++++++++++ 2 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..f8223376c0 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-GNU-4.9.3-2.25.eb @@ -0,0 +1,57 @@ +easyblock = 'MakeCp' + +name = 'RSEM' +version = '1.2.26' + +homepage = 'http://deweylab.github.io/RSEM/' +description = """RNA-Seq by Expectation-Maximization)""" +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['RSEM-1.2.26_eb_provided_zlib.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +list_of_executables = [ + "rsem_perl_utils.pm", + "rsem-bam2readdepth", + "rsem-bam2wig", + "rsem-build-read-index", + "rsem-calculate-credibility-intervals", + "rsem-calculate-expression", + "rsem-control-fdr", + "rsem-extract-reference-transcripts", + "rsem-generate-data-matrix", + "rsem-generate-ngvector", + "rsem-gen-transcript-plots", + "rsem-get-unique", + "rsem-gff3-to-gtf", + "rsem-parse-alignments", + "rsem-plot-model", + "rsem-plot-transcript-wiggles", + "rsem-prepare-reference", + "rsem-preref", + "rsem-refseq-extract-primary-assembly", + "rsem-run-ebseq", + "rsem-run-em", + "rsem-run-gibbs", + "rsem-sam-validator", + "rsem-scan-for-paired-end-reads", + "rsem-simulate-reads", + "rsem-synthesis-reference-transcripts", + "rsem-tbam2gbam", +] + +files_to_copy = [(list_of_executables, "bin"), "WHAT_IS_NEW"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch new file mode 100644 index 0000000000..7eb3522c82 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch @@ -0,0 +1,73 @@ +#Use EB provided libz +# January 11, 2016 by B. Hajgato (Vrije Ubiversiteit Brussel) +--- Makefile.orig 2016-01-08 02:23:01.000000000 +0100 ++++ Makefile 2016-01-11 16:41:25.548773718 +0100 +@@ -1,6 +1,6 @@ + CC = g++ + CFLAGS = -Wall -c -I. +-COFLAGS = -Wall -O3 -ffast-math -c -I. ++COFLAGS = -march=native -Wall -O3 -ffast-math -c -I. + PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads + + .PHONY : all ebseq clean +@@ -8,6 +8,8 @@ + all : $(PROGRAMS) + + sam/libbam.a : ++ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i sam/Makefile ++ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i sam/bcftools/Makefile + cd sam ; ${MAKE} all + + Transcript.h : utils.h +@@ -52,7 +54,7 @@ + + + rsem-parse-alignments : parseIt.o sam/libbam.a +- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread ++ $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread + + parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp + $(CC) -Wall -O2 -c -I. parseIt.cpp +@@ -87,7 +89,7 @@ + WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h + + rsem-run-em : EM.o sam/libbam.a +- $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread ++ $(CC) -o rsem-run-em EM.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread + + EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp + $(CC) $(COFLAGS) EM.cpp +@@ -97,13 +99,13 @@ + BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h + + rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a +- $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp +- $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ ++ $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp +- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ ++ $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h + $(CC) $(COFLAGS) wiggle.cpp +@@ -131,13 +133,13 @@ + $(CC) $(COFLAGS) calcCI.cpp + + rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a +- $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a +- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a +- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + ebseq : + cd EBSeq ; ${MAKE} all -- GitLab From 213e46cff340c7f90318d33e7d5c676374652693 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 13 Jan 2016 12:58:45 +1030 Subject: [PATCH 0170/2133] Added easyconfig for BBMap suite of tools --- .../b/BBMap/BBMap-35.82-Java-1.8.0_66.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb new file mode 100644 index 0000000000..3f29f51392 --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '35.82' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.8.0_66' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz' ] + +#start_dir = 'jni' +prebuildopts = 'cd jni && ' +buildopts = '-f makefile.linux' + +# put here the list of generated executables when compiling +#list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd-hit-div", "cd-hit-454"] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = ['./*'] + +sanity_check_paths = { + 'files': ['bbmap.sh'], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code." + +moduleclass = 'bio' -- GitLab From bb4be77e4feae0fddd7b46c8f88bbc1b8b1162f7 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 13 Jan 2016 13:00:22 +1030 Subject: [PATCH 0171/2133] Remove unnecessary lines --- easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb index 3f29f51392..ac6e1abb04 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb @@ -16,14 +16,9 @@ dependencies = [(java, javaver)] source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz' ] -#start_dir = 'jni' prebuildopts = 'cd jni && ' buildopts = '-f makefile.linux' -# put here the list of generated executables when compiling -#list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd-hit-div", "cd-hit-454"] - -# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" files_to_copy = ['./*'] sanity_check_paths = { -- GitLab From 10774be2c0dd4cace3b13653c1c8b078375eb1cf Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 13 Jan 2016 13:03:35 +1030 Subject: [PATCH 0172/2133] Corrected toolchain --- ...Java-1.8.0_66.eb => BBMap-35.82-foss-2015b-Java-1.8.0_66.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/b/BBMap/{BBMap-35.82-Java-1.8.0_66.eb => BBMap-35.82-foss-2015b-Java-1.8.0_66.eb} (93%) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb similarity index 93% rename from easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb rename to easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index ac6e1abb04..22ae183da3 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -6,7 +6,7 @@ version = '35.82' homepage = 'https://sourceforge.net/projects/bbmap/' description = """BBMap short read aligner, and other bioinformatic tools.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'foss', 'version': '2015b'} java = 'Java' javaver = '1.8.0_66' -- GitLab From d7740bba2a27ca80cac1ab8dbe4211ed80d844b5 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 13 Jan 2016 13:19:37 +1030 Subject: [PATCH 0173/2133] Conditionally compile JNI code depending on OS. Dummy toolchain for Java dependency --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 22ae183da3..dfcbaddec1 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -1,3 +1,5 @@ +import platform + easyblock = 'MakeCp' name = 'BBMap' @@ -11,13 +13,18 @@ toolchain = {'name': 'foss', 'version': '2015b'} java = 'Java' javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver)] +dependencies = [(java, javaver, '', True)] source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz' ] prebuildopts = 'cd jni && ' -buildopts = '-f makefile.linux' + +os_type = platform.system() +if os_type == 'Linux': + buildopts = '-f makefile.linux' +elif os_type == 'Darwin': + buildopts = '-f makefile.osx' files_to_copy = ['./*'] -- GitLab From 9396f054451883e0c353926ab63f1530ac6e0b95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Jan 2016 15:09:48 +0100 Subject: [PATCH 0174/2133] add 'import gtk' as sanity check in PyGTK easyconfig, add gtk+ as dep --- .../ATK-2.16.0-intel-2015b-GLib-2.29.92.eb | 29 +++++++++++++++++++ ...-pixbuf-2.31.4-intel-2015b-GLib-2.29.92.eb | 29 +++++++++++++++++++ .../gtk+-2.24.28-intel-2015b-GLib-2.29.92.eb | 23 +++++++++++++++ ...arfBuzz-0.9.41-intel-2015b-GLib-2.29.92.eb | 28 ++++++++++++++++++ .../Pango-1.37.1-intel-2015b-GLib-2.29.92.eb | 24 +++++++++++++++ .../PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb | 6 +++- 6 files changed, 138 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015b-GLib-2.29.92.eb create mode 100644 easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b-GLib-2.29.92.eb create mode 100644 easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b-GLib-2.29.92.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b-GLib-2.29.92.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015b-GLib-2.29.92.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015b-GLib-2.29.92.eb new file mode 100644 index 0000000000..afb1976aa4 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015b-GLib-2.29.92.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.16.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.29.92' +versionsuffix = '-GLib-%s' % glibver +dependencies = [ + ('GLib', glibver), +] + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b-GLib-2.29.92.eb new file mode 100644 index 0000000000..df97d34492 --- /dev/null +++ b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b-GLib-2.29.92.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'gdk-pixbuf' +version = '2.31.4' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.29.92' +versionsuffix = '-GLib-%s' % glibver +dependencies = [ + ('GLib', glibver), + ('libjpeg-turbo', '1.4.0'), + ('libpng', '1.6.18'), + ('LibTIFF', '4.0.3'), + +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b-GLib-2.29.92.eb new file mode 100644 index 0000000000..4fe143fa91 --- /dev/null +++ b/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b-GLib-2.29.92.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gtk+' +version = '2.24.28' +versionsuffix = '-GLib-2.29.92' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.16.0', versionsuffix), + ('gdk-pixbuf', '2.31.4', versionsuffix), + ('Pango', '1.37.1', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b-GLib-2.29.92.eb new file mode 100644 index 0000000000..890b5853fb --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b-GLib-2.29.92.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '0.9.41' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['HarfBuzz-%(version)s_no_symbolic.patch'] + +glibver = '2.29.92' +versionsuffix = '-GLib-%s' % glibver +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.2', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015b-GLib-2.29.92.eb new file mode 100644 index 0000000000..bf4f60f01b --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015b-GLib-2.29.92.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.37.1' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.29.92' +versionsuffix = '-GLib-%s' % glibver +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.2', versionsuffix), + ('HarfBuzz', '0.9.41', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb index acfff835e3..f7d18d2696 100644 --- a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb @@ -16,10 +16,12 @@ pyver_maj_min = '2.7' pyver = '%s.10' % pyver_maj_min versionsuffix = '-Python-%s' % pyver +glibver = '2.29.92' dependencies = [ ('Python', pyver), - ('GLib', '2.29.92'), + ('GLib', glibver), ('PyGObject', '2.28.6', versionsuffix), + ('gtk+', '2.24.28', '-GLib-%s' % glibver), ] sanity_check_paths = { @@ -27,4 +29,6 @@ sanity_check_paths = { 'dirs': ['lib/pygtk'], } +sanity_check_commands = [('python', "-c 'import gtk'")] + moduleclass = 'vis' -- GitLab From 13ed13b78cd8ca46675839d968cae0c8bbdf255b Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Fri, 15 Jan 2016 17:32:59 +0100 Subject: [PATCH 0175/2133] The wrapper creation process has been slightly changed, to allow for a list of host compilers --- .../CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index be0effa8e8..3480e35c4d 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -34,12 +34,11 @@ checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] # Tested, but not throughly, so it is not guaranteed to don't cause problems installopts = '-override compiler' -generate_wrapper = True -host_compiler = "icpc" +host_compilers = ["icpc", "g++"] -# Be careful and have a message consistent with the wrappers present +# Be careful and have a message consistent with the generated wrappers modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" -modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc" +modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created." moduleclass = 'system' -- GitLab From 09af072eb89d1846a00c2d4be42c44e23cddf504 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Jan 2016 22:57:23 +0100 Subject: [PATCH 0176/2133] finalize foss/2016a, add easyconfigs for toolchains + HPL --- .../f/FFTW/FFTW-3.3.4-gompi-2016a.eb | 34 +++++++++++++ easybuild/easyconfigs/f/foss/foss-2016a.eb | 12 ++--- easybuild/easyconfigs/g/gompi/gompi-2016a.eb | 20 ++++++++ .../easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb | 18 +++++++ .../h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb | 23 +++++++++ .../numactl/numactl-2.0.11-GCC-4.9.3-2.25.eb | 23 +++++++++ ...BLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb | 51 +++++++++++++++++++ .../OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb | 32 ++++++++++++ ...ompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb | 25 +++++++++ 9 files changed, 230 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016a.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2016a.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016a.eb new file mode 100644 index 0000000000..ea1354d72d --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2016a.eb b/easybuild/easyconfigs/f/foss/foss-2016a.eb index cce53461f2..0846e47261 100644 --- a/easybuild/easyconfigs/f/foss/foss-2016a.eb +++ b/easybuild/easyconfigs/f/foss/foss-2016a.eb @@ -9,10 +9,7 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain, includi toolchain = {'name': 'dummy', 'version': 'dummy'} -gccver = '4.9.3' # 20150626 -#gccver = '5.3.0' # 20151204 -binutilsver = '2.25' -tcver = '%s-binutils-%s' % (gccver, binutilsver) +gccver = '4.9.3-2.25' blaslib = 'OpenBLAS' blasver = '0.2.15' @@ -28,10 +25,9 @@ comp_mpi_tc = (comp_mpi_tc_name, version) # because of toolchain preperation functions # For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ - ('GCC', gccver, '-binutils-%s' % binutilsver), - ('binutils', binutilsver, '', ('GCC', tcver)), - ('OpenMPI', '1.10.1', '', ('GCC', '%s-%s' % (gccver, binutilsver))), - (blaslib, blasver, blassuff, ('GCC', '%s-%s' % (gccver, binutilsver))), + ('GCC', gccver), + ('OpenMPI', '1.10.1', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), ] diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016a.eb b/easybuild/easyconfigs/g/gompi/gompi-2016a.eb new file mode 100644 index 0000000000..00f9ed1bf1 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016a.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.3-2.25' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC 4.9.3 and binutils 2.25 + ('OpenMPI', '1.10.1', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb new file mode 100644 index 0000000000..e43e4270dd --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..dd384c19f8 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.2' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..cee677dd4c --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..32dd146e23 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.15' + +lapackver = '3.6.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..c91ebdd221 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.1' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.11.2')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..1326db5fe2 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blassuff = '-LAPACK-3.6.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.3-2.25'))] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From fdc0694b35a4349d85cf703524c61f75cc9c58dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 Jan 2016 00:01:53 +0200 Subject: [PATCH 0177/2133] finalize foss/2016a, add easyconfigs for toolchain components + HPL --- .../easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb | 18 +++++++++++++++ .../i/iimpi/iimpi-8.1.5-GCC-4.9.3-2.25.eb | 19 ++++++++++++++++ ...l-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb | 22 +++++++++++++++++++ easybuild/easyconfigs/i/intel/intel-2016a.eb | 4 +--- 4 files changed, 60 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-8.1.5-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb new file mode 100644 index 0000000000..a3af786ca9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-8.1.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-8.1.5-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..43b5e47c98 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-8.1.5-GCC-4.9.3-2.25.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '8.1.5' +versionsuffix = '-GCC-4.9.3-2.25' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.1.150' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.2.150', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..de96c38b15 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.3.1.150' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '8.1.5-GCC-4.9.3-2.25'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/intel/intel-2016a.eb b/easybuild/easyconfigs/i/intel/intel-2016a.eb index 367a775846..c858c20f53 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016a.eb @@ -8,16 +8,14 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} -#compver = '2015.5.223' compver = '2016.1.150' gccsuff = '-GCC-4.9.3-2.25' -#gccsuff = '-GCC-5.3.0-2.25' dependencies = [ ('icc', compver, gccsuff), ('ifort', compver, gccsuff), ('impi', '5.1.2.150', '', ('iccifort', '%s%s' % (compver, gccsuff))), - ('imkl', '11.3.1.150', '', ('iimpi', '8.4.5%s' % gccsuff)), + ('imkl', '11.3.1.150', '', ('iimpi', '8.1.5%s' % gccsuff)), ] moduleclass = 'toolchain' -- GitLab From 90eb1794c6bc71bcce9bc285b2037d9a4d9b7886 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 18 Jan 2016 12:05:06 +0100 Subject: [PATCH 0178/2133] comments implemented --- .../r/RSEM/RSEM-1.2.26-GNU-4.9.3-2.25.eb | 3 +- .../r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch | 109 ++++++++++++++---- 2 files changed, 90 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-GNU-4.9.3-2.25.eb index f8223376c0..07868df9c1 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-GNU-4.9.3-2.25.eb @@ -5,12 +5,13 @@ version = '1.2.26' homepage = 'http://deweylab.github.io/RSEM/' description = """RNA-Seq by Expectation-Maximization)""" + toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} source_urls = ['https://github.com/deweylab/RSEM/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['RSEM-1.2.26_eb_provided_zlib.patch'] +patches = ['RSEM-%(version)s_eb_provided_zlib.patch'] dependencies = [ ('ncurses', '5.9'), diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch index 7eb3522c82..8e9f764d6a 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch @@ -1,12 +1,14 @@ -#Use EB provided libz +#Use EB provided libz and use EB provided CXX and CXXFLAGS # January 11, 2016 by B. Hajgato (Vrije Ubiversiteit Brussel) --- Makefile.orig 2016-01-08 02:23:01.000000000 +0100 -+++ Makefile 2016-01-11 16:41:25.548773718 +0100 ++++ Makefile 2016-01-18 12:02:56.406105229 +0100 @@ -1,6 +1,6 @@ - CC = g++ - CFLAGS = -Wall -c -I. +-CC = g++ +-CFLAGS = -Wall -c -I. -COFLAGS = -Wall -O3 -ffast-math -c -I. -+COFLAGS = -march=native -Wall -O3 -ffast-math -c -I. ++CXX = $(CXX) ++CFLAGS = -Wall -c -I. $(CFLAGS) ++COFLAGS = $(CXXFLAGS) -Wall -c -I. PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads .PHONY : all ebseq clean @@ -19,55 +21,120 @@ cd sam ; ${MAKE} all Transcript.h : utils.h -@@ -52,7 +54,7 @@ +@@ -15,10 +17,10 @@ + Transcripts.h : utils.h my_assert.h Transcript.h + + rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp +- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts ++ $(CXX) -Wall $(CXXFLAGS) extractRef.cpp -o rsem-extract-reference-transcripts + + rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp +- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts ++ $(CXX) -Wall $(CXXFLAGS) synthesisRef.cpp -o rsem-synthesis-reference-transcripts + + BowtieRefSeqPolicy.h : RefSeqPolicy.h + +@@ -28,10 +30,10 @@ + + + rsem-preref : preRef.o +- $(CC) preRef.o -o rsem-preref ++ $(CXX) preRef.o -o rsem-preref + + preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp +- $(CC) $(COFLAGS) preRef.cpp ++ $(CXX) $(COFLAGS) preRef.cpp + + + SingleRead.h : Read.h +@@ -52,14 +54,14 @@ rsem-parse-alignments : parseIt.o sam/libbam.a - $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread -+ $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread ++ $(CXX) -o rsem-parse-alignments parseIt.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp - $(CC) -Wall -O2 -c -I. parseIt.cpp -@@ -87,7 +89,7 @@ +- $(CC) -Wall -O2 -c -I. parseIt.cpp ++ $(CXX) $(COFLAGS) parseIt.cpp + + + rsem-build-read-index : utils.h buildReadIndex.cpp +- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index ++ $(CXX) $(CXXFLAGS) buildReadIndex.cpp -o rsem-build-read-index + + + simul.h : boost/random.hpp +@@ -87,57 +89,57 @@ WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h rsem-run-em : EM.o sam/libbam.a - $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread -+ $(CC) -o rsem-run-em EM.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread ++ $(CXX) -o rsem-run-em EM.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp - $(CC) $(COFLAGS) EM.cpp -@@ -97,13 +99,13 @@ +- $(CC) $(COFLAGS) EM.cpp ++ $(CXX) $(COFLAGS) EM.cpp + + bc_aux.h : sam/bam.h + BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a - $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) $(CXXFLAGS) -Wall tbam2gbam.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp - $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ -+ $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) $(CXXFLAGS) -Wall bam2wig.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp - $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ -+ $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) $(CXXFLAGS) -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h - $(CC) $(COFLAGS) wiggle.cpp -@@ -131,13 +133,13 @@ - $(CC) $(COFLAGS) calcCI.cpp +- $(CC) $(COFLAGS) wiggle.cpp ++ $(CXX) $(COFLAGS) wiggle.cpp + + rsem-simulate-reads : simulation.o +- $(CC) -o rsem-simulate-reads simulation.o ++ $(CXX) -o rsem-simulate-reads simulation.o + + simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp +- $(CC) $(COFLAGS) simulation.cpp ++ $(CXX) $(COFLAGS) simulation.cpp + + rsem-run-gibbs : Gibbs.o +- $(CC) -o rsem-run-gibbs Gibbs.o -lpthread ++ $(CXX) -o rsem-run-gibbs Gibbs.o -lpthread + + #some header files are omitted + Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp +- $(CC) $(COFLAGS) Gibbs.cpp ++ $(CXX) $(COFLAGS) Gibbs.cpp + + Buffer.h : my_assert.h + + rsem-calculate-credibility-intervals : calcCI.o +- $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread ++ $(CXX) -o rsem-calculate-credibility-intervals calcCI.o -lpthread + + #some header files are omitted + calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp +- $(CC) $(COFLAGS) calcCI.cpp ++ $(CXX) $(COFLAGS) calcCI.cpp rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a - $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) $(CXXFLAGS) -Wall getUnique.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a - $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) $(CXXFLAGS) -Wall samValidator.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a - $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) $(CXXFLAGS) -Wall scanForPairedEndReads.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ebseq : cd EBSeq ; ${MAKE} all -- GitLab From 5b4fdbe498d4fd27b618d3872c9dce21ad7dee80 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 18 Jan 2016 12:10:52 +0100 Subject: [PATCH 0179/2133] Patch applied to sam and sam/bcftools dirs as well (use EB provided CC and CFLAGS) --- .../r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch index 8e9f764d6a..dcb5a208cd 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch @@ -138,3 +138,25 @@ ebseq : cd EBSeq ; ${MAKE} all +--- sam/Makefile.orig 2016-01-08 02:23:01.000000000 +0100 ++++ sam/Makefile 2016-01-18 12:08:43.769066188 +0100 +@@ -1,7 +1,7 @@ +-CC= gcc ++CC= $(CC) + CFLAGS_EXTRA= + #CFLAGS_EXTRA= -L/usr/include/ncurses +-CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) ++CFLAGS= $(CFLAGS) $(CFLAGS_EXTRA) + #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib + DFLAGS_EXTRA= + #DFLAGS_EXTRA= -Dexpl=exp -Dlogl=log +--- sam/bcftools/Makefile.orig 2016-01-08 02:23:01.000000000 +0100 ++++ sam/bcftools/Makefile 2016-01-18 12:09:10.076063429 +0100 +@@ -1,5 +1,5 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc ++CC= $(CC) ++CFLAGS= $(CFLAGS) + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE + LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o + OMISC= .. -- GitLab From c3f6718106ce41ded9858e005c9dc3926ec7f022 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 18 Jan 2016 14:28:14 +0100 Subject: [PATCH 0180/2133] {bio}[intel/2015b] Mothur 1.36.1 (REVIEW) --- .../g/gzip/gzip-1.6-intel-2015b.eb | 21 ++++++ ...Mothur-1.36.1-intel-2015b-Python-2.7.10.eb | 29 ++++++++ .../Mothur-1.36.1_makefile-hardcoding.patch | 68 +++++++++++++++++++ 3 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.6-intel-2015b.eb create mode 100644 easybuild/easyconfigs/m/Mothur/Mothur-1.36.1-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/m/Mothur/Mothur-1.36.1_makefile-hardcoding.patch diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-intel-2015b.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-intel-2015b.eb new file mode 100644 index 0000000000..c1b78eb897 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-intel-2015b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.6' + +homepage = 'http://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/Mothur/Mothur-1.36.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mothur/Mothur-1.36.1-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..d04ad20cc6 --- /dev/null +++ b/easybuild/easyconfigs/m/Mothur/Mothur-1.36.1-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,29 @@ +name = 'Mothur' +version = '1.36.1' +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +homepage = 'http://www.mothur.org/' +description = """Mothur is a single piece of open-source, expandable software + to fill the bioinformatics needs of the microbial ecology community.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/mothur/mothur/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['%(name)s-%(version)s_makefile-hardcoding.patch'] + +dependencies = [ + (python, pyver), + ('Boost', '1.59.0', versionsuffix), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('bzip2', '1.0.6'), + ('gzip', '1.6'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mothur/Mothur-1.36.1_makefile-hardcoding.patch b/easybuild/easyconfigs/m/Mothur/Mothur-1.36.1_makefile-hardcoding.patch new file mode 100644 index 0000000000..83e04782d6 --- /dev/null +++ b/easybuild/easyconfigs/m/Mothur/Mothur-1.36.1_makefile-hardcoding.patch @@ -0,0 +1,68 @@ +--- makefile.org 2015-07-27 16:18:26.000000000 +0200 ++++ makefile 2016-01-18 13:37:34.624809549 +0100 +@@ -18,12 +18,12 @@ + VERSION = "\"1.36.1\"" + + # Optimize to level 3: +-CXXFLAGS += -O3 ++#CXXFLAGS += -O3 + + + ifeq ($(strip $(64BIT_VERSION)),yes) + #if you are a mac user use the following line +- TARGET_ARCH += -arch x86_64 ++ #TARGET_ARCH += -arch x86_64 + + #if you using cygwin to build Windows the following line + #CXX = x86_64-w64-mingw32-g++ +@@ -58,20 +58,20 @@ + + + ifeq ($(strip $(USEMPI)),yes) +- CXX = mpic++ ++ CXX = $(MPICXX) + CXXFLAGS += -DUSE_MPI + endif + + #The boost libraries allow you to read gz files. + ifeq ($(strip $(USEBOOST)),yes) +- BOOST_INCLUDE_DIR="/usr/local/include" +- BOOST_LIBRARY_DIR="/usr/local/lib" ++ BOOST_INCLUDE_DIR=$(EBROOTBOOST)/include ++ BOOST_LIBRARY_DIR=$(EBROOTBOOST)/lib + + CXXFLAGS += -DUSE_BOOST + + LIBS += \ + ${BOOST_LIBRARY_DIR}/libboost_iostreams.a \ +- ${BOOST_LIBRARY_DIR}/zlib.a ++ ${EBROOTZLIB}/lib/libz.a + + #if linux or windows then ${BOOST_LIBRARY_DIR}/libz.a + endif +--- source/uchime_src/mk.orig 2015-07-27 16:18:26.000000000 +0200 ++++ source/uchime_src/mk 2016-01-18 14:07:56.834224506 +0100 +@@ -1,4 +1,4 @@ +-#!/bin/bash ++#!/bin/bash -v + CPPNames='addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main usort viterbifast writechhit' + ObjNames='addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o' + +@@ -7,7 +7,7 @@ + for CPPName in $CPPNames + do + echo $CPPName >> /dev/tty +- g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr ++ $CXX $ENV_GCC_OPTS -c $CXXFLAGS -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr + cat tmp.stderr + cat tmp.stderr >> mk.stderr + rm -f tmp.stderr +@@ -17,7 +17,7 @@ + if [ `uname -s` == Linux ] ; then + LINK_OPTS=-static + fi +-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o uchime $ObjNames >> mk.stdout 2>> tmp.stderr ++$CXX $CXXFLAGS $ENV_LINK_OPTS -o uchime $ObjNames >> mk.stdout 2>> tmp.stderr + cat tmp.stderr + cat tmp.stderr >> mk.stderr + rm -f tmp.stderr -- GitLab From c171f56b5a162e5c8cb12a7c6092cd5c8e69aa31 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Wed, 2 Dec 2015 16:52:49 +0100 Subject: [PATCH 0181/2133] Modified CUDA easyconfig to support wrapper creation (to enable easier use of icpc as a host compiler). Requires a modified CUDA easyblock. --- ...5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..66010feb7a --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -0,0 +1,20 @@ +name = 'CUDA' +version = '7.5.18' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} + +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux.run'] +checksums = [('md5', '4b3bcecf0dfc35928a0898793cf3e4c6')] + +moduleclass = 'system' + +generate_wrapper = True +default_host_compiler = 'icpc' -- GitLab From c4b04543037c4fe444fc3edd04d05fd31fad70ca Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Wed, 2 Dec 2015 17:13:29 +0100 Subject: [PATCH 0182/2133] Modified CUDA easyconfig to support wrapper creation (to enable easier use of icpc as a host compiler). Requires a modified CUDA easyblock. --- ...5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 28 ++++++++++++++++--- 1 file changed, 24 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 66010feb7a..91b0d98477 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -1,3 +1,17 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html +## + +#easyblock = 'ConfigureMake' + name = 'CUDA' version = '7.5.18' @@ -7,14 +21,20 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} +toolchain = {'name': 'iccifort', 'version': '2015.3.187-GCC-bare-4.9.3'} -source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] +# eg. http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run +#source_urls = ['http://developer.download.nvidia.com/compute/cuda/7_5/rel/installers/'] +source_urls = ['http://developer.download.nvidia.com/compute/cuda/7.5/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_linux.run'] checksums = [('md5', '4b3bcecf0dfc35928a0898793cf3e4c6')] +installopts = '-override compiler' + moduleclass = 'system' -generate_wrapper = True -default_host_compiler = 'icpc' +generate_intel_wrapper = True + +# Be careful and have a message consistent with the wrappers present +modloadmsg = """nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use invcc, or nvcc -ccbin=icpc""" -- GitLab From 468cfcbaa93bd664538788c7b29f31b12d2f8d40 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 3 Dec 2015 15:47:06 +0100 Subject: [PATCH 0183/2133] Small changes to better respect EB coding standards --- ...5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 91b0d98477..dcd435b3cb 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -1,8 +1,10 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University, +# Forschungszentrum Juelich # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste +# Damian Alvarez # License:: MIT/GPL # $Id$ # @@ -21,20 +23,22 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'iccifort', 'version': '2015.3.187-GCC-bare-4.9.3'} +toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} -# eg. http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run -#source_urls = ['http://developer.download.nvidia.com/compute/cuda/7_5/rel/installers/'] source_urls = ['http://developer.download.nvidia.com/compute/cuda/7.5/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_linux.run'] -checksums = [('md5', '4b3bcecf0dfc35928a0898793cf3e4c6')] +checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] +# Necessary to allow to use a GCC 4.9.3 toolchain, as CUDA by default just supports up to 4.9.2. +# Tested, but not throughly, so it is not guaranteed to don't cause problems installopts = '-override compiler' -moduleclass = 'system' - generate_intel_wrapper = True # Be careful and have a message consistent with the wrappers present -modloadmsg = """nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use invcc, or nvcc -ccbin=icpc""" +modloadmsg = """nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" ++" invcc, or nvcc -ccbin=icpc""" + +moduleclass = 'system' + -- GitLab From 0d2eecaeca519ce18a7018d8a6ccb0409f714fe3 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Fri, 4 Dec 2015 18:02:06 +0100 Subject: [PATCH 0184/2133] Updated easyblock with support for generic wrappers --- .../CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index dcd435b3cb..be0effa8e8 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -34,11 +34,12 @@ checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] # Tested, but not throughly, so it is not guaranteed to don't cause problems installopts = '-override compiler' -generate_intel_wrapper = True +generate_wrapper = True +host_compiler = "icpc" # Be careful and have a message consistent with the wrappers present -modloadmsg = """nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" -+" invcc, or nvcc -ccbin=icpc""" +modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" +modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc" moduleclass = 'system' -- GitLab From 4022cb487d0822e69064cbc22b7c9c963e2100a9 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Fri, 15 Jan 2016 17:32:59 +0100 Subject: [PATCH 0185/2133] The wrapper creation process has been slightly changed, to allow for a list of host compilers --- .../CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index be0effa8e8..3480e35c4d 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -34,12 +34,11 @@ checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] # Tested, but not throughly, so it is not guaranteed to don't cause problems installopts = '-override compiler' -generate_wrapper = True -host_compiler = "icpc" +host_compilers = ["icpc", "g++"] -# Be careful and have a message consistent with the wrappers present +# Be careful and have a message consistent with the generated wrappers modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" -modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc" +modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created." moduleclass = 'system' -- GitLab From 8a8b9e1229f019a0189c5320af1c7422d4a51147 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 18 Jan 2016 15:39:24 +0100 Subject: [PATCH 0186/2133] {bio}[intel/2015b] MIGRATE-N 4.2.2a (REVIEW) --- .../MIGRATE-N/MIGRATE-N-4.2.2a-intel-2015b.eb | 39 +++++++++++++++++++ .../m/MIGRATE-N/migrate-4.2.2a_icc.patch | 13 +++++++ .../m/MIGRATE-N/migrate-4.2.2a_install.patch | 13 +++++++ 3 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.2a-intel-2015b.eb create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.2a_icc.patch create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.2a_install.patch diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.2a-intel-2015b.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.2a-intel-2015b.eb new file mode 100644 index 0000000000..ee0f39c51a --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.2a-intel-2015b.eb @@ -0,0 +1,39 @@ +easyblock = "ConfigureMake" + +name = "MIGRATE-N" +version = "4.2.2a" + +homepage = 'http://popgen.sc.fsu.edu/Migrate/Migrate-n.html' +description = """Migrate estimates effective population sizes and past migration rates + between n population assuming a migration matrix model + with asymmetric migration tates and different subpopulation sizes.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [ + 'http://popgen.sc.fsu.edu/currentversions/', + 'http://popgen.sc.fsu.edu/oldversions/%(version_major)s.x/%(version_major_minor)s', + 'http://popgen.sc.fsu.edu/oldversions/', +] +sources = ['migrate-%(version)s.src.tar.gz'] + +patches = [ + 'migrate-%(version)s_icc.patch', + 'migrate-%(version)s_install.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-A4 "CC=$CC" STDCPLUS=-lstdc++ ' +prebuildopts = 'make mpis && make clean && ' + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['bin/migrate-n', 'bin/migrate-n-mpi'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.2a_icc.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.2a_icc.patch new file mode 100644 index 0000000000..20da05a0e4 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.2a_icc.patch @@ -0,0 +1,13 @@ +#icc does not find -lpthread, if -fast defined +#B. Hajgato January 18th, 2016 +--- src/configure.orig 2014-12-28 03:46:09.000000000 +0100 ++++ src/configure 2016-01-18 15:02:00.147089834 +0100 +@@ -3332,7 +3332,7 @@ + pgcc) CFLAGS="-B -fast "; + SYSTEM="gcc";; + # icc) CFLAGS=" -O3 -tpp7 -xKW -pad -ip "; +- icc) CFLAGS+=" -fast "; ++ icc) CFLAGS+=""; + SYSTEM="icc";; + cc) case "$host_vendor" in + ibm) CFLAGS="-O3 -Dinline='/*inline*/' -q cpluscmt -DIBM"; diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.2a_install.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.2a_install.patch new file mode 100644 index 0000000000..97957ab44e --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.2a_install.patch @@ -0,0 +1,13 @@ +#Create parent directories during install +#B. Hajgato January 18th, 2016 +--- src/configure.orig 2014-12-28 03:46:09.000000000 +0100 ++++ src/configure 2016-01-18 14:57:26.331047715 +0100 +@@ -3411,7 +3411,7 @@ + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then +- ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" ++ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c -D" + break 3 + fi + fi -- GitLab From a5271b1cca2d46ac7a7e7b642293aebec6fecce7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Jan 2016 23:29:57 +0200 Subject: [PATCH 0187/2133] add easyconfig EggLib-2.1.10-intel-2015b.eb --- .../e/EggLib/EggLib-2.1.10-intel-2015b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb diff --git a/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb b/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb new file mode 100644 index 0000000000..047574619d --- /dev/null +++ b/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'EggLib' +version = '2.1.10' + +homepage = 'http://egglib.sourceforge.net/' +description = """EggLib is a C++/Python library and program package for evolutionary genetics and genomics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [ + '%(namelower)s-cpp-%(version)s.tar.gz', + '%(namelower)s-py-%(version)s.tar.gz', +] + +dependencies = [ + ('Python', '2.7.11'), + ('GSL', '2.1'), +] + +# also install C++ part +prebuildopts = "cd %(builddir)s/egglib-cpp-%(version)s && ./configure --prefix=%(installdir)s && make && make install && " +# header files must be found when building Python library +prebuildopts += "cd %(builddir)s/egglib-py-%(version)s && CPATH=%(installdir)s/include LIBRARY_PATH=%(installdir)s/lib " + +keeppreviousinstall = True +preinstallopts = "cd %(builddir)s/egglib-py-%(version)s && CPATH=%(installdir)s/include " +installopts = "--install-lib %(installdir)s/lib/python2.7/site-packages --install-scripts %(installdir)s/bin" + +sanity_check_paths = { + 'files': ['bin/egglib', 'lib/libegglib-cpp.a'], + 'dirs': ['include/egglib-cpp', 'lib/python2.7/site-packages'], +} + +moduleclass = 'bio' -- GitLab From e93400e128298d73f320c4b2e3b795ae15b02091 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Jan 2016 10:15:00 +0200 Subject: [PATCH 0188/2133] add easyconfig Perl-5.20.3-intel-2016a.eb --- .../p/Perl/Perl-5.20.3-intel-2016a.eb | 909 ++++++++++++++++++ 1 file changed, 909 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2016a.eb new file mode 100644 index 0000000000..146a854c21 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2016a.eb @@ -0,0 +1,909 @@ +name = 'Perl' +version = '5.20.3' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.58', { + 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('TAP::Harness::Env', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.021', { + 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '0.46', { + 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.93', { + 'source_tmpl': 'DateTime-TimeZone-1.93.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.22', { + 'source_tmpl': 'Try-Tiny-0.22.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Params::Validate', '1.21', { + 'source_tmpl': 'Params-Validate-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.20', { + 'source_tmpl': 'DateTime-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Module::Build', '0.4214', { + 'source_tmpl': 'Module-Build-0.4214.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Readonly', '2.00', { + 'source_tmpl': 'Readonly-2.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.27', { + 'source_tmpl': 'Tree-DAG_Node-1.27.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.48', { + 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.72', { + 'source_tmpl': 'Shell-0.72.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.47', { + 'source_tmpl': 'PathTools-3.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::WrapTie', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.40', { + 'source_tmpl': 'Test-Exception-0.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.11', { + 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.69', { + 'source_tmpl': 'URI-1.69.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.00', { + 'source_tmpl': 'Pod-POM-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.43', { + 'source_tmpl': 'Text-Diff-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.020', { + 'source_tmpl': 'IO-Socket-SSL-2.020.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Getopt::Long', '2.47', { + 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '0.117', { + 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.000002', { + 'source_tmpl': 'Moo-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.05', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.63', { + 'source_tmpl': 'Test-Differences-0.63.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.14', { + 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9912', { + 'source_tmpl': 'version-0.9912.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + # fails: uses 'gcc' + #('XML::Bare', '0.53', { + # 'source_tmpl': 'XML-Bare-0.53.tar.gz', + # 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + #}), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.30', { + 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.11', { + 'source_tmpl': 'AnyEvent-7.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0609', { + 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::Tester', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967012', { + 'source_tmpl': 'Parse-RecDescent-1.967012.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.36', { + 'source_tmpl': 'Carp-1.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.13', { + 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT'], + }), + ('Capture::Tiny', '0.30', { + 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('LWP', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000001', { + 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.19', { + 'source_tmpl': 'File-Which-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.39', { + 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.42', { + 'source_tmpl': 'Scalar-List-Utils-1.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('IO::Scalar', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.87', { + 'source_tmpl': 'Log-Handler-0.87.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Devel::StackTrace', '2.00', { + 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1603', { + 'source_tmpl': 'Moose-2.1603.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.33', { + 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9154', { + 'source_tmpl': 'CPANPLUS-0.9154.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Harness', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.04', { + 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.14', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' -- GitLab From c6bdfe1fdba3d5c4548ca470da861b9d8bc113ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Jan 2016 11:30:44 +0200 Subject: [PATCH 0189/2133] add easyconfig GMP-6.1.0-intel-2016a.eb, add easyconfig Python-2.7.11-intel-2016a.eb, add easyconfig SQLite-3.9.2-intel-2016a.eb, add easyconfig Tcl-8.6.4-intel-2016a.eb, add easyconfig Tk-8.6.4-intel-2016a-no-X11.eb, add easyconfig bzip2-1.0.6-intel-2016a.eb, add easyconfig libreadline-6.3-intel-2016a.eb, add easyconfig ncurses-6.0-intel-2016a.eb, add easyconfig zlib-1.2.8-intel-2016a.eb --- .../b/bzip2/bzip2-1.0.6-intel-2016a.eb | 15 ++ .../g/GMP/GMP-6.1.0-intel-2016a.eb | 26 ++++ .../libreadline-6.3-intel-2016a.eb | 30 ++++ .../n/ncurses/ncurses-6.0-intel-2016a.eb | 34 +++++ .../p/Python/Python-2.7.11-intel-2016a.eb | 129 ++++++++++++++++++ .../s/SQLite/SQLite-3.9.2-intel-2016a.eb | 40 ++++++ .../t/Tcl/Tcl-8.6.4-intel-2016a.eb | 25 ++++ .../t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb | 26 ++++ .../z/zlib/zlib-1.2.8-intel-2016a.eb | 22 +++ 9 files changed, 347 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016a.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016a.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016a.eb new file mode 100644 index 0000000000..c663462b9f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016a.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016a.eb new file mode 100644 index 0000000000..c8ded809f8 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb new file mode 100644 index 0000000000..555538dfd5 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb new file mode 100644 index 0000000000..852b0df6bb --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb new file mode 100644 index 0000000000..b615ded539 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -0,0 +1,129 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), +# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb new file mode 100644 index 0000000000..a35ea6d281 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2016a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016a.eb new file mode 100644 index 0000000000..20cd9eb96c --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb new file mode 100644 index 0000000000..9f46cbbff7 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016a.eb new file mode 100644 index 0000000000..e9099d2071 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 85e058f561169beeb1eeea7d769b19f1e4c74653 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Jan 2016 11:38:26 +0100 Subject: [PATCH 0190/2133] Update impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb Provide hint on how to set defaults for `impi` to use intel compilers --- .../impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 73e4fbb027..da4a993780 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -19,6 +19,9 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' postinstallcmds = [ -- GitLab From 31d141b35103030aafcfbac8b56abda804b953ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Jan 2016 13:11:57 +0100 Subject: [PATCH 0191/2133] remove trailing whitespace --- .../a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb | 2 +- .../a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb | 2 +- .../a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb | 2 +- .../ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb | 2 +- .../a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb | 4 ++-- .../easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb | 2 +- .../easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb | 2 +- .../a/Automake/Automake-1.13.4-ictce-5.5.0.eb | 2 +- .../b/BCFtools/BCFtools-1.2-foss-2015a.eb | 2 +- .../b/BCFtools/BCFtools-1.2-intel-2015a.eb | 2 +- .../easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb | 4 ++-- .../Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/b/Bison/Bison-2.7-goolf-1.5.14.eb | 2 +- .../b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb | 2 +- .../b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb | 2 +- .../b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.8.eb | 2 +- .../b/Boost/Boost-1.57.0-foss-2015a-Python-2.7.9.eb | 2 +- .../b/Boost/Boost-1.57.0-intel-2015a-Python-2.7.9.eb | 2 +- .../b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb | 2 +- .../b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb | 2 +- .../b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb | 2 +- .../b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb | 2 +- .../b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb | 2 +- .../b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb | 2 +- .../b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb | 2 +- .../b/binutils/binutils-2.22-goolf-1.4.10.eb | 2 +- .../b/binutils/binutils-2.22-goolf-1.5.14.eb | 2 +- .../CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb | 2 +- .../easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2015a.eb | 2 +- .../easyconfigs/c/CMake/CMake-2.8.12-ictce-7.1.2.eb | 2 +- .../easyconfigs/c/CMake/CMake-2.8.12-intel-2014b.eb | 2 +- .../c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb | 4 ++-- .../c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb | 4 ++-- .../easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 2 +- .../easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb | 2 +- .../c/Clang/Clang-3.7.0-GNU-4.9.3-2.25.eb | 2 +- .../c/Clang/Clang-3.7.1-GCC-4.9.3-2.25.eb | 2 +- .../c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 4 ++-- .../d/Doxygen/Doxygen-1.8.3.1-goolf-1.5.14.eb | 2 +- .../easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb | 2 +- .../easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb | 2 +- .../easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb | 2 +- .../e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb | 2 +- .../e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb | 2 +- .../easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb | 2 +- .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 2 +- .../easyconfigs/e/Emacs/Emacs-24.3-GCC-4.8.3-bare.eb | 2 +- .../easyconfigs/e/Emacs/Emacs-24.3-GCC-4.8.3.eb | 2 +- .../ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb | 2 +- .../FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb | 2 +- .../FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb | 2 +- .../FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb | 2 +- .../FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb | 2 +- .../FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb | 12 ++++++------ .../FASTX-Toolkit-0.0.14-goolf-1.4.10.eb | 12 ++++++------ .../FASTX-Toolkit-0.0.14-intel-2015a.eb | 12 ++++++------ .../easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 2 +- .../easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb | 2 +- .../easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb | 2 +- .../easyconfigs/f/flex/flex-2.5.37-goolf-1.5.14.eb | 2 +- .../f/flex/flex-2.5.39-intel-para-2014.12.eb | 2 +- easybuild/easyconfigs/f/foss/foss-2014b.eb | 2 +- .../easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb | 2 +- .../g/GEMSTAT/GEMSTAT-1.0-goolf-1.4.10.eb | 2 +- .../g/GEOS/GEOS-3.5.0-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/g/GLPK/GLPK-4.48-ictce-5.2.0.eb | 2 +- .../easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb | 2 +- .../easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb | 2 +- .../easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb | 2 +- .../GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb | 2 +- .../GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb | 2 +- .../g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 2 +- .../easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb | 2 +- .../easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb | 2 +- .../g/gettext/gettext-0.18.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.12rc1.eb | 2 +- .../g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb | 2 +- .../g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb | 2 +- .../g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb | 8 ++++---- .../h/HDF5/HDF5-1.8.10-patch1-goolf-1.5.14.eb | 2 +- .../easyconfigs/h/HPL/HPL-2.1-gpsolf-2014.12.eb | 2 +- .../easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb | 2 +- .../easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb | 2 +- .../h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb | 2 +- .../h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b.eb | 2 +- .../h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.9.2.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb | 2 +- .../h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb | 2 +- .../h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb | 2 +- ...wloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 2 +- .../h/hwloc/hwloc-1.11.2-GNU-4.9.3-2.25.eb | 2 +- .../h/hwloc/hwloc-1.6.2-ClangGCC-1.1.3.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.6.4.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.7.2-GCC-4.8.2.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb | 2 +- easybuild/easyconfigs/h/hwloc/hwloc-1.9-GCC-4.8.3.eb | 2 +- .../i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb | 4 ++-- .../i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb | 2 +- .../i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb | 2 +- .../i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb | 2 +- .../i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb | 2 +- easybuild/easyconfigs/i/ictce/ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-4.0.6.eb | 2 +- .../i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb | 4 ++-- easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb | 2 +- .../j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb | 2 +- .../easyconfigs/j/Jansson/Jansson-2.6-GCC-4.8.3.eb | 2 +- .../j/JasPer/JasPer-1.900.1-goolf-1.5.14.eb | 2 +- .../easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb | 2 +- .../easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb | 2 +- .../easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb | 2 +- .../libX11/libX11-1.6.2-intel-2014b-Python-2.7.8.eb | 2 +- .../libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb | 2 +- .../libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb | 2 +- .../libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb | 2 +- .../libX11/libX11-1.6.3-intel-2015b-Python-2.7.10.eb | 2 +- .../libX11/libX11-1.6.3-intel-2015b-Python-2.7.11.eb | 2 +- .../libdap-3.14.0-intel-2015a-Python-2.7.10.eb | 2 +- .../libdap-3.14.0-intel-2015b-Python-2.7.10.eb | 2 +- .../libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb | 2 +- .../libpthread-stubs-0.3-goolf-1.4.10.eb | 2 +- .../libpthread-stubs-0.3-ictce-4.0.6.eb | 2 +- .../libpthread-stubs-0.3-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.2-GCC-4.9.2.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb | 2 +- .../l/libtool/libtool-2.4.5-intel-2015a.eb | 2 +- .../l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb | 2 +- .../l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.eb | 2 +- .../l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb | 2 +- .../l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb | 2 +- .../libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb | 2 +- .../l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb | 2 +- .../libxcb-1.11.1-intel-2015b-Python-2.7.10.eb | 2 +- .../libxcb-1.11.1-intel-2015b-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-goolf-1.5.14.eb | 2 +- .../m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 +++--- .../m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 6 +++--- .../m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb | 6 +++--- .../m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb | 6 +++--- .../m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 6 +++--- .../m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb | 4 ++-- .../m/MethPipe/MethPipe-3.0.1-intel-2014b.eb | 4 ++-- .../makedepend-1.0.4-goalf-1.1.0-no-OFED.eb | 2 +- .../m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb | 2 +- .../m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb | 2 +- .../m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb | 4 ++-- .../m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb | 6 +++--- .../easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb | 6 +++--- .../mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb | 2 +- .../m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb | 2 +- .../n/NCO/NCO-4.5.1-intel-2015a-Python-2.7.10.eb | 2 +- .../netCDF-Fortran-4.2-goolf-1.5.14.eb | 2 +- .../n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb | 2 +- .../easyconfigs/n/netloc/netloc-0.5-GCC-4.8.3.eb | 2 +- .../n/netloc/netloc-0.5-gcccuda-2.6.10.eb | 2 +- .../n/numpy/numpy-1.6.2-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../n/numpy/numpy-1.6.2-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb | 2 +- .../Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 4 ++-- .../o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- .../o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 2 +- .../o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 2 +- .../easyconfigs/o/o2scl/o2scl-0.913-goolf-1.4.10.eb | 2 +- .../orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb | 2 +- .../orthomcl-2.0.8-ictce-4.1.13-Perl-5.16.3.eb | 2 +- .../orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb | 2 +- .../p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb | 6 +++--- easybuild/easyconfigs/p/PCC/PCC-20131024.eb | 2 +- .../p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb | 2 +- easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb | 2 +- .../easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb | 2 +- .../p/PaStiX/PaStiX-5.2.2.22-intel-2015b.eb | 2 +- .../p/Pangomm/Pangomm-2.36.0-intel-2015a.eb | 2 +- .../p/Pangomm/Pangomm-2.36.0-intel-2015b.eb | 2 +- .../ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb | 2 +- .../ParaView-4.3.1-intel-2015a-Python-2.7.10.eb | 2 +- .../p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb | 2 +- .../p/ParaView/ParaView-4.4.0-intel-2015b.eb | 2 +- .../p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb | 2 +- .../Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb | 2 +- .../p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 12 ++++++------ .../p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb | 2 +- .../easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb | 4 ++-- .../easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb | 2 +- .../p/popt/popt-1.14-iccifort-2015.1.133.eb | 2 +- easybuild/easyconfigs/p/popt/popt-1.16-GCC-4.9.2.eb | 2 +- .../p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb | 2 +- .../p/psmpi2/psmpi2-5.0.29-GCC-4.8.2-mt.eb | 4 ++-- .../easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2.eb | 4 ++-- easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/q/qtop/qtop-53-1.eb | 2 +- .../r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb | 6 +++--- .../r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb | 2 +- .../s/SAMtools/SAMtools-1.1-foss-2014b.eb | 2 +- .../s/SAMtools/SAMtools-1.1-goolf-1.4.10.eb | 2 +- .../s/SAMtools/SAMtools-1.1-intel-2014b.eb | 2 +- .../s/SAMtools/SAMtools-1.1-intel-2015a.eb | 2 +- .../SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb | 2 +- .../s/SAMtools/SAMtools-1.2-foss-2015a.eb | 2 +- .../s/SAMtools/SAMtools-1.2-foss-2015b.eb | 2 +- .../s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb | 2 +- .../s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb | 2 +- .../SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb | 2 +- .../easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb | 2 +- .../s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb | 2 +- easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb | 2 +- .../s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb | 2 +- .../s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb | 2 +- easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb | 2 +- .../easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb | 2 +- .../easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb | 4 ++-- .../easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb | 2 +- .../s/Subversion/Subversion-1.8.14-foss-2015a.eb | 2 +- .../SuiteSparse-4.4.5-intel-2015b-METIS-5.1.0.eb | 2 +- .../easyconfigs/s/Szip/Szip-2.1-goolf-1.5.14.eb | 2 +- ...scikit-umfpack-0.2.1-intel-2015b-Python-2.7.10.eb | 2 +- .../s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb | 2 +- easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb | 2 +- .../Trilinos-10.12.2-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../Trilinos-10.12.2-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../Trilinos-12.4.2-intel-2015b-Python-2.7.11.eb | 2 +- .../easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb | 2 +- .../u/UDUNITS/UDUNITS-2.2.19-intel-2015a.eb | 2 +- .../u/UDUNITS/UDUNITS-2.2.19-intel-2015b.eb | 2 +- .../w/WRF/WRF-3.5.1-goolf-1.5.14-dmpar.eb | 2 +- .../x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb | 4 ++-- .../x/xextproto/xextproto-7.3.0-intel-2014b.eb | 2 +- .../x/xextproto/xextproto-7.3.0-intel-2015a.eb | 2 +- .../x/xextproto/xextproto-7.3.0-intel-2015b.eb | 2 +- .../x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb | 2 +- .../x/xproto/xproto-7.0.23-goolf-1.4.10.eb | 2 +- .../x/xproto/xproto-7.0.23-goolf-1.5.14.eb | 2 +- .../x/xproto/xproto-7.0.23-ictce-4.0.6.eb | 2 +- .../x/xproto/xproto-7.0.23-ictce-5.3.0.eb | 2 +- 275 files changed, 339 insertions(+), 339 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb index a0768a4fb3..a8e8be1611 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb @@ -27,7 +27,7 @@ sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] source_urls = ['http://ftp.abinit.org/'] sanity_check_paths = { - 'files': ["bin/abinit"], + 'files': ["bin/abinit"], 'dirs': [] } diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb index 0e53b02003..083d321a07 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb @@ -29,7 +29,7 @@ sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] source_urls = ['http://ftp.abinit.org/'] sanity_check_paths = { - 'files': ["bin/abinit"], + 'files': ["bin/abinit"], 'dirs': [] } diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb index 7722a1277b..5ccd2f15a7 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb @@ -30,7 +30,7 @@ sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] source_urls = ['http://ftp.abinit.org/'] sanity_check_paths = { - 'files': ["bin/abinit"], + 'files': ["bin/abinit"], 'dirs': [] } diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb index 4d319523ac..f598583eb7 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb @@ -33,7 +33,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ["bin/abinit"], + 'files': ["bin/abinit"], 'dirs': [] } diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb index cdc9d8c7ad..93b76ef8be 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb @@ -26,11 +26,11 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bcgsc.ca/downloads/abyss/'] -dependencies = [ +dependencies = [ ('sparsehash', '2.0.2'), ('Boost', '1.49.0', versionsuffix), ] - + sanity_check_paths = { 'files': ["bin/ABYSS", "bin/ABYSS-P"], 'dirs': [] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb index b32cf6ce86..f40658d141 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -dependencies = [('Java', '1.7.0_60', '', True)] +dependencies = [('Java', '1.7.0_60', '', True)] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb index 5cf3b03e64..8ba4070760 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -dependencies = [('Java', '1.7.0_60', '', True)] +dependencies = [('Java', '1.7.0_60', '', True)] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb index 66d819dd00..31ae0ccb15 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb @@ -10,7 +10,7 @@ description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) Java, C#, C++, or Python actions.""" toolchain = {'name': 'intel', 'version': '2015a'} - + source_urls = ['http://www.antlr2.org/download/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb index 555ece231a..0063135660 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb @@ -10,7 +10,7 @@ description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) Java, C#, C++, or Python actions.""" toolchain = {'name': 'intel', 'version': '2015b'} - + source_urls = ['http://www.antlr2.org/download/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb index 675782f77b..5661ddb517 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb @@ -16,7 +16,7 @@ description = "Automake: GNU Standards-compliant Makefile generator" source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb index 7aa9dcdd5b..1e64be716a 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] -parallel = 1 +parallel = 1 skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb index c997c54557..2143e1fd78 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] -parallel = 1 +parallel = 1 skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb index 1318374418..d31fc0a136 100644 --- a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'BSMAP' version = '2.74' @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TGZ] skipsteps = ['configure'] -installopts = "DESTDIR=%(installdir)s" +installopts = "DESTDIR=%(installdir)s" patches = [ 'BSMAP-2.74_makefile-modif.patch', diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb index d287d55292..baf247c07d 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb @@ -35,7 +35,7 @@ dependencies = [ sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, + 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ pyshortver), 'lib/python%s/site-packages/BioSQL' % pyshortver] diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb index eca39ee0df..96eae4f635 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb @@ -35,7 +35,7 @@ dependencies = [ sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, + 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ pyshortver), 'lib/python%s/site-packages/BioSQL' % pyshortver] diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb index 337980614f..07dcfa192d 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -23,9 +23,9 @@ sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] dependencies = [('Bowtie2', '2.0.2')] sanity_check_paths = { - 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", + 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], 'dirs': [], -} +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-goolf-1.5.14.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-goolf-1.5.14.eb index de2474fb3b..4c523b02e6 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-goolf-1.5.14.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/bison' description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb index 82b02fc155..28b4adc0bd 100644 --- a/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb @@ -24,7 +24,7 @@ sources = [SOURCE_TAR_GZ] # put here the list of generated executables when compiling list_of_executables = ["convertSamples", "estimateDE", "estimateExpression", "estimateHyperPar", "estimateVBExpression", "extractSamples", "getFoldChange", "getGeneExpression", - "getPPLR", "getVariance", "getWithinGeneExpression", "parseAlignment", + "getPPLR", "getVariance", "getWithinGeneExpression", "parseAlignment", "transposeLargeFile", "getCounts.py", "extractTranscriptInfo.py"] # this is the real EasyBuild line to copy all the executables to "bin" diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb index 88a81a73e9..54a936cee5 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb @@ -4,7 +4,7 @@ version = '1.55.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.8.eb index 39ae5a52a4..4646d38d21 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.8.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.8.eb @@ -4,7 +4,7 @@ version = '1.55.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015a-Python-2.7.9.eb index 1c2ebd212d..944128c6d5 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015a-Python-2.7.9.eb @@ -4,7 +4,7 @@ version = '1.57.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.57.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-intel-2015a-Python-2.7.9.eb index 84fbb7d38c..cf98c58fdf 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.57.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-intel-2015a-Python-2.7.9.eb @@ -4,7 +4,7 @@ version = '1.57.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb index bbef8b760b..02c7922f8d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb @@ -4,7 +4,7 @@ version = '1.58.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb index a209577bba..9d905a95e3 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb @@ -4,7 +4,7 @@ version = '1.58.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb index 7f34d18683..ead21fe6c8 100644 --- a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCE_TAR_BZ2] source_urls = ['http://bbftppro.myftp.org/'] -unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball +unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball start_dir = 'bbftpc' diff --git a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb index 8017f38954..944cb25b8b 100644 --- a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_BZ2] source_urls = ['http://bbftppro.myftp.org/'] -unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball +unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball start_dir = 'bbftpc' diff --git a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb index cf3d332d4b..8cff88ba26 100644 --- a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_BZ2] source_urls = ['http://bbftppro.myftp.org/'] -unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball +unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball start_dir = 'bbftpc' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index 09be4e2513..89688dc6f1 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -30,7 +30,7 @@ configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 037eea64d6..fc3ab9230d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -30,7 +30,7 @@ configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index 6eefeecf7f..10612dc973 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -29,7 +29,7 @@ configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb index 1922cb5d12..f0f82557eb 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -27,7 +27,7 @@ source_urls = [GNU_SOURCE] binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb index 0b72980db3..b3d2485ff0 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb @@ -29,7 +29,7 @@ list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd # this is the real EasyBuild line to copy all the executables and perl scripts to "bin" files_to_copy = [ (list_of_executables, "bin"), - (["*.pl"], 'bin'), + (["*.pl"], 'bin'), (["psi-cd-hit/*.pl"], 'bin'), "README", "doc", diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2015a.eb index 054982e2e2..0e9493dbb4 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2015a.eb @@ -19,6 +19,6 @@ builddependencies = [('CMake', '3.1.3')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +configopts = '-DCMAKE_BUILD_TYPE=Release' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-7.1.2.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-7.1.2.eb index 48bd837709..97f1c88053 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-7.1.2.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchain = {'name': 'ictce', 'version': '7.1.2'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-intel-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-intel-2014b.eb index 7749fdcd02..93127430de 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-intel-2014b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-intel-2014b.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'intel', 'version': '2014b'} +toolchain = {'name': 'intel', 'version': '2014b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb index 89d4bf6460..50c119c61c 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb @@ -31,13 +31,13 @@ installopts += 'cp -a tools/ %(installdir)s && ' installopts += 'cp -a README doc/ %(installdir)s' sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["chipcenter", "chipcor", "chipextract", "chippart", "chippeak", + 'files': ["bin/%s" % x for x in ["chipcenter", "chipcor", "chipextract", "chippart", "chippeak", "chipscore", "compactsga", "counts_filter", "countsga", "featreplace"]], 'dirs': [] } # add tools dir to PATH -modextrapaths = { +modextrapaths = { 'PATH': "tools", } diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb index d273ae8dd8..a72566ad44 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb @@ -31,13 +31,13 @@ installopts += 'cp -a tools/ %(installdir)s && ' installopts += 'cp -a README doc/ %(installdir)s' sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["chipcenter", "chipcor", "chipextract", "chippart", "chippeak", + 'files': ["bin/%s" % x for x in ["chipcenter", "chipcor", "chipextract", "chippart", "chippeak", "chipscore", "compactsga", "counts_filter", "countsga", "featreplace"]], 'dirs': [] } # add tools dir to PATH -modextrapaths = { +modextrapaths = { 'PATH': "tools", } diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 40f0a86d6f..9d5881c525 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -32,7 +32,7 @@ sources = [ dependencies = [ ('GMP', '6.0.0a'), ('ISL', '0.14'), -] +] builddependencies = [ ('CMake', '3.1.3'), diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb index 966759d71c..bb31f282f6 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb @@ -32,7 +32,7 @@ sources = [ dependencies = [ ('GMP', '6.0.0a'), ('ISL', '0.14'), -] +] builddependencies = [ ('CMake', '3.2.1'), diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.7.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/Clang/Clang-3.7.0-GNU-4.9.3-2.25.eb index 94e343f08b..a76712524b 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.7.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.7.0-GNU-4.9.3-2.25.eb @@ -32,7 +32,7 @@ sources = [ dependencies = [ ('GMP', '6.0.0a'), ('ISL', '0.15'), -] +] builddependencies = [ ('CMake', '3.3.2'), diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.7.1-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/Clang/Clang-3.7.1-GCC-4.9.3-2.25.eb index 5f5f6f2ed3..ee437ef2f2 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.7.1-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.7.1-GCC-4.9.3-2.25.eb @@ -32,7 +32,7 @@ sources = [ dependencies = [ ('GMP', '6.1.0'), ('ISL', '0.15'), -] +] builddependencies = [ ('CMake', '3.4.1', '', ('GCCcore', '4.9.3')), diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index 95405d7ce3..501824903b 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -11,7 +11,7 @@ ## name = 'Cufflinks' -version = "1.3.0" +version = "1.3.0" homepage = 'http://cole-trapnell-lab.github.io/cufflinks/' description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" @@ -30,7 +30,7 @@ dependencies = [ ] patches = [ - 'Cufflinks_GCC-4.7.patch', + 'Cufflinks_GCC-4.7.patch', 'cufflinks-1.x-ldflags.patch' ] diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.5.14.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.5.14.eb index 14b0fa7583..2e87b89a36 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.5.14.eb @@ -5,7 +5,7 @@ homepage = 'http://www.doxygen.org' description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb index 6294e11656..89cd537fc7 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb @@ -15,7 +15,7 @@ version = '2013.11' homepage = 'http://elpa.rzg.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" -toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True} # download at http://elpa.rzg.mpg.de/elpa-tar-archive diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb index c080908b42..bbbc8c56b4 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -15,7 +15,7 @@ version = '2013.11' homepage = 'http://elpa.rzg.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" -toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'usempi': True} # download at http://elpa.rzg.mpg.de/elpa-tar-archive diff --git a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb index 85c2d23a0e..5403f1fde9 100644 --- a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb @@ -26,7 +26,7 @@ buildopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ (["elph"], "bin"), "COPYRIGHT", "LICENSE", "Readme.ELPH", "VERSION" ] +files_to_copy = [ (["elph"], "bin"), "COPYRIGHT", "LICENSE", "Readme.ELPH", "VERSION" ] sanity_check_paths = { 'files': ["bin/elph"], diff --git a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb index a6057c15fd..8986e97200 100644 --- a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb @@ -26,7 +26,7 @@ buildopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ (["elph"], "bin"), "COPYRIGHT", "LICENSE", "Readme.ELPH", "VERSION" ] +files_to_copy = [ (["elph"], "bin"), "COPYRIGHT", "LICENSE", "Readme.ELPH", "VERSION" ] sanity_check_paths = { 'files': ["bin/elph"], diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb index ae4e3793e6..c8367acc34 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb @@ -31,7 +31,7 @@ configopts = " --with-hpdf=$EBROOTLIBHARU " parallel = 1 sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', 'epcre', 'eplplot', 'ezlib', 'nucleus']] + ['share/EMBOSS/jemboss/lib/jemboss.jar'], diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb index f3660e8c90..7100e7cae9 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb @@ -31,7 +31,7 @@ configopts = " --with-hpdf=$EBROOTLIBHARU " parallel = 1 sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', 'epcre', 'eplplot', 'ezlib', 'nucleus']] + ['share/EMBOSS/jemboss/lib/jemboss.jar'], diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb index f34568c037..88380bcbab 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb @@ -31,7 +31,7 @@ configopts = " --with-hpdf=$EBROOTLIBHARU " parallel = 1 sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', 'epcre', 'eplplot', 'ezlib', 'nucleus']] + ['share/EMBOSS/jemboss/lib/jemboss.jar'], diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb index f270612d5f..9ec46d296f 100644 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -27,7 +27,7 @@ configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include'" dependencies = [ ('netCDF', '4.1.3') ] sanity_check_paths = { - 'files': ["bin/etsf_io"], + 'files': ["bin/etsf_io"], 'dirs': [] } diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-24.3-GCC-4.8.3-bare.eb b/easybuild/easyconfigs/e/Emacs/Emacs-24.3-GCC-4.8.3-bare.eb index 68f945c239..8e47359be1 100644 --- a/easybuild/easyconfigs/e/Emacs/Emacs-24.3-GCC-4.8.3-bare.eb +++ b/easybuild/easyconfigs/e/Emacs/Emacs-24.3-GCC-4.8.3-bare.eb @@ -10,7 +10,7 @@ description = """GNU Emacs is an extensible, customizable text editor—and more with extensions to support text editing.""" toolchain = {'name': 'GCC', 'version': '4.8.3'} -toolchainopts = {} +toolchainopts = {} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-24.3-GCC-4.8.3.eb b/easybuild/easyconfigs/e/Emacs/Emacs-24.3-GCC-4.8.3.eb index cb835bb8cd..485bc70664 100644 --- a/easybuild/easyconfigs/e/Emacs/Emacs-24.3-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/e/Emacs/Emacs-24.3-GCC-4.8.3.eb @@ -9,7 +9,7 @@ description = """GNU Emacs is an extensible, customizable text editor—and more with extensions to support text editing.""" toolchain = {'name': 'GCC', 'version': '4.8.3'} -toolchainopts = {} +toolchainopts = {} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb index 4e009be5c9..570e7eb37f 100644 --- a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb +++ b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb @@ -16,7 +16,7 @@ configopts = '--without-javac ' sanity_check_paths = { 'files': ['bin/erl'], - 'dirs': ['lib/erlang/bin', 'lib/erlang/lib'], + 'dirs': ['lib/erlang/bin', 'lib/erlang/lib'], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb index ce824a5e56..2fa88fc7e0 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb @@ -33,7 +33,7 @@ sanity_check_paths = { 'artifacts_filter', 'reverse_complement', 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + + 'nucleotide_distribution_line_graph.sh']] + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb index d68850c297..b2711aa2a6 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb @@ -33,7 +33,7 @@ sanity_check_paths = { 'artifacts_filter', 'reverse_complement', 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + + 'nucleotide_distribution_line_graph.sh']] + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb index c0fdac7c35..aaddc8190a 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb @@ -35,7 +35,7 @@ sanity_check_paths = { 'artifacts_filter', 'reverse_complement', 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + + 'nucleotide_distribution_line_graph.sh']] + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb index f7fa06667c..02992118cc 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb @@ -36,7 +36,7 @@ sanity_check_paths = { 'artifacts_filter', 'reverse_complement', 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + + 'nucleotide_distribution_line_graph.sh']] + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb index b4ea7cb7ba..46d174be2c 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb @@ -28,15 +28,15 @@ sources = ['fastx_toolkit-%(version)s.tar.bz2'] builddependencies = [('libgtextutils', '0.7')]; sanity_check_paths = { - 'files': - ['bin/fastx_%s' % x for x in + 'files': + ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in - ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', 'quality_trimmer', 'masker']], 'dirs': ['.'] } diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb index 96c1129290..16426d6788 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb @@ -29,15 +29,15 @@ sources = ['%s-%%(version)s.tar.bz2' % altname] dependencies = [('libgtextutils', '0.6.1')]; sanity_check_paths = { - 'files': - ['bin/fastx_%s' % x for x in + 'files': + ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in - ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', 'quality_trimmer', 'masker']], 'dirs': ['.'] } diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb index 13d9d1cb72..18c56837a0 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb @@ -29,15 +29,15 @@ sources = ['%s-%%(version)s.tar.bz2' % altname] dependencies = [('libgtextutils', '0.6.1')]; sanity_check_paths = { - 'files': - ['bin/fastx_%s' % x for x in + 'files': + ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in - ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', 'quality_trimmer', 'masker']], 'dirs': ['.'] } diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 902b240c04..4af4d1b872 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -37,7 +37,7 @@ cmds_map = [ files_to_copy = [(['fastqz', 'fapack'], 'bin')] sanity_check_paths = { - 'files': ["bin/fastqz", "bin/fapack"], + 'files': ["bin/fastqz", "bin/fapack"], 'dirs': [] } diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb index 36569d20af..4abf658ad6 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb +++ b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb @@ -20,7 +20,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + - ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb index a9bbbfc3c1..4461759fe7 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb +++ b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb @@ -20,7 +20,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + - ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.37-goolf-1.5.14.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-goolf-1.5.14.eb index 3f5206f66c..852837bf5b 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.37-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-goolf-1.5.14.eb @@ -5,7 +5,7 @@ homepage = 'http://flex.sourceforge.net/' description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb index 469e32f3d7..7cd93ab5fc 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb @@ -5,7 +5,7 @@ homepage = 'http://flex.sourceforge.net/' description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" -toolchain = {'name': 'intel-para', 'version': '2014.12'} +toolchain = {'name': 'intel-para', 'version': '2014.12'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/f/foss/foss-2014b.eb b/easybuild/easyconfigs/f/foss/foss-2014b.eb index 5ff6c5693e..538536a696 100644 --- a/easybuild/easyconfigs/f/foss/foss-2014b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2014b.eb @@ -28,7 +28,7 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # because of toolchain preperation functions dependencies = [ ('GCC', '4.8.3'), - ('OpenMPI', '1.8.1', '', comp), + ('OpenMPI', '1.8.1', '', comp), (blaslib, blasver, blassuff, comp), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), diff --git a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb index 0f7a6c3ea5..c4cf3f3ff7 100644 --- a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb @@ -24,7 +24,7 @@ source_urls = [SOURCEFORGE_SOURCE] files_to_copy = [(['fqz_comp'], 'bin')] sanity_check_paths = { - 'files': ["bin/fqz_comp"], + 'files': ["bin/fqz_comp"], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/GEMSTAT/GEMSTAT-1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GEMSTAT/GEMSTAT-1.0-goolf-1.4.10.eb index c3c35140d3..71eda7f181 100644 --- a/easybuild/easyconfigs/g/GEMSTAT/GEMSTAT-1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GEMSTAT/GEMSTAT-1.0-goolf-1.4.10.eb @@ -30,7 +30,7 @@ buildopts = ' GSL_DIR=$EBROOTGSL' files_to_copy = [ (["seq2expr"], 'bin'), - "README.txt", "data" + "README.txt", "data" ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2015b-Python-2.7.10.eb index 6d5cb52fe8..35073f5ad2 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2015b-Python-2.7.10.eb @@ -18,7 +18,7 @@ versionsuffix = '-Python-%s' % pyver dependencies = [('Python', pyver)] builddependencies = [('SWIG', '3.0.7', versionsuffix)] - + configopts = '--enable-python' modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.2.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.2.0.eb index afaaab1f33..42150fd75f 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.2.0.eb @@ -10,7 +10,7 @@ written in ANSI C and organized in the form of a callable library.""" toolchain = {'name': 'ictce', 'version': '5.2.0'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True} - + sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb index 4716a30ce5..c0b7a97231 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb @@ -10,7 +10,7 @@ written in ANSI C and organized in the form of a callable library.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True} - + sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/%(namelower)s'] diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb index 9aae296531..4525095b97 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb @@ -9,7 +9,7 @@ programming (LP), mixed integer programming (MIP), and other related problems. I written in ANSI C and organized in the form of a callable library.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} - + sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/%(namelower)s'] diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb index b55056667c..aabef669ba 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb @@ -10,7 +10,7 @@ written in ANSI C and organized in the form of a callable library.""" toolchain = {'name': 'ictce', 'version': '6.2.5'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True} - + sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/%(namelower)s'] diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb index 3ce82b5b2d..5fbe4acc9a 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' version = '2014-01-21' diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb index 746e7c4f53..d83527abe3 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' version = "2014-06-10" diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 41de713278..4e828aad87 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -17,7 +17,7 @@ checksums = ['829319325bbdb83f5c81379a8f86f38f'] dependencies = [ ('zlib', '1.2.8'), - ('libpng', '1.6.17'), + ('libpng', '1.6.17'), ('freetype', '2.6'), ('fontconfig', '2.11.94'), ('GLib', '2.44.1'), diff --git a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb index 8e1cb764c0..f946da12a2 100644 --- a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libgtkmm-2.4.so.1'], + 'files': ['lib/libgtkmm-2.4.so.1'], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb index f4d4f0209a..60c1e59723 100644 --- a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb +++ b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb @@ -20,7 +20,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libgtkmm-2.4.so.1'], + 'files': ['lib/libgtkmm-2.4.so.1'], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.1.13.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.1.13.eb index ea88dd569c..cff1cf8e33 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """GNU `gettext' is an important step for the GNU Translation Proj build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" -toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.12rc1.eb index c3fb773c88..50901901bf 100644 --- a/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.12rc1.eb @@ -32,6 +32,6 @@ dependencies = [ (blaslib, blasver, blassuff, comp_mpi_tc), ('FFTW', '3.3.3', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), -] +] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb index 8746928b55..9315e9e792 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb @@ -21,7 +21,7 @@ configopts = "--with-guile-site-dir=$EBROOTGUILE" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'danetool', 'gnutls-cli', 'gnutls-cli-debug', - 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + ['lib/libgnutls%s' % x for x in ['.a', 'xx.a', '-xssl.a', '-openssl.a']], 'dirs': ['include/gnutls'], } diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb index 110dff5cb7..0fc5d46401 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb @@ -20,7 +20,7 @@ configopts = "--with-guile-site-dir=$EBROOTGUILE" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'danetool', 'gnutls-cli', 'gnutls-cli-debug', - 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + ['lib/libgnutls%s' % x for x in ['.a', 'xx.a', '-xssl.a', '-openssl.a']], 'dirs': ['include/gnutls'], } diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb index a1b5c74cda..d883037773 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb @@ -31,7 +31,7 @@ configopts = "--with-guile-site-dir=$EBROOTGUILE --enable-openssl-compatibility sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'crywrap', 'gnutls-cli', 'gnutls-cli-debug', - 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]] + ['lib/guile/%s/guile-gnutls-v-2.so' % guileshortver], 'dirs': ['include/gnutls'], diff --git a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb index aeb9e7c8b0..ab9d5fd44f 100644 --- a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb +++ b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb @@ -15,10 +15,10 @@ dependencies = [('Java', '1.7.0_80')] parallel = 1 -sanity_check_paths = { - 'files': ["bin/hbase"], - 'dirs': ["conf", "docs", "hbase-webapps", "lib"] -} +sanity_check_paths = { + 'files': ["bin/hbase"], + 'dirs': ["conf", "docs", "hbase-webapps", "lib"] +} modextravars = {'HBASE_HOME': '%(installdir)s'} diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.5.14.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.5.14.eb index 89abbbefcf..c83b2a6347 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.5.14.eb @@ -5,7 +5,7 @@ homepage = 'http://www.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gpsolf-2014.12.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gpsolf-2014.12.eb index 26abf7963c..8b166299eb 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gpsolf-2014.12.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gpsolf-2014.12.eb @@ -5,7 +5,7 @@ homepage = 'http://www.netlib.org/benchmark/hpl/' description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'gpsolf', 'version': '2014.12'} +toolchain = {'name': 'gpsolf', 'version': '2014.12'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb index b56af425fe..0ad29d6c94 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb @@ -5,7 +5,7 @@ homepage = 'http://www.netlib.org/benchmark/hpl/' description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'intel-para', 'version': '2014.12'} +toolchain = {'name': 'intel-para', 'version': '2014.12'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb index 99632e1361..d99049bc6c 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'HTSlib' version = '1.1' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb index 77c75fbe48..aa9159ceb5 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('GLib', '2.41.2'), ] -sanity_check_paths = { +sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b.eb index ce42351add..82ca87f89c 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('GLib', '2.41.2'), ] -sanity_check_paths = { +sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb index bd8c70bf67..bece15fbe3 100644 --- a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb @@ -19,7 +19,7 @@ source_urls = ['http://ccb.jhu.edu/software/hisat/downloads/'] checksums = ['9524a0170d85c5b560b51e0087f4cf46'] -executables = [name, 'hisat-build', 'hisat-inspect', 'hisat-build-s', 'hisat-inspect-s', 'hisat-align-s', +executables = [name, 'hisat-build', 'hisat-inspect', 'hisat-build-s', 'hisat-inspect-s', 'hisat-align-s', 'hisat-build-l', 'hisat-inspect-l', 'hisat-align-l'] files_to_copy = [(executables, 'bin')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.9.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.9.2.eb index f86d5d11ab..2481673293 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.9.2.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb index 6adedf3a5d..ec22112547 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb @@ -19,5 +19,5 @@ sources = [SOURCE_TAR_GZ] dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" - + moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb index 33b2aeafd6..afa499ff97 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb index 086602c3aa..5b67b5f490 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index e2d5ab4c7f..50bcad92f3 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GNU-4.9.3-2.25.eb index 4a93ec7e70..41a09546a0 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GNU-4.9.3-2.25.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ClangGCC-1.1.3.eb index 21df483130..3e12868a78 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ClangGCC-1.1.3.eb @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.6.4.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.6.4.eb index 3c07bbe614..ca74b09ce1 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.6.4.eb @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'GCC', 'version': '4.6.4'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb index 19d34c3d1a..58f69d8db5 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb index 35e5b4d3bc..4a1f0300da 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-GCC-4.8.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-GCC-4.8.2.eb index ade75969bd..13051e6d81 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-GCC-4.8.2.eb @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb index bbe1c894d7..459fa88c69 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb index b8de1f4777..b61501e141 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'gcccuda', 'version': '2.6.10'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb index cb11169e92..ea7fbe41dd 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb index dd1343eaa7..82f551b247 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'GCC', 'version': '4.8.3'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.9-GCC-4.8.3.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.9-GCC-4.8.3.eb index c21425bb3c..5353d4e58c 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.9-GCC-4.8.3.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.3'} dependencies = [('numactl', '2.0.9')] configopts = "--enable-libnuma=$EBROOTNUMACTL" - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb index 0ee4a4f740..776e9a7846 100644 --- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -8,7 +8,7 @@ easyblock = 'MakeCp' name = 'IDBA-UD' -version = '1.1.1' +version = '1.1.1' homepage = 'http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads @@ -31,7 +31,7 @@ prebuildopts = './configure && ' buildopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' files_to_copy = ["bin", "script", "README", "ChangeLog", "NEWS"] - + sanity_check_paths = { 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", "idba_ud", "parallel_blat", "idba_tran_test"]], diff --git a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb index 2aebd3c1b6..2f880e4689 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb @@ -25,7 +25,7 @@ sources = [SOURCE_TGZ] # gmake all -- IOR with POSIX, MPIIO, HDF5, and NCMPI interfaces buildopts = ' mpiio' -files_to_copy = [(['src/C/IOR'], 'bin'), +files_to_copy = [(['src/C/IOR'], 'bin'), "README", "RELEASE_LOG", "UNDOCUMENTED_OPTIONS", "USER_GUIDE", "scripts", "testing"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb index 50f1a0bd7d..ac67b88a09 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb @@ -25,7 +25,7 @@ sources = [SOURCE_TGZ] # gmake all -- IOR with POSIX, MPIIO, HDF5, and NCMPI interfaces buildopts = ' mpiio' -files_to_copy = [(['src/C/IOR'], 'bin'), +files_to_copy = [(['src/C/IOR'], 'bin'), "README", "RELEASE_LOG", "UNDOCUMENTED_OPTIONS", "USER_GUIDE", "scripts", "testing"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb index 7dc3787320..5f71030257 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb @@ -20,7 +20,7 @@ sources = [ ] source_urls = ['http://www.cs.ucr.edu/~jianxing'] -dependencies = [ +dependencies = [ ('QuadProg++', '1.2.1'), ('GLPK', '4.53'), ('GSL', '1.16') diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb index 436dd9a680..10342bedf0 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb @@ -20,7 +20,7 @@ sources = [ ] source_urls = ['http://www.cs.ucr.edu/~jianxing'] -dependencies = [ +dependencies = [ ('QuadProg++', '1.2.1'), ('GLPK', '4.53'), ('GSL', '1.16') diff --git a/easybuild/easyconfigs/i/ictce/ictce-4.0.6.eb b/easybuild/easyconfigs/i/ictce/ictce-4.0.6.eb index 72df26b46c..77fb61dc74 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-4.0.6.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-4.0.6.eb @@ -9,7 +9,7 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2011.6.233' -dependencies = [ +dependencies = [ ('icc', compver), ('ifort', compver), ('impi', '4.0.2.003', '', ('iccifort', compver)), diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-4.0.6.eb b/easybuild/easyconfigs/i/iimpi/iimpi-4.0.6.eb index ffa9bd3843..51b3aa5c0f 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-4.0.6.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-4.0.6.eb @@ -9,7 +9,7 @@ description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2011.6.233' -dependencies = [ +dependencies = [ ('icc', compver), ('ifort', compver), ('impi', '4.0.2.003', '', ('iccifort', compver)), diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb index a44565b87f..58af733372 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb @@ -1,12 +1,12 @@ name = 'imkl' -version = "11.2.1.133" +version = "11.2.1.133" homepage = 'http://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'ipsmpi', 'version': '2014.12'} +toolchain = {'name': 'ipsmpi', 'version': '2014.12'} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb index 5f9a44b8c2..0e49c82636 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb @@ -17,7 +17,7 @@ sources = ['ispc-v%(version)s-linux.tar.gz'] source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] sanity_check_paths = { - 'files': ["ispc"], + 'files': ["ispc"], 'dirs': [] } diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb index d889b3d0b2..949fa04983 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb @@ -13,7 +13,7 @@ description = """Jansson is a C library for encoding, decoding and manipulating * Extensive test suite""" toolchain = {'name': 'gcccuda', 'version': '2.6.10'} - + # fi. https://github.com/akheron/jansson/archive/2.5.zip source_urls = ['https://github.com/akheron/jansson/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.6-GCC-4.8.3.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.6-GCC-4.8.3.eb index 0803b327c8..6da2045abd 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.6-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.6-GCC-4.8.3.eb @@ -13,7 +13,7 @@ description = """Jansson is a C library for encoding, decoding and manipulating * Extensive test suite""" toolchain = {'name': 'GCC', 'version': '4.8.3'} - + # fi. https://github.com/akheron/jansson/archive/2.5.zip source_urls = ['https://github.com/akheron/jansson/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goolf-1.5.14.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goolf-1.5.14.eb index e398d414f1..8d3aa6f5fe 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goolf-1.5.14.eb @@ -6,7 +6,7 @@ version = '1.900.1' homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_ZIP] diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb index d296c6ae8c..3280a4d8e4 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb @@ -6,7 +6,7 @@ version = '1.0.8' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X Inter-Client Exchange library for freedesktop.org""" -toolchain = {'name': 'intel', 'version': '2014b'} +toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb index 57f6a9f4e3..c7f664c8c8 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb @@ -6,7 +6,7 @@ version = '1.0.9' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X Inter-Client Exchange library for freedesktop.org""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb index 061d77840d..87ccf251e1 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb @@ -6,7 +6,7 @@ version = '1.0.9' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X Inter-Client Exchange library for freedesktop.org""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2014b-Python-2.7.8.eb index 491d7b754b..6dc47a39ef 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2014b-Python-2.7.8.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-2.7.8' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X11 client-side library""" -toolchain = {'name': 'intel', 'version': '2014b'} +toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb index 3f72262d57..ee582416a0 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-2.7.9' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X11 client-side library""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb index 9c513d4634..a4a7437300 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-2.7.10' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X11 client-side library""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb index aec9e4570d..fa0d2300e6 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-2.7.9' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X11 client-side library""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.10.eb index 81992bc475..90a1e61002 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.10.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-2.7.10' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X11 client-side library""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.11.eb index 061bf0062c..ce11a9ade3 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.11.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-2.7.11' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X11 client-side library""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015a-Python-2.7.10.eb index f396c996d1..63172f59f4 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015a-Python-2.7.10.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'libdap' version = '3.14.0' -versionsuffix = "-Python-2.7.10" +versionsuffix = "-Python-2.7.10" homepage = 'http://opendap.org/download/libdap' description = """A C++ SDK which contains an implementation of DAP 2.0 diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015b-Python-2.7.10.eb index ab0f0f65d0..f70b2b33c4 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015b-Python-2.7.10.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'libdap' version = '3.14.0' -versionsuffix = "-Python-2.7.10" +versionsuffix = "-Python-2.7.10" homepage = 'http://opendap.org/download/libdap' description = """A C++ SDK which contains an implementation of DAP 2.0 diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb index f829f915ab..9739f76ef1 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] + 'dirs': [] } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goolf-1.4.10.eb index 1b25208919..1a74d61a74 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goolf-1.4.10.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] + 'dirs': [] } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb index 9f980a8c82..f71c39521b 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} sanity_check_paths = { 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] + 'dirs': [] } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.3.0.eb index 1c780648c6..8789568941 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.3.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] + 'dirs': [] } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.9.2.eb index fdeaf140c1..a0d2e1edbd 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.9.2.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.""" -toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb index a0c6a258a8..51c79ac40a 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.""" -toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb index a0bfd7ae8e..dd9022e00e 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb index f29d89e1c6..6daa86f14e 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.""" -toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.eb index 99efd1e796..7143101605 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.""" -toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb index 33c6f3867e..290aa77f30 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.""" -toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} +toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb index 1ae3d3fbc4..930f6a164f 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -toolchain = {'name': 'intel', 'version': '2014b'} +toolchain = {'name': 'intel', 'version': '2014b'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb index c1b10ef129..09a13b616d 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb index 7d20038412..68acb79d5b 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb index d5d178d52d..482b2014e9 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb index b3c206c1f5..c9239b151b 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-goolf-1.5.14.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-goolf-1.5.14.eb index b2b4474146..0cb44a3cfb 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-goolf-1.5.14.eb @@ -10,7 +10,7 @@ It is mostly SVR4 compatible although it has some extensions GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. """ -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index f703162700..9fed17ec40 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -35,7 +35,7 @@ builddependencies = [ ('glproto', '1.4.17'), ('M4', '1.4.17') ] - + dependencies = [ ('Python', pythonver), ('libxml2', '2.9.2', versionsuffix), diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 8493b40437..071c95fba2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -33,8 +33,8 @@ dependencies = [ osdependencies = [ 'libX11-devel', # Xlibs.h 'xorg-x11-proto-devel', # X.h, glproto, xproto - 'libXdamage-devel', - 'libXext-devel', + 'libXdamage-devel', + 'libXext-devel', 'libXfixes-devel', ] @@ -46,7 +46,7 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' -sanity_check_paths = { +sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index dae84ea70b..3fa0d3f751 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -32,8 +32,8 @@ dependencies = [ osdependencies = [ 'libX11-devel', # Xlibs.h 'xorg-x11-proto-devel', # X.h, glproto, xproto - 'libXdamage-devel', - 'libXext-devel', + 'libXdamage-devel', + 'libXext-devel', 'libXfixes-devel', ] @@ -45,7 +45,7 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' -sanity_check_paths = { +sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb index ce1d47d02a..864dc0bea3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb @@ -33,8 +33,8 @@ dependencies = [ osdependencies = [ 'libX11-devel', # Xlibs.h 'xorg-x11-proto-devel', # X.h, glproto, xproto - 'libXdamage-devel', - 'libXext-devel', + 'libXdamage-devel', + 'libXext-devel', 'libXfixes-devel', ] @@ -46,7 +46,7 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' -sanity_check_paths = { +sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb index 490f0bad9f..4ae1b34911 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb @@ -33,8 +33,8 @@ dependencies = [ osdependencies = [ 'libX11-devel', # Xlibs.h 'xorg-x11-proto-devel', # X.h, glproto, xproto - 'libXdamage-devel', - 'libXext-devel', + 'libXdamage-devel', + 'libXext-devel', 'libXfixes-devel', ] @@ -46,7 +46,7 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' -sanity_check_paths = { +sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 226d771609..8f7b8fd9e1 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -34,8 +34,8 @@ dependencies = [ osdependencies = [ 'libX11-devel', # Xlibs.h 'xorg-x11-proto-devel', # X.h, glproto, xproto - 'libXdamage-devel', - 'libXext-devel', + 'libXdamage-devel', + 'libXext-devel', 'libXfixes-devel', ] @@ -47,7 +47,7 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' -sanity_check_paths = { +sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', diff --git a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb index 852c1e3066..5ee01321f8 100644 --- a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb @@ -32,8 +32,8 @@ files_to_copy = ["bin", "docs"] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["allelicmeth", "amrfinder", "amrtester", "bsrate", "dmr", - "duplicate-remover", "hmr", "hmr_plant", "lc_approx","levels", - "merge-bsrate", "merge-methcounts", "methcounts","methdiff", + "duplicate-remover", "hmr", "hmr_plant", "lc_approx","levels", + "merge-bsrate", "merge-methcounts", "methcounts","methdiff", "methstates", "pmd", "rmapbs", "rmapbs-pe", "roimethstat", "to-mr"]], 'dirs': ['docs'], } diff --git a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb index 2c109b3557..546db6338a 100644 --- a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb +++ b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb @@ -32,8 +32,8 @@ files_to_copy = ["bin", "docs"] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["allelicmeth", "amrfinder", "amrtester", "bsrate", "dmr", - "duplicate-remover", "hmr", "hmr_plant", "lc_approx","levels", - "merge-bsrate", "merge-methcounts", "methcounts","methdiff", + "duplicate-remover", "hmr", "hmr_plant", "lc_approx","levels", + "merge-bsrate", "merge-methcounts", "methcounts","methdiff", "methstates", "pmd", "rmapbs", "rmapbs-pe", "roimethstat", "to-mr"]], 'dirs': ['docs'], } diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb index 10d8f0fdb3..529c59d6ab 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb index ff1abe6893..df5d7baa12 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb @@ -11,7 +11,7 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb index 790eefcde4..3d0c89f8f2 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb @@ -14,7 +14,7 @@ source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] patches = ['makedepend_icc-sigaction.patch'] -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb index 94b2544e16..fa3bc9877b 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb index c0f71c373d..3f3fa2cba5 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb index 39683b811c..653ce13c66 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb @@ -13,7 +13,7 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb index 34e982133e..a42c1e4ac5 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb @@ -14,7 +14,7 @@ source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] patches = ['makedepend_icc-sigaction.patch'] -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb index 6c2df30046..f389f06807 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb @@ -25,8 +25,8 @@ parallel = 1 buildopts = ' CC="$CC"' files_to_copy = [ - (['mdtest'], 'bin'), - "README", + (['mdtest'], 'bin'), + "README", "COPYRIGHT", ] diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb index d5a5cb84d4..9444c160fd 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb @@ -25,8 +25,8 @@ parallel = 1 buildopts = ' CC="$CC"' files_to_copy = [ - (['mdtest'], 'bin'), - "README", + (['mdtest'], 'bin'), + "README", "COPYRIGHT", ] diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb index aaa3515150..a7dcc82e62 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb @@ -25,9 +25,9 @@ parallel = 1 buildopts = ' CC="$CC"' files_to_copy = [ - (['mdtest'], 'bin'), - (['mdtest.1'], 'man/man1'), - "README", + (['mdtest'], 'bin'), + (['mdtest.1'], 'man/man1'), + "README", "RELEASE_LOG", "scripts" ] diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb index 28fb4bd0ad..2085a445de 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb @@ -25,9 +25,9 @@ parallel = 1 buildopts = ' CC="$CC"' files_to_copy = [ - (['mdtest'], 'bin'), - (['mdtest.1'], 'man/man1'), - "README", + (['mdtest'], 'bin'), + (['mdtest.1'], 'man/man1'), + "README", "RELEASE_LOG", "scripts" ] diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 98f6b375df..de5230e1fa 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -14,7 +14,7 @@ source_urls = [ GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] - + python = 'Python' pyver = '2.7.3' versionsuffix = '-%s-%s' % (python, pyver) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb index 58e1efec95..c04cd339fd 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -14,7 +14,7 @@ source_urls = [ GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] - + python = 'Python' pyver = '2.7.3' versionsuffix = '-%s-%s' % (python, pyver) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb index 8d1017dab1..bc0d20fdcb 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb @@ -15,7 +15,7 @@ source_urls = [ GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] - + python = 'Python' pyver = '3.2.3' versionsuffix = '-%s-%s' % (python, pyver) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb index fff549de1f..ad06de5d4f 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb @@ -14,7 +14,7 @@ source_urls = [ GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] - + python = 'Python' pyver = '2.7.3' versionsuffix = '-%s-%s' % (python, pyver) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb index 9fe2a5f319..c69d7c6073 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb @@ -14,7 +14,7 @@ source_urls = [ GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] - + python = 'Python' pyver = '2.7.3' versionsuffix = '-%s-%s' % (python, pyver) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb index eaf599c8ab..94b5a9f2f8 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb @@ -14,7 +14,7 @@ source_urls = [ GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] - + python = 'Python' pyver = '2.7.3' versionsuffix = '-%s-%s' % (python, pyver) diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb index 5ddc8fef62..b849d1d7cc 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb @@ -16,7 +16,7 @@ description = """The NCO toolkit manipulates and analyzes data stored in netCDF- toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'cstd': 'c99'} - + source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.5.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/NCO/NCO-4.5.1-intel-2015a-Python-2.7.10.eb index 3612474f0c..a6ab3c607d 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.5.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.5.1-intel-2015a-Python-2.7.10.eb @@ -16,7 +16,7 @@ description = """The NCO toolkit manipulates and analyzes data stored in netCDF- toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'cstd': 'c99'} - + source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb index bd158f66c5..3d072019b1 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb @@ -6,7 +6,7 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb index 4527973704..113ec9d3b8 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb @@ -6,7 +6,7 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/n/netloc/netloc-0.5-GCC-4.8.3.eb b/easybuild/easyconfigs/n/netloc/netloc-0.5-GCC-4.8.3.eb index 025be1d81d..26ee8e7734 100644 --- a/easybuild/easyconfigs/n/netloc/netloc-0.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/netloc/netloc-0.5-GCC-4.8.3.eb @@ -10,7 +10,7 @@ description = """The Portable Network Locality (netloc) software package provide It is provided as a companion to the Portable Hardware Locality (hwloc) package.""" toolchain = {'name': 'GCC', 'version': '4.8.3'} - + source_urls = [homepage + '/v%(version_major_minor)s/downloads'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb b/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb index 6b5126f478..71e8c66169 100644 --- a/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb @@ -10,7 +10,7 @@ description = """The Portable Network Locality (netloc) software package provide It is provided as a companion to the Portable Hardware Locality (hwloc) package.""" toolchain = {'name': 'gcccuda', 'version': '2.6.10'} - + dependencies = [ ('hwloc', '1.8'), ('Jansson', '2.5'), diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.0.6-Python-2.7.3.eb index 32146789ef..cd51989f63 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.0.6-Python-2.7.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] - + patches = ['numpy-1.6.2_distutils_multiple-lib-dirs.patch'] python = 'Python' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb index 6f22931653..0c0f829203 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] - + patches = ['numpy-%(version)s_distutils_multiple-lib-dirs.patch'] python = 'Python' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-5.3.0-Python-2.7.3.eb index 0ea594ac42..72587faf5d 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-5.3.0-Python-2.7.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] - + patches = ['numpy-1.6.2_distutils_multiple-lib-dirs.patch'] python = 'Python' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb index 722f3cab2c..9211de2ef5 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb @@ -14,7 +14,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['numpy-1.7.1_distutils_multiple-lib-dirs.patch'] - + python = 'Python' pyver = '2.7.5' versionsuffix = '-%s-%s' % (python, pyver) diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 2e5794c12d..15b1424e0d 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -28,9 +28,9 @@ options = {'modulename': name} sanity_check_paths = { 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in + 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in [ - 'datasets', 'evaluation', 'examples', 'gradient', + 'datasets', 'evaluation', 'examples', 'gradient', 'nodes', 'parallel', 'tests', 'utils', ] ] diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb index ca77bdf1b1..95e21e11e7 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb @@ -29,9 +29,9 @@ options = {'modulename': name} sanity_check_paths = { 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in + 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in [ - 'datasets', 'evaluation', 'examples', 'gradient', + 'datasets', 'evaluation', 'examples', 'gradient', 'nodes', 'parallel', 'tests', 'utils', ] ] diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb index 96fa8be936..e5cd3a5503 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb @@ -28,7 +28,7 @@ options = {'modulename': name} sanity_check_paths = { 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in + 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in ['datasets', 'evaluation', 'examples', 'gradient', 'nodes', 'parallel', 'tests', 'utils'] ] } diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb index 3a51160584..a04089fb7d 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb @@ -29,7 +29,7 @@ options = {'modulename': name} sanity_check_paths = { 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in + 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in ['datasets', 'evaluation', 'examples', 'gradient', 'nodes', 'parallel', 'tests', 'utils'] ] } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 8b588833b0..4310e30ba0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.6.2')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index ccbc9394ec..b176332293 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = [ +patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index ce23f55355..da09b2dec4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = [ +patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index c6b40582c8..192e287657 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = [ +patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 2afbc4733e..6714cfb974 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = [ +patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 8af372736a..dcc884ec54 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = [ +patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index 2ae7377c37..ef8df74e30 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = [ +patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index 10774dff41..0d0d8c2243 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'gcccuda', 'version': '2.6.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = [ +patches = [ 'OpenMPI-%(version)s_common-cuda-lib.patch', 'OpenMPI-%(version)s-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/o2scl/o2scl-0.913-goolf-1.4.10.eb b/easybuild/easyconfigs/o/o2scl/o2scl-0.913-goolf-1.4.10.eb index 539e278a55..665ae52c04 100644 --- a/easybuild/easyconfigs/o/o2scl/o2scl-0.913-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/o2scl/o2scl-0.913-goolf-1.4.10.eb @@ -20,7 +20,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [ +dependencies = [ ('Eigen', '3.1.4'), ('libreadline', '6.2'), ('HDF5', '1.8.11'), diff --git a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb index 54437d6a78..2cbfe2886f 100644 --- a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb @@ -27,7 +27,7 @@ sanity_check_paths = { 'ExtractProteinIdsFromGroupsFile', 'ExtractProteinPairsFromGroupsFile', 'FilterFasta', 'InstallSchema', 'LoadBlast', 'MclToGroups', 'Pairs', 'ReduceFasta', 'ReduceGroups', 'RemoveIdenticalGroups', 'Singletons', - 'SortGroupMembersByScore', 'SortGroupsFile']], + 'SortGroupMembersByScore', 'SortGroupsFile']], 'dirs': ['lib/perl/OrthoMCLEngine'], } diff --git a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-4.1.13-Perl-5.16.3.eb index 0bcdb50b2f..b5689400cf 100644 --- a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-4.1.13-Perl-5.16.3.eb @@ -27,7 +27,7 @@ sanity_check_paths = { 'ExtractProteinIdsFromGroupsFile', 'ExtractProteinPairsFromGroupsFile', 'FilterFasta', 'InstallSchema', 'LoadBlast', 'MclToGroups', 'Pairs', 'ReduceFasta', 'ReduceGroups', 'RemoveIdenticalGroups', 'Singletons', - 'SortGroupMembersByScore', 'SortGroupsFile']], + 'SortGroupMembersByScore', 'SortGroupsFile']], 'dirs': ['lib/perl/OrthoMCLEngine'], } diff --git a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb index 4cb9385e59..2fe0311606 100644 --- a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb @@ -27,7 +27,7 @@ sanity_check_paths = { 'ExtractProteinIdsFromGroupsFile', 'ExtractProteinPairsFromGroupsFile', 'FilterFasta', 'InstallSchema', 'LoadBlast', 'MclToGroups', 'Pairs', 'ReduceFasta', 'ReduceGroups', 'RemoveIdenticalGroups', 'Singletons', - 'SortGroupMembersByScore', 'SortGroupsFile']], + 'SortGroupMembersByScore', 'SortGroupsFile']], 'dirs': ['lib/perl/OrthoMCLEngine'], } diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb index e0822f5ef3..e1ffffe615 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'PBZIP2' -version = '1.1.8' +version = '1.1.8' homepage = 'http://compression.ca/pbzip2/' description = """ PBZIP2 is a parallel implementation of the bzip2 block-sorting file @@ -24,7 +24,7 @@ buildopts = " CC=$CXX" parallel = 1 files_to_copy = [(["pbzip2"], "bin"), (["pbzip2.1"], "man/man1"), "README", "ChangeLog"] - + sanity_check_paths = { 'files': ["bin/pbzip2"], 'dirs': [], diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb index a1befffbe4..795cc4f409 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'PBZIP2' -version = '1.1.8' +version = '1.1.8' homepage = 'http://compression.ca/pbzip2/' description = """ PBZIP2 is a parallel implementation of the bzip2 block-sorting file @@ -14,7 +14,7 @@ description = """ PBZIP2 is a parallel implementation of the bzip2 block-sorting of this version is fully compatible with bzip2 v1.0.2 or newer (ie: anything compressed with pbzip2 can be decompressed with bzip2).""" -toolchain = {'name': 'ictce', 'version': '6.2.5'} +toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = ['http://compression.ca/pbzip2/'] sources = [SOURCELOWER_TAR_GZ] @@ -24,7 +24,7 @@ buildopts = " CC=$CXX" parallel = 1 files_to_copy = [(["pbzip2"], "bin"), (["pbzip2.1"], "man/man1"), "README", "ChangeLog"] - + sanity_check_paths = { 'files': ["bin/pbzip2"], 'dirs': [], diff --git a/easybuild/easyconfigs/p/PCC/PCC-20131024.eb b/easybuild/easyconfigs/p/PCC/PCC-20131024.eb index be6e59a2e9..c40392b771 100644 --- a/easybuild/easyconfigs/p/PCC/PCC-20131024.eb +++ b/easybuild/easyconfigs/p/PCC/PCC-20131024.eb @@ -28,7 +28,7 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ["bin/pcc"], + 'files': ["bin/pcc"], 'dirs': ["lib"] } diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb index 4cff265549..72b0ef23a9 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'PETSc_ranlib-fix.patch', 'PETSc-%(version)s-zlibfix.patch', -] +] parmetis = 'ParMETIS' parmetis_ver = '4.0.3' diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb index 50bb76fbb3..7f7c8b29a2 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb @@ -14,7 +14,7 @@ source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] checksums = ['fd0bafeda42151b20534e4f97b0d97df'] files_to_copy = [ - 'plink', + 'plink', 'gPLINK.jar', 'test.map', 'test.ped', diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb index 2060e3874c..34a1760e0e 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -22,7 +22,7 @@ source_urls = ['http://download.osgeo.org/proj/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', 'bin/nad2bin', 'bin/proj'], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb index 427477bf96..1a6432b2aa 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -22,7 +22,7 @@ source_urls = ['http://download.osgeo.org/proj/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', 'bin/nad2bin', 'bin/proj'], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/PaStiX/PaStiX-5.2.2.22-intel-2015b.eb b/easybuild/easyconfigs/p/PaStiX/PaStiX-5.2.2.22-intel-2015b.eb index 82b29f84c1..34d2da9e2f 100644 --- a/easybuild/easyconfigs/p/PaStiX/PaStiX-5.2.2.22-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PaStiX/PaStiX-5.2.2.22-intel-2015b.eb @@ -32,7 +32,7 @@ buildopts += 'MPCXXPROG="$MPICXX -cxx=$CXX -Wall" ' runtest = "examples && ./example/bin/simple -lap 100" -installopts = "PREFIX=%(installdir)s" +installopts = "PREFIX=%(installdir)s" sanity_check_paths = { 'files': ['bin/pastix-conf', 'lib/libmatrix_driver.a', 'lib/libpastix.a', 'lib/libpastix_murge.a'], diff --git a/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb b/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb index 3ad20e9bd1..d0dd1f9907 100644 --- a/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb @@ -21,6 +21,6 @@ dependencies = [ sanity_check_paths = { 'files': ['lib/libpangomm-1.4.%s' % SHLIB_EXT], 'dirs': [], -} +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015b.eb b/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015b.eb index 1c45a9716d..71f5cdfd45 100644 --- a/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015b.eb @@ -21,6 +21,6 @@ dependencies = [ sanity_check_paths = { 'files': ['lib/libpangomm-1.4.%s' % SHLIB_EXT], 'dirs': [], -} +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb index 003394e4e2..96e7b3b1b8 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb @@ -33,7 +33,7 @@ builddependencies = [('CMake', '3.2.2')] separate_build_dir = True -maxparallel = 4 +maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb index db99151738..a80a2bae48 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb @@ -32,7 +32,7 @@ builddependencies = [('CMake', '3.2.2')] separate_build_dir = True -maxparallel = 4 +maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb index fb6b899d90..9449cd74f2 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb @@ -33,7 +33,7 @@ builddependencies = [('CMake', '3.3.2')] separate_build_dir = True -maxparallel = 4 +maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb index 00106458b8..cb5acbbae9 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb @@ -32,7 +32,7 @@ builddependencies = [('CMake', '3.3.2')] separate_build_dir = True -maxparallel = 4 +maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb index 524dd9ba3d..aededa4507 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb @@ -7,7 +7,7 @@ homepage = 'http://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'foss', 'version': '2015a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb index 04c7f0efa3..07b42e823b 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb @@ -7,7 +7,7 @@ homepage = 'http://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index 65d0c45c59..864b80e95c 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -28,14 +28,14 @@ dependencies = [ ] cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] - + files_to_copy = [ (['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), - "demo", - "gmt", - "gmt-web", - "test", - "README.md", + "demo", + "gmt", + "gmt-web", + "test", + "README.md", "RELEASE" ] diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb index fa5b729bcb..8678c70192 100644 --- a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -28,6 +28,6 @@ files_to_copy = [(['pBWA','qualfa2fq.pl','solid2fastq.pl' ], 'bin')] sanity_check_paths = { 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], 'dirs': ['.'], -} +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb index 2c50b49d22..292fb226d3 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'pigz' -version = '2.3.1' +version = '2.3.1' homepage = 'http://zlib.net/pigz/' description = """ pigz, which stands for parallel implementation of gzip, is a fully @@ -27,7 +27,7 @@ buildopts = ' CC=$CC' parallel = 1 files_to_copy = [(["pigz", "unpigz"], "bin")] - + sanity_check_paths = { 'files': ["bin/pigz", "bin/unpigz"], 'dirs': [""], diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb index ec92fe5f04..770c70dd5f 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'pigz' -version = '2.3.1' +version = '2.3.1' homepage = 'http://zlib.net/pigz/' description = """ pigz, which stands for parallel implementation of gzip, is a fully @@ -27,7 +27,7 @@ buildopts = ' CC=$CC' parallel = 1 files_to_copy = [(["pigz", "unpigz"], "bin")] - + sanity_check_paths = { 'files': ["bin/pigz", "bin/unpigz"], 'dirs': [""], diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb index a4a1fb5b25..e95cb85cb9 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb @@ -30,7 +30,7 @@ buildopts = ' CC=$CC' parallel = 1 files_to_copy = [(["pigz", "unpigz"], "bin")] - + sanity_check_paths = { 'files': ["bin/pigz", "bin/unpigz"], 'dirs': [""], diff --git a/easybuild/easyconfigs/p/popt/popt-1.14-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/popt/popt-1.14-iccifort-2015.1.133.eb index da01178a4c..24a941cf28 100644 --- a/easybuild/easyconfigs/p/popt/popt-1.14-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/popt/popt-1.14-iccifort-2015.1.133.eb @@ -5,7 +5,7 @@ version = '1.14' homepage = "http://freecode.com/projects/popt" description = """Popt is a C library for parsing command line parameters.""" -toolchain = {'name': 'iccifort', 'version': '2015.1.133'} +toolchain = {'name': 'iccifort', 'version': '2015.1.133'} source_urls = ['http://rpm5.org/files/popt/'] diff --git a/easybuild/easyconfigs/p/popt/popt-1.16-GCC-4.9.2.eb b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-4.9.2.eb index 544e28528a..07519cbd9a 100644 --- a/easybuild/easyconfigs/p/popt/popt-1.16-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-4.9.2.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'popt' -version = "1.16" +version = "1.16" homepage = "http://freecode.com/projects/popt" description = """Popt is a C library for parsing command line parameters.""" diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb index 66ec7c7853..3b463debfc 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb @@ -4,7 +4,7 @@ name = 'pscom' version = '5.0.44-1' homepage = 'http://www.par-tec.com' description = """ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.""" -toolchain = {'name': 'iccifort', 'version': '2015.1.133'} +toolchain = {'name': 'iccifort', 'version': '2015.1.133'} source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] diff --git a/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2-mt.eb b/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2-mt.eb index 8690e4b98b..d7fb1e75ef 100644 --- a/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2-mt.eb +++ b/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2-mt.eb @@ -33,8 +33,8 @@ prebuildopts = "echo '%(version)s-1' > VERSION && " preinstallopts = prebuildopts sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', + 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', + 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', ('lib/libfmpich.a', 'lib64/libfmpich.a'), ('lib/libfmpich.%s' % SHLIB_EXT, 'lib64/libfmpich.%s' % SHLIB_EXT), ('lib/libmpich.a', 'lib64/libmpich.a'), diff --git a/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2.eb b/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2.eb index 101fec1094..9c3dd66c77 100644 --- a/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2.eb @@ -32,8 +32,8 @@ prebuildopts = "echo '%(version)s-1' > VERSION && " preinstallopts = prebuildopts sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', + 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', + 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', ('lib/libfmpich.a', 'lib64/libfmpich.a'), ('lib/libfmpich.%s' % SHLIB_EXT, 'lib64/libfmpich.%s' % SHLIB_EXT), ('lib/libmpich.a', 'lib64/libmpich.a'), diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb index 785cdca42b..5406e997c6 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb @@ -4,7 +4,7 @@ version = '4.8.5' homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." -toolchain = {'name': 'gmpolf', 'version': '1.4.8'} +toolchain = {'name': 'gmpolf', 'version': '1.4.8'} source_urls = [ 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb index eb4b11b03a..c5c6c8344b 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb @@ -4,7 +4,7 @@ version = '4.8.5' homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', diff --git a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb index 1cda3a4011..e4973548b5 100644 --- a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb @@ -23,7 +23,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] sanity_check_paths = { - 'files': ["bin/quip"], + 'files': ["bin/quip"], 'dirs': [] } diff --git a/easybuild/easyconfigs/q/qtop/qtop-53-1.eb b/easybuild/easyconfigs/q/qtop/qtop-53-1.eb index c04c0cb73d..1e12105e71 100644 --- a/easybuild/easyconfigs/q/qtop/qtop-53-1.eb +++ b/easybuild/easyconfigs/q/qtop/qtop-53-1.eb @@ -27,7 +27,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [homepage] sanity_check_paths = { - 'files': ["qtop"], + 'files': ["qtop"], 'dirs': [] } diff --git a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb index 418cc4118e..d832fcca93 100644 --- a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb @@ -30,7 +30,7 @@ prebuildopts = 'export BIOINFOGSLDIR=$EBROOTGSL && export BIOINFOCONFDIR=conf && prebuildopts += 'cd bios && make && make prod && cd - && ' # now move to "mrf" folder, re-export the needed env var and run make prebuildopts += 'cd mrf && export BIOINFOCONFDIR=../bios/conf/ && ' - + parallel = 1 # these are all the binaries compiled in "mrf" folder @@ -38,8 +38,8 @@ binary_files = ["psl2mrf", "bowtie2mrf", "singleExport2mrf", "mrfSubsetByTargetN "mrfQuantifier", "mrfAnnotationCoverage", "mrf2wig", "mrf2gff", "mrfSampler", "mrf2bgr", "wigSegmenter", "mrfMappingBias", "mrfSelectRegion", "mrfSelectSpliced", "mrfSelectAnnotated", "createSpliceJunctionLibrary", "gff2interval", "export2fastq", - "mergeTranscripts", "interval2gff", "interval2sequences", "bed2interval", - "interval2bed", "mrf2sam", "sam2mrf", "mrfValidate", "bgrQuantifier", + "mergeTranscripts", "interval2gff", "interval2sequences", "bed2interval", + "interval2bed", "mrf2sam", "sam2mrf", "mrfValidate", "bgrQuantifier", "bgrSegmenter", "mrfCountRegion"] files_to_copy = [ diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb index 463de39baa..7c80c0fb24 100644 --- a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://pypi.python.org/packages/source/r/%(name)s'] sources = [SOURCE_TAR_GZ] - + python = 'Python' pyver = '2.7.3' pyshortver = '.'.join(pyver.split('.')[:2]) diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb index 5287791d7c..2ad8592b89 100644 --- a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://pypi.python.org/packages/source/r/%(name)s'] sources = [SOURCE_TAR_GZ] - + python = 'Python' pyver = '3.2.3' pyshortver = '.'.join(pyver.split('.')[:2]) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-foss-2014b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-foss-2014b.eb index a7bfe7aa51..37118ac1e1 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-foss-2014b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-foss-2014b.eb @@ -28,6 +28,6 @@ dependencies = [ ('zlib', '1.2.7'), ] -parallel = 1 +parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-goolf-1.4.10.eb index 48efe7e0a7..ffeec869d8 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-goolf-1.4.10.eb @@ -30,6 +30,6 @@ dependencies = [ ('zlib', '1.2.7'), ] -parallel = 1 +parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2014b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2014b.eb index 9993040cdb..f6766acbd2 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2014b.eb @@ -30,6 +30,6 @@ dependencies = [ ('zlib', '1.2.7'), ] -parallel = 1 +parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb index 91e58c27f0..805874583a 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb @@ -30,6 +30,6 @@ dependencies = [ ('zlib', '1.2.8'), ] -parallel = 1 +parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb index c7743a27f3..3835083700 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb @@ -33,6 +33,6 @@ dependencies = [ ('zlib', '1.2.8'), ] -parallel = 1 +parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb index 227c52d47d..be9360b7e5 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb @@ -28,6 +28,6 @@ dependencies = [ ('zlib', '1.2.8'), ] -parallel = 1 +parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015b.eb index 64891e6e5f..598ba6e51e 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015b.eb @@ -28,6 +28,6 @@ dependencies = [ ('zlib', '1.2.8'), ] -parallel = 1 +parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb index 15cb82566e..97a147d8ec 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb @@ -28,6 +28,6 @@ dependencies = [ ('zlib', '1.2.7'), ] -parallel = 1 +parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb index 695f8c6b45..e3ff7301d8 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb @@ -28,6 +28,6 @@ dependencies = [ ('zlib', '1.2.8'), ] -parallel = 1 +parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb index ccd0092201..2896876819 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb @@ -33,6 +33,6 @@ dependencies = [ ('zlib', '1.2.8'), ] -parallel = 1 +parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb index f442020c76..d732b448eb 100644 --- a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb @@ -30,7 +30,7 @@ buildopts = '-C zlib-1.2.8 && make all' files_to_copy = [(['scalce'], 'bin')] sanity_check_paths = { - 'files': ["bin/scalce"], + 'files': ["bin/scalce"], 'dirs': [] } diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb index edac27cad0..ba1a0a43d1 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb @@ -1,6 +1,6 @@ name = 'SCOTCH' version = '6.0.4' -versionsuffix = '-64bitint' +versionsuffix = '-64bitint' homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, diff --git a/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb b/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb index b97860755c..a74b423aa7 100644 --- a/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb +++ b/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb @@ -35,7 +35,7 @@ builddependencies = [ configopts = "--disable-pic14-port --disable-pic16-port" sanity_check_paths = { - 'files': ["bin/sdcc"], + 'files': ["bin/sdcc"], 'dirs': [] } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb index ecc7ac751e..aaac9462ce 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb @@ -9,7 +9,7 @@ version = '4.16.4' homepage = 'http://www.riverbankcomputing.com/software/sip/' description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb index 0710574135..f0dcc913e9 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb @@ -9,7 +9,7 @@ version = '4.16.4' homepage = 'http://www.riverbankcomputing.com/software/sip/' description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb index c965b7304f..0e8750aa56 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb @@ -28,7 +28,7 @@ sanity_check_paths = { } # add the installation dir to PATH -modextrapaths = { +modextrapaths = { 'PATH': "", } diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb index bb97c237d9..ea1f495c8a 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb @@ -28,7 +28,7 @@ sanity_check_paths = { } # add the installation dir to PATH -modextrapaths = { +modextrapaths = { 'PATH': "", } diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb index c428723fec..c819f307db 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.3.0e' +version = '2.3.0e' homepage = 'https://code.google.com/p/rna-star/' description = """ STAR aligns RNA-seq reads to a reference genome using @@ -25,7 +25,7 @@ prebuildopts = 'rm STAR && ' parallel = 1 files_to_copy = [(["STAR"], "bin"), "README.txt"] - + sanity_check_paths = { 'files': ["bin/STAR"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb index 128fc5121a..2a0e1ca5db 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.5.0a' +version = '2.5.0a' homepage = 'https://code.google.com/p/rna-star/' description = """ STAR aligns RNA-seq reads to a reference genome using @@ -23,7 +23,7 @@ prebuildopts = 'rm -fr bin/ && ' parallel = 1 files_to_copy = [(["source/STAR"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] - + sanity_check_paths = { 'files': ["bin/STAR"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb index 6a4e930918..ab46efb39c 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.5.0a' +version = '2.5.0a' homepage = 'https://code.google.com/p/rna-star/' description = """ STAR aligns RNA-seq reads to a reference genome using @@ -23,7 +23,7 @@ prebuildopts = 'rm -fr bin/ && ' parallel = 1 files_to_copy = [(["source/STAR"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] - + sanity_check_paths = { 'files': ["bin/STAR"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb index febe7d2fb6..0676f01766 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb @@ -30,7 +30,7 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" sanity_check_paths = { - 'files': ['include/serf-1/serf.h'] + + 'files': ['include/serf-1/serf.h'] + ['lib/libserf-1.%s' % x for x in ['a', 'so']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb index 9bae8b637e..be6f1332e2 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb @@ -31,4 +31,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.5-intel-2015b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.5-intel-2015b-METIS-5.1.0.eb index 49a8ba6fea..36dee081ed 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.5-intel-2015b-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.5-intel-2015b-METIS-5.1.0.eb @@ -11,7 +11,7 @@ source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] patches = [ - 'SuiteSparse-%(version)s_AMD_GNUMakefile.patch', + 'SuiteSparse-%(version)s_AMD_GNUMakefile.patch', 'SuiteSparse-%(version)s_UMFPACK_GNUMakefile.patch', ] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.14.eb index ab15e56447..af86122037 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.14.eb @@ -6,7 +6,7 @@ version = '2.1' homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] diff --git a/easybuild/easyconfigs/s/scikit-umfpack/scikit-umfpack-0.2.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/scikit-umfpack/scikit-umfpack-0.2.1-intel-2015b-Python-2.7.10.eb index c30e04d554..f47e1ccb98 100644 --- a/easybuild/easyconfigs/s/scikit-umfpack/scikit-umfpack-0.2.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/scikit-umfpack/scikit-umfpack-0.2.1-intel-2015b-Python-2.7.10.eb @@ -23,7 +23,7 @@ dependencies = [ builddependencies = [ ('SWIG', '3.0.7', versionsuffix), -] +] options = {'modulename': 'scikits'} diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb index ebdf0c48b0..f3db34a07a 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb @@ -7,7 +7,7 @@ homepage = 'http://spglib.sourceforge.net/' description = """Spglib is a C library for finding and handling crystal symmetries.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'dynamic': True, } +toolchainopts = {'dynamic': True, } source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb b/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb index e7a38fab79..9fc79c204d 100644 --- a/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb +++ b/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb @@ -27,7 +27,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://download.savannah.nongnu.org/releases/tinycc/'] sanity_check_paths = { - 'files': ["bin/tcc"], + 'files': ["bin/tcc"], 'dirs': [] } diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-4.0.6-Python-2.7.3.eb index cc0fc985e0..fea45f6e5c 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-4.0.6-Python-2.7.3.eb @@ -29,5 +29,5 @@ builddependencies = [('CMake', '2.8.4')] # Kokkos build is broken with ictce/4.0.6 # yields internal error: 0_1670 for packages/kokkos/LinAlg/Kokkos_DefaultArithmetic.hpp (line 827) skip_exts = ["Kokkos", "Tpetra"] - + moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-5.3.0-Python-2.7.3.eb index a7d22afde0..84613e0ab2 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-5.3.0-Python-2.7.3.eb @@ -30,5 +30,5 @@ builddependencies = [('CMake', '2.8.4')] # Kokkos build is broken with ictce/4.0.6 # yields internal error: 0_1670 for packages/kokkos/LinAlg/Kokkos_DefaultArithmetic.hpp (line 827) skip_exts = ["Kokkos", "Tpetra"] - + moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.4.2-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.4.2-intel-2015b-Python-2.7.11.eb index 465a84d1bb..57bd77ec8b 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.4.2-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.4.2-intel-2015b-Python-2.7.11.eb @@ -33,5 +33,5 @@ skip_exts = ['STKClassic', 'STKDoc_tests'] # too parallel is too slow, and may cause build/tests to fail maxparallel = 10 - + moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.5.14.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.5.14.eb index 2e710f4a1d..5e7647f183 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.5.14.eb @@ -21,7 +21,7 @@ description = """Tcsh is an enhanced, but completely compatible version of the B processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = [ diff --git a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb index cd1b05dd17..b34529fe92 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb @@ -19,7 +19,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/tmux'], + 'files': ['bin/tmux'], 'dirs': [] } diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015a.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015a.eb index e9af43d201..964a50f27f 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015a.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015a.eb @@ -28,7 +28,7 @@ source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] dependencies = [('expat', '2.1.0')] sanity_check_paths = { - 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], 'dirs': ['share'], } diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015b.eb index 45c7bafac5..efdb4ae86f 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015b.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015b.eb @@ -28,7 +28,7 @@ source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] dependencies = [('expat', '2.1.0')] sanity_check_paths = { - 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], 'dirs': ['share'], } diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.5.1-goolf-1.5.14-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.5.1-goolf-1.5.14-dmpar.eb index aca6ed1e40..8654cbea4e 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.5.1-goolf-1.5.14-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.5.1-goolf-1.5.14-dmpar.eb @@ -6,7 +6,7 @@ description = """The Weather Research and Forecasting (WRF) Model is a next-gene numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 sources = ['%(name)sV%(version)s.TAR.gz'] diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb index c1f4fa485c..d9881b2ef7 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -7,10 +7,10 @@ description = "Xmipp is a suite of image processing programs, primarily aimed at source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] sources = ['Xmipp-%(version)s-src.tar.gz'] - + toolchain = {'name': 'goolf', 'version': '1.4.10'} # note: all other dependencies are taken care of by Xmipp itself dependencies = [('Java', '1.7.0_80', '', True)] - + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb index 4ef466e9c6..d03ad18e50 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb @@ -6,7 +6,7 @@ version = '7.3.0' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" -toolchain = {'name': 'intel', 'version': '2014b'} +toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb index ee0ab26f86..01075a73cf 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb @@ -6,7 +6,7 @@ version = '7.3.0' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb index 5e95a7e8bd..983804175f 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb @@ -6,7 +6,7 @@ version = '7.3.0' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb index bb6336c340..51a00b2812 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb @@ -14,7 +14,7 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb index 6e21bf0fdc..d17e8eb76f 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb @@ -14,7 +14,7 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb index 2837728722..f34a19a932 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb @@ -14,7 +14,7 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb index d005dadc8e..fd2b06fd61 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb @@ -14,7 +14,7 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb index 096a07bd53..dad31a77b4 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], -- GitLab From cb23aae8f3c34f63546221bb9785cf2b9feae3ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Jan 2016 17:47:47 +0200 Subject: [PATCH 0192/2133] add easyconfig Bison-3.0.4-intel-2016a.eb, add easyconfig M4-1.4.17-intel-2016a.eb, add easyconfig flex-2.5.39-intel-2016a.eb, add easyconfig flex-2.6.0-intel-2016a.eb --- .../b/Bison/Bison-3.0.4-intel-2016a.eb | 22 ++++++++++++++++++ .../f/flex/flex-2.5.39-intel-2016a.eb | 14 +++++++++++ .../f/flex/flex-2.6.0-intel-2016a.eb | 16 +++++++++++++ .../easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb | 23 +++++++++++++++++++ 4 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016a.eb new file mode 100644 index 0000000000..df48dd47dd --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb new file mode 100644 index 0000000000..419266740d --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb new file mode 100644 index 0000000000..f451c3ed90 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb new file mode 100644 index 0000000000..519be6b6b3 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 8d29e1f78fe4b7cdcb06f5f789f676d5a5115d8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Jan 2016 17:57:09 +0200 Subject: [PATCH 0193/2133] add easyconfig CMake-3.4.1-intel-2016a.eb --- .../c/CMake/CMake-3.4.1-intel-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb new file mode 100644 index 0000000000..db841bbaef --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 3c13a535e38d244579ad9675fefd8a5bfbedfdb7 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 19 Jan 2016 17:04:49 +0100 Subject: [PATCH 0194/2133] Add velvet 1.2.10-intel-2015b --- .../v/Velvet/Velvet-1.2.10-intel-2015b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb new file mode 100644 index 0000000000..e7cf6bb7c1 --- /dev/null +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb @@ -0,0 +1,27 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Velvet' +version = '1.2.10' + +homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +description = """Sequence assembler for very short reads""" + + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%s_%s.tgz' % (name.lower(), version)] +source_urls = ['http://www.ebi.ac.uk/~zerbino/%s' % name.lower()] + +moduleclass = 'bio' + -- GitLab From 0a4ec86224cb865b311f9be2adb15a42a6b3bb8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Jan 2016 18:05:54 +0200 Subject: [PATCH 0195/2133] add easyconfig Boost-1.57.0-foss-2015b-Python-2.7.10.eb --- .../Boost-1.57.0-foss-2015b-Python-2.7.10.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..f89cb288d3 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.57.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 8fd1f03e903ffc479f69fefd241af961a402c141 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Jan 2016 17:16:25 +0100 Subject: [PATCH 0196/2133] style fixes --- easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb index e7cf6bb7c1..bc6b0ab068 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb @@ -16,12 +16,10 @@ version = '1.2.10' homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' description = """Sequence assembler for very short reads""" - toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s_%s.tgz' % (name.lower(), version)] -source_urls = ['http://www.ebi.ac.uk/~zerbino/%s' % name.lower()] +sources = ['%(namelower)s_%(version)s.tgz'] +source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] moduleclass = 'bio' - -- GitLab From 0ea4f7b95bdeca5509a5630d42848a33e0737c10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Jan 2016 17:20:33 +0100 Subject: [PATCH 0197/2133] sync with existing Velvet 1.2.10 easyconfigs (versionsuffix, default kmer) + update header --- ...15b.eb => Velvet-1.2.10-intel-2015b-mt-kmer_31.eb} | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/v/Velvet/{Velvet-1.2.10-intel-2015b.eb => Velvet-1.2.10-intel-2015b-mt-kmer_31.eb} (59%) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb similarity index 59% rename from easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb rename to easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb index bc6b0ab068..fff6a988ab 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb @@ -1,8 +1,9 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Cedric Laczny , Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute +# Authors:: Cedric Laczny , Fotis Georgatos , +# Thekla Loizou , Andreas Panteli # License:: MIT/GPL # $Id$ # @@ -12,14 +13,18 @@ name = 'Velvet' version = '1.2.10' +versionsuffix = '-mt-kmer_31' homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' description = """Sequence assembler for very short reads""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} sources = ['%(namelower)s_%(version)s.tgz'] source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] +# by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous +buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] + moduleclass = 'bio' -- GitLab From 01b47bbb2a57cc69786e33a23ce6dac6ea507205 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 11:57:14 +0100 Subject: [PATCH 0198/2133] add CMake as runtime dep for Instant, define and in Instant module file --- .../i/Instant/Instant-1.6.0-intel-2015b-Python-2.7.11.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.6.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/i/Instant/Instant-1.6.0-intel-2015b-Python-2.7.11.eb index 608ac917b3..a2476ddb2c 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.6.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.6.0-intel-2015b-Python-2.7.11.eb @@ -18,8 +18,15 @@ versionsuffix = '-Python-%s' % pyver dependencies = [ ('Python', pyver), ('SWIG', '3.0.8', versionsuffix), + ('CMake', '3.1.4'), # runtime dep! ] +# compiler-related variables *must* be set, since Instant does runtime compilation and remembers $CFLAGS/$CXXFLAGS +modextravars = { + 'CC': 'icc', + 'CXX': 'icpc', +} + pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], -- GitLab From dde8f9ce22d203708e36a73ab17b03e122fb7346 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 12:05:15 +0100 Subject: [PATCH 0199/2133] fix typo --- .../i/Instant/Instant-1.6.0-intel-2015b-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.6.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/i/Instant/Instant-1.6.0-intel-2015b-Python-2.7.11.eb index a2476ddb2c..84082aadb4 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.6.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.6.0-intel-2015b-Python-2.7.11.eb @@ -18,7 +18,7 @@ versionsuffix = '-Python-%s' % pyver dependencies = [ ('Python', pyver), ('SWIG', '3.0.8', versionsuffix), - ('CMake', '3.1.4'), # runtime dep! + ('CMake', '3.4.1'), # runtime dep! ] # compiler-related variables *must* be set, since Instant does runtime compilation and remembers $CFLAGS/$CXXFLAGS -- GitLab From 16d89f2dd07331523ce65d2f2e856cfe65144ff2 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 20 Jan 2016 12:48:45 +0100 Subject: [PATCH 0200/2133] Add SOAPdenovo2 based on intel2015b. This is based on the 2015a eb cfg. --- .../SOAPdenovo2-r240-intel-2015b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb new file mode 100644 index 0000000000..0df8fa5210 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb @@ -0,0 +1,40 @@ +# With <3 for EasyBuild +# +# EasyConfig for SOAPdenovo2: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = "MakeCp" + +name = 'SOAPdenovo2' +version = 'r240' + +homepage = 'http://soap.genomics.org.cn/index.html' +description = """SOAPdenovo is a novel short-read assembly method that can build a + de novo draft assembly for human-sized genomes. The program is specially designed to + assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. + SOAPdenovo2 is the successor of SOAPdenovo.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tgz'] + +patches = ['SOAPdenovo2-fix-unistd-includes.patch'] + +# parallel build is broken +maxparallel = 1 + +files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 01e61b469f6cb761e5709ea2803c21a1c36dcfe6 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 Jan 2016 14:50:03 +0100 Subject: [PATCH 0201/2133] patch corrected + intel version added --- .../r/RSEM/RSEM-1.2.26-intel-2015b.eb | 57 +++++++++++++++++++ .../r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch | 32 +++++------ 2 files changed, 73 insertions(+), 16 deletions(-) create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-intel-2015b.eb diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-intel-2015b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-intel-2015b.eb new file mode 100644 index 0000000000..c3eaea845a --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-intel-2015b.eb @@ -0,0 +1,57 @@ +easyblock = 'MakeCp' + +name = 'RSEM' +version = '1.2.26' + +homepage = 'http://deweylab.github.io/RSEM/' +description = """RNA-Seq by Expectation-Maximization)""" +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['RSEM-1.2.26_eb_provided_zlib.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +list_of_executables = [ + "rsem_perl_utils.pm", + "rsem-bam2readdepth", + "rsem-bam2wig", + "rsem-build-read-index", + "rsem-calculate-credibility-intervals", + "rsem-calculate-expression", + "rsem-control-fdr", + "rsem-extract-reference-transcripts", + "rsem-generate-data-matrix", + "rsem-generate-ngvector", + "rsem-gen-transcript-plots", + "rsem-get-unique", + "rsem-gff3-to-gtf", + "rsem-parse-alignments", + "rsem-plot-model", + "rsem-plot-transcript-wiggles", + "rsem-prepare-reference", + "rsem-preref", + "rsem-refseq-extract-primary-assembly", + "rsem-run-ebseq", + "rsem-run-em", + "rsem-run-gibbs", + "rsem-sam-validator", + "rsem-scan-for-paired-end-reads", + "rsem-simulate-reads", + "rsem-synthesis-reference-transcripts", + "rsem-tbam2gbam", +] + +files_to_copy = [(list_of_executables, "bin"), "WHAT_IS_NEW"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch index dcb5a208cd..c1f315d2d7 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26_eb_provided_zlib.patch @@ -6,9 +6,9 @@ -CC = g++ -CFLAGS = -Wall -c -I. -COFLAGS = -Wall -O3 -ffast-math -c -I. -+CXX = $(CXX) -+CFLAGS = -Wall -c -I. $(CFLAGS) -+COFLAGS = $(CXXFLAGS) -Wall -c -I. ++#CC = g++ ++#CFLAGS = -Wall -c -I. ++COFLAGS = ${CXXFLAGS} -Wall -c -I. PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads .PHONY : all ebseq clean @@ -26,11 +26,11 @@ rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp - $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts -+ $(CXX) -Wall $(CXXFLAGS) extractRef.cpp -o rsem-extract-reference-transcripts ++ $(CXX) -Wall ${CXXFLAGS} extractRef.cpp -o rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp - $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts -+ $(CXX) -Wall $(CXXFLAGS) synthesisRef.cpp -o rsem-synthesis-reference-transcripts ++ $(CXX) -Wall ${CXXFLAGS} synthesisRef.cpp -o rsem-synthesis-reference-transcripts BowtieRefSeqPolicy.h : RefSeqPolicy.h @@ -61,7 +61,7 @@ rsem-build-read-index : utils.h buildReadIndex.cpp - $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index -+ $(CXX) $(CXXFLAGS) buildReadIndex.cpp -o rsem-build-read-index ++ $(CXX) ${CXXFLAGS} buildReadIndex.cpp -o rsem-build-read-index simul.h : boost/random.hpp @@ -82,15 +82,15 @@ rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a - $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) $(CXXFLAGS) -Wall tbam2gbam.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall tbam2gbam.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp - $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) $(CXXFLAGS) -Wall bam2wig.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall bam2wig.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp - $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) $(CXXFLAGS) -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h - $(CC) $(COFLAGS) wiggle.cpp @@ -126,15 +126,15 @@ rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a - $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) $(CXXFLAGS) -Wall getUnique.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall getUnique.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a - $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) $(CXXFLAGS) -Wall samValidator.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall samValidator.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a - $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) $(CXXFLAGS) -Wall scanForPairedEndReads.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall scanForPairedEndReads.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ ebseq : cd EBSeq ; ${MAKE} all @@ -142,11 +142,11 @@ +++ sam/Makefile 2016-01-18 12:08:43.769066188 +0100 @@ -1,7 +1,7 @@ -CC= gcc -+CC= $(CC) ++#CC= gcc CFLAGS_EXTRA= #CFLAGS_EXTRA= -L/usr/include/ncurses -CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) -+CFLAGS= $(CFLAGS) $(CFLAGS_EXTRA) ++#CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib DFLAGS_EXTRA= #DFLAGS_EXTRA= -Dexpl=exp -Dlogl=log @@ -155,8 +155,8 @@ @@ -1,5 +1,5 @@ -CC= gcc -CFLAGS= -g -Wall -O2 #-m64 #-arch ppc -+CC= $(CC) -+CFLAGS= $(CFLAGS) ++#CC= gcc ++#CFLAGS= -g -Wall -O2 #-m64 #-arch ppc DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o OMISC= .. -- GitLab From 3bd0fa3952d634f0c1275c4ff19b054ae00480d1 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 20 Jan 2016 17:06:52 +0100 Subject: [PATCH 0202/2133] hanythingondemand 3.0.4 --- .../hanythingondemand-3.0.4-cli.eb | 42 +++++++++++++++++++ ...ndemand-3.0.4-intel-2015b-Python-2.7.10.eb | 35 ++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb new file mode 100644 index 0000000000..754319d620 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.0.4' +versionsuffix = '-cli' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) +dependencies = [ + ('pbs_python', '4.6.0'), + ('vsc-base', '2.4.2'), +] + +use_easy_install = True +zipped_egg = True + +# use 'hod' rather than 'hanythingondemand' in module name +modaltsoftname = 'hod' + +options = {'modulename': 'hod'} + +modextravars = { + # site-specific settings, hence commented out + # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) + #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # specify location on shared 'scratch' filesystem for HOD working directories + #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', +} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..a9eb0b66e9 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.0.4' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.10' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime +dependencies = [ + (python, pythonver), # provides netaddr, netifaces, mpi4py + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), + ('setuptools', '1.4.2', '', True), +] + +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'hod'} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' -- GitLab From 8575242ea8bb7d0074de3756081bfcc997fb8ee6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 18:15:34 +0200 Subject: [PATCH 0203/2133] add easyconfig make-4.1-GCC-4.9.2.eb --- .../easyconfigs/m/make/make-4.1-GCC-4.9.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..e061820bb1 --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.1' + +homepage = 'http://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +sources = ['make-%(version)s.tar.bz2'] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sanity_check_paths = { + 'files': ['bin/make'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 487635689eeb7bf76652267e1a82b6a41a57310f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 18:17:33 +0200 Subject: [PATCH 0204/2133] modify easyconfig make-4.1-GCC-4.9.2.eb --- easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb index e061820bb1..59504d7383 100644 --- a/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb @@ -15,6 +15,7 @@ easyblock = 'ConfigureMake' name = 'make' version = '4.1' +# Alan doens't like this homepage = 'http://www.gnu.org/software/make/make.html' description = "GNU version of make utility" -- GitLab From 3d2c80eb9608f635480ee5fbf46aac81b19b4644 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 21:29:42 +0100 Subject: [PATCH 0205/2133] move up 'toolchain', drop silly comment --- easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb index 59504d7383..083b66b471 100644 --- a/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb @@ -9,21 +9,19 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/ ## - easyblock = 'ConfigureMake' name = 'make' version = '4.1' -# Alan doens't like this homepage = 'http://www.gnu.org/software/make/make.html' description = "GNU version of make utility" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + sources = ['make-%(version)s.tar.bz2'] source_urls = [GNU_SOURCE] -toolchain = {'name': 'GCC', 'version': '4.9.2'} - sanity_check_paths = { 'files': ['bin/make'], 'dirs': [] -- GitLab From 6eabc55f2582cd44388151ad7dea998d3021e876 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 22:16:59 +0100 Subject: [PATCH 0206/2133] fix remark --- easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb index 083b66b471..bff321b4b2 100644 --- a/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb @@ -19,8 +19,8 @@ description = "GNU version of make utility" toolchain = {'name': 'GCC', 'version': '4.9.2'} -sources = ['make-%(version)s.tar.bz2'] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_BZ2] sanity_check_paths = { 'files': ['bin/make'], -- GitLab From d4699ef070ee177d4badd55f3b8476c0b2860646 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 23:34:17 +0200 Subject: [PATCH 0207/2133] add easyconfig Boost-1.59.0-intel-2016a-Python-2.7.11.eb --- .../Boost-1.59.0-intel-2016a-Python-2.7.11.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..df6d6d14c6 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.59.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.11' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 67759bbd3453b2905154afa620394bf98d99aca9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 23:42:18 +0200 Subject: [PATCH 0208/2133] add easyconfig GMP-6.1.0-foss-2016a.eb, add easyconfig Python-2.7.11-foss-2016a.eb, add easyconfig SQLite-3.9.2-foss-2016a.eb, add easyconfig Tcl-8.6.4-foss-2016a.eb, add easyconfig Tk-8.6.4-foss-2016a-no-X11.eb, add easyconfig bzip2-1.0.6-foss-2016a.eb, add easyconfig libreadline-6.3-foss-2016a.eb, add easyconfig ncurses-6.0-foss-2016a.eb, add easyconfig zlib-1.2.8-foss-2016a.eb --- .../b/bzip2/bzip2-1.0.6-foss-2016a.eb | 15 ++ .../easyconfigs/g/GMP/GMP-6.1.0-foss-2016a.eb | 26 ++++ .../libreadline/libreadline-6.3-foss-2016a.eb | 30 ++++ .../n/ncurses/ncurses-6.0-foss-2016a.eb | 34 +++++ .../p/Python/Python-2.7.11-foss-2016a.eb | 129 ++++++++++++++++++ .../s/SQLite/SQLite-3.9.2-foss-2016a.eb | 40 ++++++ .../easyconfigs/t/Tcl/Tcl-8.6.4-foss-2016a.eb | 25 ++++ .../t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb | 26 ++++ .../z/zlib/zlib-1.2.8-foss-2016a.eb | 22 +++ 9 files changed, 347 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016a.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016a.eb new file mode 100644 index 0000000000..4620787ebb --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016a.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2016a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2016a.eb new file mode 100644 index 0000000000..6816b3d777 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb new file mode 100644 index 0000000000..4d15c99139 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb new file mode 100644 index 0000000000..6029357e96 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb new file mode 100644 index 0000000000..4bce06c8fe --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -0,0 +1,129 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), +# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb new file mode 100644 index 0000000000..47bee4f624 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2016a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2016a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2016a.eb new file mode 100644 index 0000000000..3884765bf6 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb new file mode 100644 index 0000000000..6f98f7076c --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016a.eb new file mode 100644 index 0000000000..8e13f1aa09 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From fccc2f93d713e3a2212738c510b5ac2980c1c52f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 23:47:04 +0200 Subject: [PATCH 0209/2133] add easyconfig Bison-3.0.4-foss-2016a.eb, add easyconfig M4-1.4.17-foss-2016a.eb, add easyconfig flex-2.5.39-foss-2016a.eb, add easyconfig flex-2.6.0-foss-2016a.eb --- .../b/Bison/Bison-3.0.4-foss-2016a.eb | 22 ++++++++++++++++++ .../f/flex/flex-2.5.39-foss-2016a.eb | 14 +++++++++++ .../f/flex/flex-2.6.0-foss-2016a.eb | 16 +++++++++++++ .../easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb | 23 +++++++++++++++++++ 4 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2016a.eb new file mode 100644 index 0000000000..e479dbbdd8 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb new file mode 100644 index 0000000000..352bff8334 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb new file mode 100644 index 0000000000..13ec4d5ea6 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb new file mode 100644 index 0000000000..0d030e3264 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 756fe78aeb6b8470e62b8fcb88c90c1043bcd766 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 23:50:28 +0200 Subject: [PATCH 0210/2133] add easyconfig Perl-5.20.3-foss-2016a.eb --- .../p/Perl/Perl-5.20.3-foss-2016a.eb | 909 ++++++++++++++++++ 1 file changed, 909 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2016a.eb new file mode 100644 index 0000000000..0dbde8ec2c --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2016a.eb @@ -0,0 +1,909 @@ +name = 'Perl' +version = '5.20.3' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.58', { + 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('TAP::Harness::Env', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.021', { + 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '0.46', { + 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.93', { + 'source_tmpl': 'DateTime-TimeZone-1.93.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.22', { + 'source_tmpl': 'Try-Tiny-0.22.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Params::Validate', '1.21', { + 'source_tmpl': 'Params-Validate-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.20', { + 'source_tmpl': 'DateTime-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Module::Build', '0.4214', { + 'source_tmpl': 'Module-Build-0.4214.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Readonly', '2.00', { + 'source_tmpl': 'Readonly-2.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.27', { + 'source_tmpl': 'Tree-DAG_Node-1.27.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.48', { + 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.72', { + 'source_tmpl': 'Shell-0.72.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.47', { + 'source_tmpl': 'PathTools-3.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::WrapTie', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.40', { + 'source_tmpl': 'Test-Exception-0.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.11', { + 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.69', { + 'source_tmpl': 'URI-1.69.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.00', { + 'source_tmpl': 'Pod-POM-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.43', { + 'source_tmpl': 'Text-Diff-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.020', { + 'source_tmpl': 'IO-Socket-SSL-2.020.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Getopt::Long', '2.47', { + 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '0.117', { + 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.000002', { + 'source_tmpl': 'Moo-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.05', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.63', { + 'source_tmpl': 'Test-Differences-0.63.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.14', { + 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9912', { + 'source_tmpl': 'version-0.9912.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + # fails: uses 'gcc' + #('XML::Bare', '0.53', { + # 'source_tmpl': 'XML-Bare-0.53.tar.gz', + # 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + #}), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.30', { + 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.11', { + 'source_tmpl': 'AnyEvent-7.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0609', { + 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::Tester', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967012', { + 'source_tmpl': 'Parse-RecDescent-1.967012.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.36', { + 'source_tmpl': 'Carp-1.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.13', { + 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT'], + }), + ('Capture::Tiny', '0.30', { + 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('LWP', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000001', { + 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.19', { + 'source_tmpl': 'File-Which-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.39', { + 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.42', { + 'source_tmpl': 'Scalar-List-Utils-1.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('IO::Scalar', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.87', { + 'source_tmpl': 'Log-Handler-0.87.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Devel::StackTrace', '2.00', { + 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1603', { + 'source_tmpl': 'Moose-2.1603.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.33', { + 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9154', { + 'source_tmpl': 'CPANPLUS-0.9154.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Harness', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.04', { + 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.14', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' -- GitLab From 22f167ad1e078b117b6b89350fb2253e4b2638c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 23:52:45 +0200 Subject: [PATCH 0211/2133] add easyconfig CMake-3.4.1-foss-2016a.eb --- .../c/CMake/CMake-3.4.1-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb new file mode 100644 index 0000000000..87dc8ebec4 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 8d67798f64489917e52fc079d94ddf6f9099fdd0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Jan 2016 23:54:32 +0200 Subject: [PATCH 0212/2133] add easyconfig Boost-1.59.0-foss-2016a-Python-2.7.11.eb --- .../Boost-1.59.0-foss-2016a-Python-2.7.11.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.59.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..5a890ee8ea --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.59.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.11' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From e2fd16eeac3d7e38b582404122c1be5ff510689b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Jan 2016 12:44:55 +0200 Subject: [PATCH 0213/2133] add easyconfig Velvet-1.2.10-intel-2015b-mt-kmer_100.eb --- .../Velvet-1.2.10-intel-2015b-mt-kmer_100.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb new file mode 100644 index 0000000000..70b05647b0 --- /dev/null +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute +# Authors:: Cedric Laczny , Fotis Georgatos , +# Thekla Loizou , Andreas Panteli +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Velvet' +version = '1.2.10' +versionsuffix = '-mt-kmer_100' + +homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +description = """Sequence assembler for very short reads""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} + +sources = ['%(namelower)s_%(version)s.tgz'] +source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] + +buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] + +moduleclass = 'bio' -- GitLab From 46d5f0a1514aaf139e4672e19c6f02d82da4f4e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Jan 2016 13:34:41 +0100 Subject: [PATCH 0214/2133] use EggLib easyblock --- .../e/EggLib/EggLib-2.1.10-intel-2015b.eb | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb b/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb index 047574619d..c13f8036ed 100644 --- a/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb +++ b/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'EggLib' version = '2.1.10' @@ -19,18 +17,4 @@ dependencies = [ ('GSL', '2.1'), ] -# also install C++ part -prebuildopts = "cd %(builddir)s/egglib-cpp-%(version)s && ./configure --prefix=%(installdir)s && make && make install && " -# header files must be found when building Python library -prebuildopts += "cd %(builddir)s/egglib-py-%(version)s && CPATH=%(installdir)s/include LIBRARY_PATH=%(installdir)s/lib " - -keeppreviousinstall = True -preinstallopts = "cd %(builddir)s/egglib-py-%(version)s && CPATH=%(installdir)s/include " -installopts = "--install-lib %(installdir)s/lib/python2.7/site-packages --install-scripts %(installdir)s/bin" - -sanity_check_paths = { - 'files': ['bin/egglib', 'lib/libegglib-cpp.a'], - 'dirs': ['include/egglib-cpp', 'lib/python2.7/site-packages'], -} - moduleclass = 'bio' -- GitLab From 65bbcf0b27c194dbb4ac55365ead1bf16ee1e6cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Jan 2016 14:53:18 +0100 Subject: [PATCH 0215/2133] bump toolchain to intel/2016a --- ...-2015b.eb => EggLib-2.1.10-intel-2016a.eb} | 2 +- .../easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb | 19 +++++++++++++++++++ 2 files changed, 20 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/e/EggLib/{EggLib-2.1.10-intel-2015b.eb => EggLib-2.1.10-intel-2016a.eb} (89%) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb b/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2016a.eb similarity index 89% rename from easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb rename to easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2016a.eb index c13f8036ed..d32e7db616 100644 --- a/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2015b.eb +++ b/easybuild/easyconfigs/e/EggLib/EggLib-2.1.10-intel-2016a.eb @@ -4,7 +4,7 @@ version = '2.1.10' homepage = 'http://egglib.sourceforge.net/' description = """EggLib is a C++/Python library and program package for evolutionary genetics and genomics.""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [ diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb new file mode 100644 index 0000000000..4184830813 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.1' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, + special functions and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' -- GitLab From 44507a2f25fd4dad666f2019f984f8730ec7d812 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 21 Jan 2016 15:48:46 +0100 Subject: [PATCH 0216/2133] Use domspec in CHARMM --- .../c/CHARMM/CHARMM-37b2-intel-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb new file mode 100644 index 0000000000..518f529427 --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb @@ -0,0 +1,28 @@ +# Authors:: Ward Poelmans + +name = 'CHARMM' +version = '37b2' + +homepage = "http://www.charmm.org" +description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile +and widely used molecular simulation program with broad application to many-particle systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = ["c%(version)s.tar.gz"] + +patches = [ + "qmmm-pme-%(version)s.patch", + "use-xhost-%(version)s.patch", + "main-case-fix-%(version)s.patch", + 'CHARMM-37b2_fix-qgas-double-declared.patch', +] + +# MKL activated automatically when the ictce toolchain is used +build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" + +# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' -- GitLab From 42d1cef0e68315c9763200ac4618a0816efb66bb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 21 Jan 2016 16:32:50 +0100 Subject: [PATCH 0217/2133] Fix remarks --- .../c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb | 2 +- .../easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb | 2 +- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb | 6 +++--- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb | 6 +++--- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb | 4 ++-- 6 files changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb index 928c867d0a..2c1fee6bd7 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb @@ -18,7 +18,7 @@ patches = [ ] # FFTW will automatically be used because of the toolchain -build_options = "FULL COLFFT PIPF" +build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" # Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb index 3485ce9ee9..76ce2fdf5b 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb @@ -20,7 +20,7 @@ patches = [ ] # MKL activated automatically when the MKL is found, same for g09 -build_options = "FULL COLFFT PIPF" +build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" # Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb index 81f90923f0..89826fa9da 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb @@ -19,7 +19,7 @@ patches = [ ] # MKL activated automatically when the ictce toolchain is used -build_options = "FULL COLFFT PIPF" +build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" # Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb index 155eb5a8ae..2c9c3d3bc3 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb @@ -16,11 +16,11 @@ patches = [ "qmmm-pme-%(version)s.patch", "use-xhost-%(version)s.patch", "main-case-fix-%(version)s.patch", - 'CHARMM-37b2_fix-qgas-double-declared.patch', + 'CHARMM-%(version)s_fix-qgas-double-declared.patch', ] -# MKL activated automatically when the ictce toolchain is used -build_options = "FULL COLFFT PIPF" +# MKL activated automatically when the intel toolchain is used +build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" # Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb index 417f7a8785..537a0d5087 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb @@ -16,11 +16,11 @@ patches = [ "qmmm-pme-%(version)s.patch", "use-xhost-%(version)s.patch", "main-case-fix-%(version)s.patch", - 'CHARMM-37b2_fix-qgas-double-declared.patch', + 'CHARMM-%(version)s_fix-qgas-double-declared.patch', ] -# MKL activated automatically when the ictce toolchain is used -build_options = "FULL COLFFT PIPF" +# MKL activated automatically when the intel toolchain is used +build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" # Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb index 518f529427..c818c7a654 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb @@ -16,10 +16,10 @@ patches = [ "qmmm-pme-%(version)s.patch", "use-xhost-%(version)s.patch", "main-case-fix-%(version)s.patch", - 'CHARMM-37b2_fix-qgas-double-declared.patch', + 'CHARMM-%(version)s_fix-qgas-double-declared.patch', ] -# MKL activated automatically when the ictce toolchain is used +# MKL activated automatically when the intel toolchain is used build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" # Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce -- GitLab From 8a6266f8468d0c0d1c6606f13124db29d3085f39 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 21 Jan 2016 16:33:25 +0100 Subject: [PATCH 0218/2133] Spell fix --- .../easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb | 2 +- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb | 2 +- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb | 2 +- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb | 2 +- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb index 2c1fee6bd7..01ff6a2329 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb @@ -20,7 +20,7 @@ patches = [ # FFTW will automatically be used because of the toolchain build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" -# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +# Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb index 76ce2fdf5b..5a484cda95 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb @@ -22,7 +22,7 @@ patches = [ # MKL activated automatically when the MKL is found, same for g09 build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" -# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +# Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb index 89826fa9da..d7cd0f51f6 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb @@ -21,7 +21,7 @@ patches = [ # MKL activated automatically when the ictce toolchain is used build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" -# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +# Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb index 2c9c3d3bc3..894f7b2297 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb @@ -22,7 +22,7 @@ patches = [ # MKL activated automatically when the intel toolchain is used build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" -# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +# Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb index 537a0d5087..de51fe23be 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb @@ -22,7 +22,7 @@ patches = [ # MKL activated automatically when the intel toolchain is used build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" -# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +# Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb index c818c7a654..100fe61003 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb @@ -22,7 +22,7 @@ patches = [ # MKL activated automatically when the intel toolchain is used build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" -# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +# Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" moduleclass = 'chem' -- GitLab From 334f040ede6ea98174eea99093d5e6bef1aebac6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Jan 2016 17:53:04 +0200 Subject: [PATCH 0219/2133] add easyconfig matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb, add easyconfig libpng-1.6.21-intel-2016a.eb, add easyconfig freetype-2.6.2-intel-2016a.eb --- .../f/freetype/freetype-2.6.2-intel-2016a.eb | 22 +++++++++++++ .../l/libpng/libpng-1.6.21-intel-2016a.eb | 26 +++++++++++++++ ...plotlib-1.5.1-intel-2016a-Python-2.7.11.eb | 32 +++++++++++++++++++ 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb new file mode 100644 index 0000000000..ce2c31a36a --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2016a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2016a.eb new file mode 100644 index 0000000000..7ea89634eb --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' %(majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..192e60d3a1 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'matplotlib' +version = '1.5.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'vis' -- GitLab From 07aaa0202f7e46b6a3bba913a5bf3bb2c82b5980 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Jan 2016 18:02:40 +0200 Subject: [PATCH 0220/2133] add easyconfig PyYAML-3.11-intel-2016a-Python-2.7.11.eb, add easyconfig libyaml-0.1.6-intel-2016a.eb --- .../l/libyaml/libyaml-0.1.6-intel-2016a.eb | 28 +++++++++++++++++ .../PyYAML-3.11-intel-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016a.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016a.eb new file mode 100644 index 0000000000..c715793903 --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016a.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.1.6' + +homepage = 'http://pyyaml.org/wiki/LibYAML' +description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['yaml-%(version)s.tar.gz'] +source_urls = ['http://pyyaml.org/download/libyaml/'] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.%s" % SHLIB_EXT], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..b476753678 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.11' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('libyaml', '0.1.6'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/yaml' % pyshortver], +} + +moduleclass = 'lib' -- GitLab From aa8800ae1eb88551754f2da979fa10be34cad8eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Jan 2016 18:02:57 +0200 Subject: [PATCH 0221/2133] add easyconfig lxml-3.5.0-intel-2016a-Python-2.7.11.eb, add easyconfig libxml2-2.9.3-intel-2016a-Python-2.7.11.eb, add easyconfig libxslt-1.1.28-intel-2016a-Python-2.7.11.eb --- ...libxml2-2.9.3-intel-2016a-Python-2.7.11.eb | 28 +++++++++++++++++ ...ibxslt-1.1.28-intel-2016a-Python-2.7.11.eb | 25 ++++++++++++++++ .../lxml-3.5.0-intel-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 3 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..41e4fc099e --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pyver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..c1402800ba --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3', versionsuffix), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..76a6e93d59 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '3.5.0' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('libxml2', '2.9.3', versionsuffix), + ('libxslt', '1.1.28', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s' % pyshortver], +} + +moduleclass = 'lib' -- GitLab From e55e823924d7cfef43e6de0eef9ae45d0188a7b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Jan 2016 19:40:56 +0200 Subject: [PATCH 0222/2133] simplify/fix sanity check dir for lxml --- .../easyconfigs/l/lxml/lxml-3.5.0-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2016a-Python-2.7.11.eb index 76a6e93d59..e06da544f2 100644 --- a/easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2016a-Python-2.7.11.eb @@ -24,7 +24,7 @@ dependencies = [ sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pyshortver], + 'dirs': ['lib/python%s/site-packages' % pyshortver], } moduleclass = 'lib' -- GitLab From 6134c9bd20cb8203e22201ee5a2cd5d539a9e087 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Jan 2016 20:30:29 +0200 Subject: [PATCH 0223/2133] add easyconfig phonopy-1.10.1-intel-2016a-Python-2.7.11.eb --- ...honopy-1.10.1-intel-2016a-Python-2.7.11.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-1.10.1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.10.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.10.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..8ce0f20b14 --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.10.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '1.10.1' + +homepage = 'http://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('matplotlib', '1.5.1', versionsuffix), + ('lxml', '3.5.0', versionsuffix), + ('PyYAML', '3.11', versionsuffix), +] + + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s' % pyshortver], +} + +moduleclass = 'lib' -- GitLab From afcbcf13877fee7cdb69454c36d615cefbffb6cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Jan 2016 21:27:25 +0100 Subject: [PATCH 0224/2133] last minute bump of OpenMPI to 1.10.2 in foss/2016a --- easybuild/easyconfigs/f/foss/foss-2016a.eb | 2 +- easybuild/easyconfigs/g/gompi/gompi-2016a.eb | 2 +- .../OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb | 32 +++++++++++++++++++ 3 files changed, 34 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2016a.eb b/easybuild/easyconfigs/f/foss/foss-2016a.eb index 0846e47261..d0ff96c9d1 100644 --- a/easybuild/easyconfigs/f/foss/foss-2016a.eb +++ b/easybuild/easyconfigs/f/foss/foss-2016a.eb @@ -26,7 +26,7 @@ comp_mpi_tc = (comp_mpi_tc_name, version) # For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ ('GCC', gccver), - ('OpenMPI', '1.10.1', '', ('GCC', gccver)), + ('OpenMPI', '1.10.2', '', ('GCC', gccver)), (blaslib, blasver, blassuff, ('GCC', gccver)), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016a.eb b/easybuild/easyconfigs/g/gompi/gompi-2016a.eb index 00f9ed1bf1..793e78b5ef 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016a.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016a.eb @@ -14,7 +14,7 @@ gccver = '4.9.3-2.25' # compiler toolchain dependencies dependencies = [ ('GCC', gccver), # includes both GCC 4.9.3 and binutils 2.25 - ('OpenMPI', '1.10.1', '', ('GCC', gccver)), + ('OpenMPI', '1.10.2', '', ('GCC', gccver)), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..6afba2f292 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.11.2')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' -- GitLab From 808e5d1f1e922d920d7e38149cd3d000d684597d Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Aug 2015 23:04:57 -0400 Subject: [PATCH 0225/2133] Add easyconfig for PGI 15.7 using GCC 4.9.2 libraries. --- .../p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb diff --git a/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..7ec36c07ec --- /dev/null +++ b/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb @@ -0,0 +1,22 @@ +name = 'pgi' +version = '15.7' +year = '2015' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['pgilinux-'+year+'-%(version_major)s%(version_minor)s-x86_64.tar.gz'] + +gnu = 'GNU' +gnuver = '4.9.2-2.25' +versionsuffix = '-%s-%s' % (gnu, gnuver) + +dependencies = [(gnu, gnuver)] + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") + +moduleclass = 'compiler' -- GitLab From 34368a3d21deee22453ed2ccac582c754e830d06 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 7 Aug 2015 22:17:23 -0400 Subject: [PATCH 0226/2133] Incorporate comments from Kenneth Hoste in PGI easyconfig. --- easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb index 7ec36c07ec..7833cffa39 100644 --- a/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb @@ -1,13 +1,12 @@ name = 'pgi' version = '15.7' -year = '2015' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} -sources = ['pgilinux-'+year+'-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] gnu = 'GNU' gnuver = '4.9.2-2.25' -- GitLab From 72050f1fe6a60fea0bad013225ce5256895f18af Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 10 Sep 2015 15:25:10 -0400 Subject: [PATCH 0227/2133] Add pgi easyconfig for GNU-4.9.3-2.25 --- .../p/pgi/pgi-15.7-GNU-4.9.3-2.25.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..1d5241fd48 --- /dev/null +++ b/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +name = 'pgi' +version = '15.7' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] + +gnu = 'GNU' +gnuver = '4.9.3-2.25' +versionsuffix = '-%s-%s' % (gnu, gnuver) + +dependencies = [(gnu, gnuver)] + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") + +moduleclass = 'compiler' -- GitLab From d58005d08d558bdfd328dab90d3f975f77c32a4c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 21 Jan 2016 23:35:19 +0000 Subject: [PATCH 0228/2133] Add first version of R-3.2.3 incorporating work from Simon Thompson --- .../easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 400 ++++++++++++++++++ 1 file changed, 400 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb new file mode 100644 index 0000000000..25f244aa40 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -0,0 +1,400 @@ +name = 'R' +version = '3.2.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML +# ('GDAL', '2.0.1'), # for rgdal +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 21st 2016 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + #('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('Rmpi', '0.6-5', ext_options), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + #('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('geometry', '0.3-6', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.3', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.9', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2.1', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5.1', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-22', ext_options), + ('mime', '0.4', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.1', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.7-0', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-3', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.60.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('checkmate', '1.6.3', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-4', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.1', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.0.2', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.3-0', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringi', '1.0-1', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.8', ext_options), + ('logspline', '2.1.8', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.6-1', ext_options), + ('randomForest', '4.6-12', ext_options), + ('scatterplot3d', '0.3-36', ext_options), + ('SparseM', '1.7', ext_options), + ('tripack', '1.3-7', ext_options), + ('irace', '1.07', ext_options), + ('rJava', '0.9-7', ext_options), + ('lattice', '0.20-33', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-3', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.12.2', ext_options), + ('RcppArmadillo', '0.6.400.2.2', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.3', ext_options), + ('rlecuyer', '0.3-4', ext_options), + ('snow', '0.4-1', ext_options), + ('MASS', '7.3-45', ext_options), + ('tree', '1.0-36', ext_options), + ('pls', '2.5-0', ext_options), + ('class', '7.3-14', ext_options), + ('e1071', '1.6-7', ext_options), + ('nnet', '7.3-11', ext_options), + ('nlme', '3.1-122', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.5.1', ext_options), + ('MatrixModels', '0.4-1', ext_options), + ('quantreg', '5.19', ext_options), + ('mgcv', '1.8-10', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-5', ext_options), + ('sp', '1.2-1', ext_options), + ('zoo', '1.7-12', ext_options), + ('lmtest', '0.9-34', ext_options), + ('vcd', '1.4-1', ext_options), + ('snowfall', '1.84-6.1', ext_options), + ('rpart', '4.1-10', ext_options), + ('survival', '2.38-3', ext_options), + ('mice', '2.25', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-12', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-17', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.3', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.18-1', ext_options), + ('codetools', '0.2-14', ext_options), + ('foreach', '1.4.3', ext_options), + ('doMC', '1.3.4', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-66', ext_options), + ('gam', '1.12', ext_options), + ('gamlss.data', '4.3-2', ext_options), + ('gamlss.dist', '4.3-5', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-0', ext_options), + ('quantmod', '0.4-5', ext_options), + ('mnormt', '1.5-3', ext_options), + ('mvtnorm', '1.0-3', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.1', ext_options), + ('prodlim', '1.5.7', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-4', ext_options), + ('sfsmisc', '1.0-28', ext_options), + ('spatial', '7.3-11', ext_options), + ('VGAM', '1.0-0', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.8-0', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.12', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.2.5', ext_options), + ('R.utils', '2.2.0', ext_options), + ('R.matlab', '3.3.0', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-1', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('reshape2', '1.4.1', ext_options), + ('gtable', '0.1.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.3.0', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '2.0.0', ext_options), + ('gridExtra', '2.0.0', ext_options), + ('Hmisc', '3.17-1', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-47', ext_options), + ('data.table', '1.9.6', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.10', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '2.0.0', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.13', ext_options), + ('ape', '3.4', ext_options), + ('htmltools', '0.3', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.17.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.3', ext_options), + ('R6', '2.1.1', ext_options), + ('jsonlite', '0.9.19', ext_options), + ('rjson', '0.2.15', ext_options), + ('shiny', '0.12.2', ext_options), + ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), + ('spdep', '0.5-92', ext_options), + ('assertthat', '0.1', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.3', ext_options), + ('adegenet', '2.0.0', ext_options), + ('rncl', '0.6.0', ext_options), + ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('praise', '1.0.0', ext_options), + ('testthat', '0.11.0', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.11', ext_options), + ('rmarkdown', '0.9.2', ext_options), + ('curl', '0.9.4', ext_options), + ('httr', '1.0.0', ext_options), + ('reshape', '0.8.5', ext_options), + ('bold', '0.3.0', ext_options), + ('taxize', '0.7.0', ext_options), + ('tidyr', '0.3.1', ext_options), + ('uuid', '0.1-2', ext_options), + ('RNeXML', '2.0.5', ext_options), + ('phylobase', '0.8.0', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.4', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), +# ('synchronicity', '1.1.9', ext_options), + ('bigmemory', '4.5.8', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.5-2', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.999-0', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.3-6', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.6', ext_options), + ('glmnet', '2.0-2', ext_options), + ('rgl', '0.95.1441', ext_options), + ('labdsv', '1.7-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.5-0', ext_options), + ('msm', '1.6', ext_options), + ('nor1mix', '1.2-1', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('polspline', '1.1.12', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-1', ext_options), + ('rms', '4.4-1', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6-2', ext_options), + ('TraMineR', '1.8-11', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-5', ext_options), + ('statmod', '1.4.23', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.3-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('optparse', '1.3.2', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '1.0.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.50.1', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-10', ext_options), + ('pbkrtest', '0.4-4', ext_options), + ('car', '2.1-1', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.31.4', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-10', ext_options), + ('BiasedUrn', '1.07', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '1.1', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.9.1', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.1.3', ext_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('VennDiagram', '1.6.16', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-2', ext_options), + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.8-37', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.44-1', ext_options), +# ('rgdal', '1.1-3', ext_options), +# ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.8.8', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-4', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), + ('SuperLearner', '2.0-15', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('caret', '6.0-64', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.6', ext_options), + ('ggvis', '0.4.2', ext_options), + ('mlr', '2.7', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-7', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.10', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.2', ext_options), +] + +moduleclass = 'lang' -- GitLab From f7d1eaea9b0dc54da38cf8f3d5305b3effbada4d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 21 Jan 2016 23:39:30 +0000 Subject: [PATCH 0229/2133] Add Java 1.8u72, required by R-3.2.3 --- easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb new file mode 100644 index 0000000000..1c2b638642 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb @@ -0,0 +1,41 @@ +# Built with EasyBuild version 2.5.0 on 2016-01-21_18-39-33 +name = 'Java' +version = "1.8.0_72" + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.5.0", + "easybuild-easyblocks_version": "2.5.0", + "timestamp": 1453401573, + "build_time": 7.9, + "install_size": 366003609, + "command_line": ['--buildpath=/tmp/centos', '--configfiles=/opt/soft/apps/EasyBuild/easybuild.cfg', '--installpath=/opt/soft', '--module-syntax=Lua', '--modules-tool=Lmod', '--repositorypath=/opt/soft/ebfiles', '--robot=/opt/soft/ebfiles:/opt/soft/apps/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs', '--robot-paths=/opt/soft/ebfiles:', '--sourcepath=/opt/soft/source', '--subdir-software=apps', '--tmp-logdir=/tmp/centos', '--tmpdir=/tmp/centos', '--try-software-version=1.8.0_72', 'Java-1.8.0_66.eb'], + "modules_tool": ('Lmod', '/opt/soft/apps/lmod/lmod/libexec/lmod', '6.0.9'), + "core_count": 16, + "cpu_model": "Intel Xeon E312xx (Sandy Bridge)", + "cpu_speed": 2399.998, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper; Target: x86_64-redhat-linux; Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux; Thread model: posix; gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC) ; ", + "glibc_version": "2.17", + "hostname": "easybuild-6.novalocal", + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.2.1511", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 20 2015, 02:00:19) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]", + "system_gcc_path": "/usr/bin/gcc", + "system_python_path": "/usr/bin/python", +}] -- GitLab From 611a73f4d63009e5e5ba5e3784865d5677da79ee Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 21 Jan 2016 20:09:58 -0500 Subject: [PATCH 0230/2133] PGI: fix capitalization --- .../PGI-15.7-GNU-4.9.2-2.25.eb} | 2 +- .../PGI-15.7-GNU-4.9.3-2.25.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/{pgi/pgi-15.7-GNU-4.9.2-2.25.eb => PGI/PGI-15.7-GNU-4.9.2-2.25.eb} (97%) rename easybuild/easyconfigs/p/{pgi/pgi-15.7-GNU-4.9.3-2.25.eb => PGI/PGI-15.7-GNU-4.9.3-2.25.eb} (97%) diff --git a/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb similarity index 97% rename from easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb rename to easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb index 7833cffa39..d3260f31f8 100644 --- a/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb @@ -1,4 +1,4 @@ -name = 'pgi' +name = 'PGI' version = '15.7' homepage = 'http://www.pgroup.com/' diff --git a/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb similarity index 97% rename from easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.3-2.25.eb rename to easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb index 1d5241fd48..6589eba972 100644 --- a/easybuild/easyconfigs/p/pgi/pgi-15.7-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -name = 'pgi' +name = 'PGI' version = '15.7' homepage = 'http://www.pgroup.com/' -- GitLab From f3210f5da70f8dbb56f51fa4f3606875e04a578b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 22 Jan 2016 10:16:42 +0000 Subject: [PATCH 0231/2133] Remove unnecessary parts, as per PR 2364 comments --- easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb index 1c2b638642..9d370ddcef 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.5.0 on 2016-01-21_18-39-33 name = 'Java' version = "1.8.0_72" @@ -14,28 +13,3 @@ altver = '%su%s' % (vp.split('.')[1], vs) sources = ['jdk-%s-linux-x64.tar.gz' % altver] moduleclass = 'lang' - -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.5.0", - "easybuild-easyblocks_version": "2.5.0", - "timestamp": 1453401573, - "build_time": 7.9, - "install_size": 366003609, - "command_line": ['--buildpath=/tmp/centos', '--configfiles=/opt/soft/apps/EasyBuild/easybuild.cfg', '--installpath=/opt/soft', '--module-syntax=Lua', '--modules-tool=Lmod', '--repositorypath=/opt/soft/ebfiles', '--robot=/opt/soft/ebfiles:/opt/soft/apps/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs', '--robot-paths=/opt/soft/ebfiles:', '--sourcepath=/opt/soft/source', '--subdir-software=apps', '--tmp-logdir=/tmp/centos', '--tmpdir=/tmp/centos', '--try-software-version=1.8.0_72', 'Java-1.8.0_66.eb'], - "modules_tool": ('Lmod', '/opt/soft/apps/lmod/lmod/libexec/lmod', '6.0.9'), - "core_count": 16, - "cpu_model": "Intel Xeon E312xx (Sandy Bridge)", - "cpu_speed": 2399.998, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper; Target: x86_64-redhat-linux; Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux; Thread model: posix; gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC) ; ", - "glibc_version": "2.17", - "hostname": "easybuild-6.novalocal", - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.2.1511", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 20 2015, 02:00:19) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]", - "system_gcc_path": "/usr/bin/gcc", - "system_python_path": "/usr/bin/python", -}] -- GitLab From b2918c22540eb531f1a017754e880cc959df7b3f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 22 Jan 2016 10:20:14 +0000 Subject: [PATCH 0232/2133] Re-enabled GDAL and related extensions --- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index 25f244aa40..b8b4f7fc7c 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -24,7 +24,7 @@ dependencies = [ ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl ('libxml2', '2.9.2'), # for XML -# ('GDAL', '2.0.1'), # for rgdal + ('GDAL', '2.0.1'), # for rgdal ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -371,8 +371,8 @@ exts_list = [ ('polyclip', '1.3-2', ext_options), ('goftest', '1.0-3', ext_options), ('spatstat', '1.44-1', ext_options), -# ('rgdal', '1.1-3', ext_options), -# ('gdalUtils', '2.0.1.7', ext_options), + ('rgdal', '1.1-3', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), ('pracma', '1.8.8', ext_options), ('RCurl', '1.95-4.7', ext_options), ('bio3d', '2.2-4', ext_options), -- GitLab From 31e8dbc901016cca666b8a0b4985bdad88d268e5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 22 Jan 2016 10:22:37 +0000 Subject: [PATCH 0233/2133] Re-enable synchronicity --- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index b8b4f7fc7c..4b3bbee5c5 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -278,7 +278,7 @@ exts_list = [ ('adephylo', '1.1-6', ext_options), ('animation', '2.4', ext_options), ('bigmemory.sri', '0.1.3', ext_options), -# ('synchronicity', '1.1.9', ext_options), + ('synchronicity', '1.1.9', ext_options), ('bigmemory', '4.5.8', ext_options), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), -- GitLab From a808ad8f0ac188e7efba6a26aceebdb9712c0fff Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 22 Jan 2016 11:24:57 +0100 Subject: [PATCH 0234/2133] pinned version for intel --- easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb | 1 + easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb index eb0449a963..5ee5f118a3 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-intel/5.2.82', EXTERNAL_MODULE), + ('intel/15.0.1.133', EXTERNAL_MODULE), ('craype/2.4.0', EXTERNAL_MODULE), ('cray-libsci/13.0.4', EXTERNAL_MODULE), ('cray-mpich/7.2.2', EXTERNAL_MODULE), diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb index 1ae0fb83c7..7846b2d7c5 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-intel/5.2.82', EXTERNAL_MODULE), + ('intel/15.0.1.133', EXTERNAL_MODULE), ('craype/2.4.2', EXTERNAL_MODULE), ('cray-libsci/13.2.0', EXTERNAL_MODULE), ('cray-mpich/7.2.6', EXTERNAL_MODULE), -- GitLab From e901191050988401a105bb3f6ccc464a61c115ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Jan 2016 13:38:37 +0200 Subject: [PATCH 0235/2133] add easyconfig BoltzTraP-1.2.5-intel-2016a.eb --- .../BoltzTraP/BoltzTraP-1.2.5-intel-2016a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/BoltzTraP/BoltzTraP-1.2.5-intel-2016a.eb diff --git a/easybuild/easyconfigs/b/BoltzTraP/BoltzTraP-1.2.5-intel-2016a.eb b/easybuild/easyconfigs/b/BoltzTraP/BoltzTraP-1.2.5-intel-2016a.eb new file mode 100644 index 0000000000..db484f3beb --- /dev/null +++ b/easybuild/easyconfigs/b/BoltzTraP/BoltzTraP-1.2.5-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'BoltzTraP' +version = '1.2.5' + +homepage = 'http://www.icams.de/content/departments/cmat/boltztrap/' +description = """Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport + coefficients.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# download from http://www.icams.de/content/uploads/boltztrap/BoltzTraP.tar.bz2, and rename to include version +sources = [SOURCE_TAR_BZ2] +checksums = ['6623d4393bce2e178b073f75f283eee6'] + +skipsteps = ['configure'] + +start_dir = 'src' +parallel = 1 +buildopts = 'FC="${FC}" FOPT="$FFLAGS" LIBS="$LIBLAPACK"' + +files_to_copy = [(['BoltzTraP'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/BoltzTraP'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From d21c973e4eaed7b66f589fa29b7ce8d42c444ed8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 22 Jan 2016 12:19:01 +0000 Subject: [PATCH 0236/2133] Add GDAL 2.0.1 for foss-2015b --- .../g/GDAL/GDAL-2.0.1-foss-2015b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb new file mode 100644 index 0000000000..f602285a99 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.1' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.3.3.1'), + ('expat', '2.1.0'), + ('libxml2', '2.9.2'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' -- GitLab From 6a69cfee3e7899af9224f89f14b4542e3cf8a857 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 22 Jan 2016 14:03:56 +0100 Subject: [PATCH 0237/2133] Don't use DOMSPEC in non-mpi builds --- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb index 5a484cda95..18d4e7d4ab 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb @@ -20,7 +20,7 @@ patches = [ ] # MKL activated automatically when the MKL is found, same for g09 -build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" +build_options = "FULL COLFFT PIPF" # Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" -- GitLab From 960db19d07bf6ca8ee2597cfbfba79c309a3f9e4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 22 Jan 2016 15:00:20 +0000 Subject: [PATCH 0238/2133] Fix typo in foss toolchain version --- easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb index f602285a99..99a0b765d4 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb @@ -9,7 +9,7 @@ description = """GDAL is a translator library for raster geospatial data formats to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'foss', 'version': '2015b'} source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] sources = [SOURCELOWER_TAR_XZ] -- GitLab From d225cc745139083b70d971e97fa53df314a21ef1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 22 Jan 2016 15:02:32 +0000 Subject: [PATCH 0239/2133] Remove irrelevant Intel compiler patch references --- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index 4b3bbee5c5..13055be87d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -54,11 +54,10 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - #('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('Rmpi', '0.6-5', ext_options), ('Rmpi', '0.6-5', ext_options), ('abind', '1.4-3', ext_options), ('magic', '1.5-6', ext_options), - #('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), ('geometry', '0.3-6', ext_options), ('bit', '1.1-12', ext_options), ('filehash', '2.3', ext_options), -- GitLab From 57ed1da00980d5ceeba80fb4c01c30023aaaafe3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 22 Jan 2016 16:33:44 +0000 Subject: [PATCH 0240/2133] Add GDAL and deps for R-3.2.3 foss 2015b --- .../b/Bison/Bison-3.0.4-foss-2015b.eb | 22 ++++++++++++ .../c/cURL/cURL-7.45.0-foss-2015b.eb | 31 +++++++++++++++++ .../d/Doxygen/Doxygen-1.8.10-foss-2015b.eb | 19 +++++++++++ .../e/expat/expat-2.1.0-foss-2015b.eb | 16 +++++++++ .../g/GDAL/GDAL-2.0.1-foss-2015b.eb | 1 + .../h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb | 23 +++++++++++++ .../easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb | 23 +++++++++++++ .../n/netCDF/netCDF-4.3.3.1-foss-2015b.eb | 34 +++++++++++++++++++ .../easyconfigs/s/Szip/Szip-2.1-foss-2015b.eb | 23 +++++++++++++ 9 files changed, 192 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2015b.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.45.0-foss-2015b.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-foss-2015b.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015b.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2015b.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2015b.eb new file mode 100644 index 0000000000..5555d066b8 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2015b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.45.0-foss-2015b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.45.0-foss-2015b.eb new file mode 100644 index 0000000000..dad17a3944 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.45.0-foss-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.45.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-foss-2015b.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-foss-2015b.eb new file mode 100644 index 0000000000..2185cbf1af --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-foss-2015b.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.10' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.1'), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015b.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015b.eb new file mode 100644 index 0000000000..f7e3a65441 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015b.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb index 99a0b765d4..304e10cc99 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015b.eb @@ -10,6 +10,7 @@ description = """GDAL is a translator library for raster geospatial data formats data translation and processing.""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'usempi': True} source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] sources = [SOURCELOWER_TAR_XZ] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb new file mode 100644 index 0000000000..8b6038c4ee --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.15-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb new file mode 100644 index 0000000000..b66775c7a6 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015b.eb new file mode 100644 index 0000000000..d5f3ba2170 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.3.3.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.15-patch1'), + ('cURL', '7.45.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.10'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2015b.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2015b.eb new file mode 100644 index 0000000000..ecef46c63a --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2015b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 33143a486f7f845179ace7393a8cd041f56a00c3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 22 Jan 2016 17:03:30 +0000 Subject: [PATCH 0241/2133] Fix incorrect cURL dep --- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index 13055be87d..b1f4627e3f 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -22,7 +22,7 @@ dependencies = [ ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk - ('cURL', '7.43.0'), # for RCurl + ('cURL', '7.45.0'), # for RCurl ('libxml2', '2.9.2'), # for XML ('GDAL', '2.0.1'), # for rgdal ] -- GitLab From 667085e1f13217af9f2346fb5d82bcfe4451697a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 23 Jan 2016 00:06:31 +0100 Subject: [PATCH 0242/2133] don't hardcode toolchain for Autotools build dep --- .../a/Autoconf/Autoconf-2.69-foss-2015a.eb | 25 ++++++++++++++ .../a/Autoconf/Autoconf-2.69-intel-2015b.eb | 25 ++++++++++++++ .../a/Automake/Automake-1.15-GCC-4.7.2.eb | 33 +++++++++++++++++++ .../a/Automake/Automake-1.15-foss-2015a.eb | 33 +++++++++++++++++++ .../a/Automake/Automake-1.15-intel-2015b.eb | 33 +++++++++++++++++++ .../Autotools/Autotools-20150215-GCC-4.7.2.eb | 17 ++++++++++ .../Autotools/Autotools-20150215-GCC-4.8.4.eb | 17 ++++++++++ .../Autotools-20150215-foss-2015a.eb | 17 ++++++++++ .../Autotools-20150215-intel-2015b.eb | 17 ++++++++++ .../easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb | 2 +- .../g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb | 2 +- .../g/GMP/GMP-6.0.0a-foss-2015a.eb | 2 +- .../g/GMP/GMP-6.0.0a-intel-2015b.eb | 2 +- .../g/GMP/GMP-6.1.0-GCC-4.9.3-2.25.eb | 4 +++ .../easyconfigs/g/GMP/GMP-6.1.0-foss-2016a.eb | 4 +++ .../g/GMP/GMP-6.1.0-intel-2015b.eb | 4 +++ .../g/GMP/GMP-6.1.0-intel-2016a.eb | 4 +++ .../l/libtool/libtool-2.4.6-GCC-4.7.2.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-GCC-4.8.4.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-foss-2015a.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-intel-2015b.eb | 17 ++++++++++ .../easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb | 23 +++++++++++++ 25 files changed, 331 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015a.eb create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015b.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.7.2.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015a.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.7.2.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015b.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015a.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015a.eb new file mode 100644 index 0000000000..1001ba837c --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically + configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like + systems without manual user intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015b.eb new file mode 100644 index 0000000000..801b643ac0 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically + configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like + systems without manual user intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb new file mode 100644 index 0000000000..05705b029e --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCC', 'version': '4.7.2'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb new file mode 100644 index 0000000000..7303c3d70e --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb new file mode 100644 index 0000000000..8a059d28e6 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.7.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.7.2.eb new file mode 100644 index 0000000000..7f04debe9c --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.7.2.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GCC', 'version': '4.7.2'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.8.4.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.8.4.eb new file mode 100644 index 0000000000..357867c586 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.8.4.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015a.eb new file mode 100644 index 0000000000..6a68f164a9 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015a.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015b.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015b.eb new file mode 100644 index 0000000000..7677218c94 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015b.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb index 864ca72292..ebcf354128 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb @@ -13,7 +13,7 @@ sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215'), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb index 3eda44f8a9..f6165358fa 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb @@ -13,7 +13,7 @@ sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215'), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb index 9bccbc6b38..0ea694664d 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb @@ -13,7 +13,7 @@ sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215'), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb index c570e2437e..d4d4addc7c 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb @@ -13,7 +13,7 @@ sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215'), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb index af8067c083..3328cb4883 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb @@ -13,7 +13,7 @@ sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215'), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb index 09a8825768..70ef38387d 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215'), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb index 9c4dc8d9de..1497e83746 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = [GNU_SOURCE] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215'), ] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-GCC-4.9.3-2.25.eb index e1c0c0929d..3a35abe64e 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-GCC-4.9.3-2.25.eb @@ -13,6 +13,10 @@ toolchainopts = {'pic': True, 'precise': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] +builddependencies = [ + ('Autotools', '20150215'), +] + # enable C++ interface configopts = '--enable-cxx' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2016a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2016a.eb index 6816b3d777..5a43c93bf3 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2016a.eb @@ -13,6 +13,10 @@ toolchainopts = {'pic': True, 'precise': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] +builddependencies = [ + ('Autotools', '20150215'), +] + # enable C++ interface configopts = '--enable-cxx' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2015b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2015b.eb index 04e471f0d6..531c5382b9 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2015b.eb @@ -13,6 +13,10 @@ toolchainopts = {'pic': True, 'precise': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] +builddependencies = [ + ('Autotools', '20150215'), +] + # enable C++ interface configopts = '--enable-cxx' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016a.eb index c8ded809f8..c0c58b69fb 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016a.eb @@ -13,6 +13,10 @@ toolchainopts = {'pic': True, 'precise': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] +builddependencies = [ + ('Autotools', '20150215'), +] + # enable C++ interface configopts = '--enable-cxx' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.7.2.eb new file mode 100644 index 0000000000..45aff7a013 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.7.2.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCC', 'version': '4.7.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.8.4.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.8.4.eb new file mode 100644 index 0000000000..e93fcc4049 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.8.4.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015a.eb new file mode 100644 index 0000000000..d420dbd013 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015a.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015b.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015b.eb new file mode 100644 index 0000000000..f1364b279c --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015b.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb new file mode 100644 index 0000000000..b62284872a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCC', 'version': '4.7.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 4ae7345b8bd9f98b2b73662366c8ee35523cc357 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 23 Jan 2016 00:42:02 +0100 Subject: [PATCH 0243/2133] add missing easyconfigs --- .../Autoconf/Autoconf-2.69-GCC-4.9.3-2.25.eb | 26 +++++++++++++++ .../a/Autoconf/Autoconf-2.69-foss-2016a.eb | 26 +++++++++++++++ .../a/Autoconf/Autoconf-2.69-intel-2016a.eb | 26 +++++++++++++++ .../Automake/Automake-1.15-GCC-4.9.3-2.25.eb | 33 +++++++++++++++++++ .../a/Automake/Automake-1.15-foss-2016a.eb | 33 +++++++++++++++++++ .../a/Automake/Automake-1.15-intel-2016a.eb | 33 +++++++++++++++++++ .../Autotools-20150215-GCC-4.9.3-2.25.eb | 17 ++++++++++ .../Autotools-20150215-foss-2016a.eb | 17 ++++++++++ .../Autotools-20150215-intel-2016a.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-GCC-4.9.3-2.25.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-foss-2016a.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-intel-2016a.eb | 17 ++++++++++ .../m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb | 23 +++++++++++++ 13 files changed, 302 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016a.eb create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016a.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016a.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..1ea18e5a7c --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.9.3-2.25.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016a.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016a.eb new file mode 100644 index 0000000000..34de43acd4 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016a.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016a.eb new file mode 100644 index 0000000000..9014da6c86 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..a37c1d9e3b --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb new file mode 100644 index 0000000000..f73c4759ee --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb new file mode 100644 index 0000000000..06fbc9d74b --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..8870d76965 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016a.eb new file mode 100644 index 0000000000..a07bbf4e25 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016a.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016a.eb new file mode 100644 index 0000000000..0810dfe536 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016a.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..d4e8dd2add --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016a.eb new file mode 100644 index 0000000000..d14a6fa24f --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016a.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016a.eb new file mode 100644 index 0000000000..f2ac301f56 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016a.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..0fa72c61c9 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 792c069e7c3482444ac19c589f66f7f0db684f12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 23 Jan 2016 09:52:10 +0100 Subject: [PATCH 0244/2133] fix version conflict on M4 --- easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.7.2.eb index 45aff7a013..81c5e4cf65 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-4.7.2.eb @@ -12,6 +12,6 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -dependencies = [('M4', '1.4.17')] +dependencies = [('M4', '1.4.16')] moduleclass = 'lib' -- GitLab From 5e9d08817d5d6c13f9f40d95e0d5444442f441cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 23 Jan 2016 14:15:01 +0200 Subject: [PATCH 0245/2133] add easyconfig binutils-2.25.1.eb --- .../easyconfigs/b/binutils/binutils-2.25.1.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb new file mode 100644 index 0000000000..6e4fce3123 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25.1' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), +] + +# statically link with zlib, to avoid runtime dependency on zlib +# further, add the system library path in the rpath: this should 'harden' the +# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' +prebuildopts = preconfigopts + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 9a024f5881e7857ff63039249bd81d7e80877748 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Sat, 23 Jan 2016 11:34:22 -0500 Subject: [PATCH 0246/2133] Add easyconfig for PGI 15.10 using GCCcore 4.9.3. --- .../p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..e722b3a3d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '15.10' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['cae307f7ad467a1811a5d5da758048ab'] + +gccver = '4.9.3' +binutilsver = '2.25' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") + +moduleclass = 'compiler' -- GitLab From bdfae8049e6adad2cbd79ddc837562001db1cf1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 23 Jan 2016 20:40:41 +0100 Subject: [PATCH 0247/2133] fix easyconfig filename for MACS2 --- ...2.7.3.eb => MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MACS2/{MACS2-2.1.0-20150731-goolf-1.4.10-Python-2.7.3.eb => MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb} (100%) diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0-20150731-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/MACS2/MACS2-2.1.0-20150731-goolf-1.4.10-Python-2.7.3.eb rename to easybuild/easyconfigs/m/MACS2/MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb -- GitLab From a223aa534e4f98cccea010a250cf3b5d743bc29b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 23 Jan 2016 23:22:26 +0200 Subject: [PATCH 0248/2133] add easyconfig mympingpong-0.7.0-intel-2015b-Python-2.7.10.eb, add easyconfig matplotlib-1.5.1-intel-2015b-Python-2.7.10.eb, add easyconfig freetype-2.6.2-intel-2015b.eb, add easyconfig libpng-1.6.21-intel-2015b.eb --- .../f/freetype/freetype-2.6.2-intel-2015b.eb | 22 ++++++++++++ .../l/libpng/libpng-1.6.21-intel-2015b.eb | 26 ++++++++++++++ ...plotlib-1.5.1-intel-2015b-Python-2.7.10.eb | 32 +++++++++++++++++ ...ingpong-0.7.0-intel-2015b-Python-2.7.10.eb | 36 +++++++++++++++++++ 4 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb new file mode 100644 index 0000000000..0811253154 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb new file mode 100644 index 0000000000..b76c98f402 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' %(majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..e3cf47e553 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'matplotlib' +version = '1.5.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +pyver = '2.7.10' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..dc119b0460 --- /dev/null +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'mympingpong' +version = '0.7.0' + +homepage = 'https://github.com/hpcugent/mympingpong' +description = """A mpi4py based random pair pingpong network stress test.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.10' +versionsuffix = '-Python-%s' % pyver + +vsc_base_ver = '2.4.16' + +dependencies = [ + ('Python', pyver), + ('vsc-base', vsc_base_ver, versionsuffix), + ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-%s' % vsc_base_ver), + ('matplotlib', '1.5.1', versionsuffix), + ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.15-patch1'), + ('mpi4py', '1.3.1', versionsuffix + '-timed-pingpong'), +] + +options = {'modulename': 'vsc.mympingpong'} + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/mympingpong', 'bin/mympingponganalysis'], + 'dirs': ['lib/python%(pyver)s/site-packages/mympingpong-%%(version)s-py%(pyver)s.egg' % {'pyver': pyshortver}], +} + +moduleclass = 'perf' -- GitLab From 506ad994637671131b59b38b829f14a10431f74f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 23 Jan 2016 22:43:17 +0000 Subject: [PATCH 0249/2133] Disable synchronicity owing to new Boost dep --- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index b1f4627e3f..4d294b2bb3 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -277,7 +277,8 @@ exts_list = [ ('adephylo', '1.1-6', ext_options), ('animation', '2.4', ext_options), ('bigmemory.sri', '0.1.3', ext_options), - ('synchronicity', '1.1.9', ext_options), + #Moved to separate easyconfig owing to new Boost dep + #('synchronicity', '1.1.9', ext_options), ('bigmemory', '4.5.8', ext_options), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), -- GitLab From f83f6e80135c56bcc1cbbf9d01692a62d31550b0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 24 Jan 2016 10:26:55 +0000 Subject: [PATCH 0250/2133] Add PROJ for foss 2015b, needed by rgdal/GDAL --- .../p/PROJ/PROJ-4.8.0-foss-2015b.eb | 56 +++++++++++++++++++ .../easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 1 + 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb new file mode 100644 index 0000000000..7121f9c66c --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb @@ -0,0 +1,56 @@ +# Built with EasyBuild version 2.5.0 on 2016-01-24_10-09-18 +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.8.0' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.5.0", + "easybuild-easyblocks_version": "2.5.0", + "timestamp": 1453630158, + "build_time": 21.19, + "install_size": 3603179, + "command_line": ['--buildpath=/tmp/centos', '--configfiles=/opt/soft/apps/EasyBuild/easybuild.cfg', '--debug', '--installpath=/opt/soft', '--module-syntax=Lua', '--modules-tool=Lmod', '--repositorypath=/opt/soft/ebfiles', '--robot=/opt/soft/apps/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs', '--sourcepath=/opt/soft/source', '--subdir-software=apps', '--tmp-logdir=/tmp/centos', '--tmpdir=/tmp/centos', '--try-toolchain="[\'foss\', \'2015b\']"', '/opt/soft/apps/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb'], + "modules_tool": ('Lmod', '/opt/soft/apps/lmod/lmod/libexec/lmod', '6.0.9'), + "core_count": 16, + "cpu_model": "Intel Xeon E312xx (Sandy Bridge)", + "cpu_speed": 2399.998, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/opt/soft/apps/GCC/4.9.3-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/opt/soft/apps/GCC/4.9.3-binutils-2.25 --with-local-prefix=/opt/soft/apps/GCC/4.9.3-binutils-2.25; Thread model: posix; gcc version 4.9.3 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "easybuild-6.novalocal", + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.2.1511", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 20 2015, 02:00:19) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]", + "system_gcc_path": "/opt/soft/apps/GCC/4.9.3-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index 4d294b2bb3..151d5f6819 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -25,6 +25,7 @@ dependencies = [ ('cURL', '7.45.0'), # for RCurl ('libxml2', '2.9.2'), # for XML ('GDAL', '2.0.1'), # for rgdal + ('PROJ', '4.8.0'), # for rgdal ] name_tmpl = '%(name)s_%(version)s.tar.gz' -- GitLab From 80088a8f62072b0cec4f74735127ba7d027c9e7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 24 Jan 2016 18:47:05 +0100 Subject: [PATCH 0251/2133] bump version to 2.6.0 and update release notes --- RELEASE_NOTES | 26 +++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 26 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index ad3268bea1..cae9e41ed7 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,33 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 4,819 easyconfig files, for 778 different software packages, +The latest version of easybuild-easyconfig provides 5,093 easyconfig files, for 799 different software packages, 34 different (compiler) toolchains, 12 software bundles and 1 meta-package. +v2.6.0 (January 26th 2016) +-------------------------- + +feature + bugfix release +- add easyconfigs for foss/2016a and intel/2016 common toolchains (#2310, #2311, #2339, #2363) + incl. easyconfigs for Boost, CMake, Python, Perl using these toolchains +- added example easyconfig files for 21 new software packages: + BLASR (#922), BioKanga (#2247), BoltzTraP (#2365), basemap (#2221), CppUnit (#2271), EggLib (#2335), + FLASH (#2281), GLM (#2288), hub (#2249), MACS2 (#1983), MotEvo (#843), numba (#2243), PGI (#1833, #2367), + PLY (#2305), PaStiX (#2319, #2326), patchelf (#2327), pip (#2284), RSEM (#2316), RcppArmadillo (#2289), + SCDE (#2289), slepc4py (#2318) +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including BamTools 2.4.0, Boost 1.60.0, Clang 3.7.1, DOLFIN/FFC/FIAT/Instant/UFL 1.6.0, GATE 7.0, GCC 5.3.0, LLVM 3.7.1, pandas 0.17.1, PETSc 3.6.3, SAMtools 1.3, scipy 0.16.1, SLEPc 3.6.2, Trilinos 12.4.2, Trinity 2.1.1, VTK 6.3.0 +- various other enhancements, including: + - added new Cray* toolchain versions with pinned dependency versions (#2222) + - don't hardcode .so, use SHLIB_EXT constant instead (#2245) + - add custom sanity check in GEOS easyconfigs (#2285) +- various bug fixes, including: + - add Autotools (M4) as a build dependency in GMP v6.x easyconfigs (#2096) + - remove argparse from list of extensions in Python 3.2+ easyconfigs, since it became part of stdlib (#2323) +- various style fixes, including: + - get rid of tabs (#2302) + - remove trailing whitespace (#2341) + v2.5.0 (December 17th 2015) --------------------------- diff --git a/setup.py b/setup.py index e369b435aa..caeb9346b1 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.6.0.dev0' +VERSION = '2.6.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 2bbd86bdff5b2f215d7ba5660886e0d9f9163ef2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 24 Jan 2016 19:45:47 +0100 Subject: [PATCH 0252/2133] fix long line --- RELEASE_NOTES | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index cae9e41ed7..a3e8287af7 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -18,7 +18,9 @@ feature + bugfix release PLY (#2305), PaStiX (#2319, #2326), patchelf (#2327), pip (#2284), RSEM (#2316), RcppArmadillo (#2289), SCDE (#2289), slepc4py (#2318) - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... - including BamTools 2.4.0, Boost 1.60.0, Clang 3.7.1, DOLFIN/FFC/FIAT/Instant/UFL 1.6.0, GATE 7.0, GCC 5.3.0, LLVM 3.7.1, pandas 0.17.1, PETSc 3.6.3, SAMtools 1.3, scipy 0.16.1, SLEPc 3.6.2, Trilinos 12.4.2, Trinity 2.1.1, VTK 6.3.0 + including BamTools 2.4.0, Boost 1.60.0, Clang 3.7.1, DOLFIN/FFC/FIAT/Instant/UFL 1.6.0, GATE 7.0, GCC 5.3.0, + LLVM 3.7.1, pandas 0.17.1, PETSc 3.6.3, SAMtools 1.3, scipy 0.16.1, SLEPc 3.6.2, Trilinos 12.4.2, + Trinity 2.1.1, VTK 6.3.0 - various other enhancements, including: - added new Cray* toolchain versions with pinned dependency versions (#2222) - don't hardcode .so, use SHLIB_EXT constant instead (#2245) -- GitLab From c7d4de5c2c421ddc65afed359d7b0cfa50a22f4e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 25 Jan 2016 08:39:34 +0100 Subject: [PATCH 0253/2133] added extra line --- easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-intel-2015b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-intel-2015b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-intel-2015b.eb index c3eaea845a..c63ccbd6bf 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-intel-2015b.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.26-intel-2015b.eb @@ -5,12 +5,13 @@ version = '1.2.26' homepage = 'http://deweylab.github.io/RSEM/' description = """RNA-Seq by Expectation-Maximization)""" + toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/deweylab/RSEM/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['RSEM-1.2.26_eb_provided_zlib.patch'] +patches = ['RSEM-%(version)s_eb_provided_zlib.patch'] dependencies = [ ('ncurses', '5.9'), -- GitLab From 45342b3d44e370fd17a26103d310938ab8565021 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Jan 2016 10:29:34 +0000 Subject: [PATCH 0254/2133] Remove disabled synchronicity --- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index 4d294b2bb3..e8890010d8 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -277,8 +277,6 @@ exts_list = [ ('adephylo', '1.1-6', ext_options), ('animation', '2.4', ext_options), ('bigmemory.sri', '0.1.3', ext_options), - #Moved to separate easyconfig owing to new Boost dep - #('synchronicity', '1.1.9', ext_options), ('bigmemory', '4.5.8', ext_options), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), -- GitLab From d34809710cbec4db43d80ce41436eb7f4b4ea433 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Jan 2016 10:31:34 +0000 Subject: [PATCH 0255/2133] Remove try-toolchain cruft from PROJ for foss-2015b --- .../p/PROJ/PROJ-4.8.0-foss-2015b.eb | 27 ------------------- 1 file changed, 27 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb index 7121f9c66c..8e0db7e9a1 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb @@ -1,5 +1,3 @@ -# Built with EasyBuild version 2.5.0 on 2016-01-24_10-09-18 -## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute @@ -29,28 +27,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.5.0", - "easybuild-easyblocks_version": "2.5.0", - "timestamp": 1453630158, - "build_time": 21.19, - "install_size": 3603179, - "command_line": ['--buildpath=/tmp/centos', '--configfiles=/opt/soft/apps/EasyBuild/easybuild.cfg', '--debug', '--installpath=/opt/soft', '--module-syntax=Lua', '--modules-tool=Lmod', '--repositorypath=/opt/soft/ebfiles', '--robot=/opt/soft/apps/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs', '--sourcepath=/opt/soft/source', '--subdir-software=apps', '--tmp-logdir=/tmp/centos', '--tmpdir=/tmp/centos', '--try-toolchain="[\'foss\', \'2015b\']"', '/opt/soft/apps/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb'], - "modules_tool": ('Lmod', '/opt/soft/apps/lmod/lmod/libexec/lmod', '6.0.9'), - "core_count": 16, - "cpu_model": "Intel Xeon E312xx (Sandy Bridge)", - "cpu_speed": 2399.998, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/opt/soft/apps/GCC/4.9.3-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/opt/soft/apps/GCC/4.9.3-binutils-2.25 --with-local-prefix=/opt/soft/apps/GCC/4.9.3-binutils-2.25; Thread model: posix; gcc version 4.9.3 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "easybuild-6.novalocal", - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.2.1511", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 20 2015, 02:00:19) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]", - "system_gcc_path": "/opt/soft/apps/GCC/4.9.3-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] -- GitLab From a5965e7a9e0133e17be5fbc26bfa677b98690222 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 26 Jan 2016 10:46:13 +1300 Subject: [PATCH 0256/2133] Re-enable checksum verification --- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 54c92da4c6..3ea34a9824 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -12,10 +12,10 @@ source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] # Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version # numbering. Also, the authors are prone (alas) to stealth upgrades, so that two # tarballs with the same version number can have different checksums. For this -# reason, it is suggested to manually download and rename the tarball, and the -# checksum input has been disabled. +# reason, it is suggested to manually download and rename the tarball. The +# checksum may also need updating from time to time. sources = ['dftd3-%(version)s.tgz'] -#checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] +checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From e0384385e174945a7172015fdbe1de4a8118e3a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Jan 2016 16:17:27 +0100 Subject: [PATCH 0257/2133] bump version to 2.7.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index caeb9346b1..fecf010363 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.6.0' +VERSION = '2.7.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From b3043269951023b9270888c1c53be8ae64c7b279 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Jan 2016 17:19:54 +0200 Subject: [PATCH 0258/2133] add easyconfig EasyBuild-2.6.0.eb --- .../e/EasyBuild/EasyBuild-2.6.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb new file mode 100644 index 0000000000..01e4502a09 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.6.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.4.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 7f930d9b5f858596ebb58b39f93e232617968454 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 27 Jan 2016 00:11:59 +0100 Subject: [PATCH 0259/2133] Add ncdf4 for a user. I tried to also do it for intel-2015b w/ netCDF-4.3.3.1 but it has conflicting dependencies that won't work with R-3.2.1-intel-2015b (cURL 7.43 vs 7.45). --- .../n/ncdf4/ncdf4-1.15-intel-2015a-R-3.2.1.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdf4/ncdf4-1.15-intel-2015a-R-3.2.1.eb diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.15-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.15-intel-2015a-R-3.2.1.eb new file mode 100644 index 0000000000..ea4c448508 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.15-intel-2015a-R-3.2.1.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.15' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.2.1' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.3.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + +moduleclass = 'math' -- GitLab From 07a4cfceb7ce37a9079523fd8698e8b80c1503f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Jan 2016 11:22:33 +0200 Subject: [PATCH 0260/2133] add easyconfig numpy-1.10.1-foss-2015b-Python-2.7.10.eb --- .../numpy-1.10.1-foss-2015b-Python-2.7.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..9160880ad1 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.10.1' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' -- GitLab From d442be6a8769d0f3624269107b6026936f40604f Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Wed, 27 Jan 2016 14:35:35 +0100 Subject: [PATCH 0261/2133] Removed empty ending line --- .../c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 3480e35c4d..0bcd8423d9 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -41,4 +41,3 @@ modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icp modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created." moduleclass = 'system' - -- GitLab From 878ecd06428e7c345d0f238741514ad8527dca70 Mon Sep 17 00:00:00 2001 From: damianam Date: Wed, 27 Jan 2016 16:20:09 +0100 Subject: [PATCH 0262/2133] Update CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb --- .../c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 0bcd8423d9..3638002800 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University, # Forschungszentrum Juelich # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste -# Damian Alvarez +# Authors:: Damian Alvarez # License:: MIT/GPL # $Id$ # -- GitLab From fec595f5f348f51dc6ad01b4ef234386747a7664 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 10:21:31 +0100 Subject: [PATCH 0263/2133] Drop trailing spaces --- easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb | 2 +- .../easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb | 2 +- .../easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-intel-2015a.eb | 2 +- easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb | 2 +- .../easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb | 2 +- .../easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb | 2 +- .../easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb | 2 +- .../easyconfigs/f/FFTW/FFTW-3.3.3-ictce-4.1.13-single.eb | 2 +- easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.2.0-single.eb | 2 +- easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.3.0-single.eb | 2 +- .../easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb | 2 +- .../g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb | 2 +- .../GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb | 4 ++-- .../g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb | 2 +- .../easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 2 +- .../i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb | 2 +- .../easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 2 +- .../easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb | 2 +- .../easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 2 +- .../easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb | 2 +- .../easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 2 +- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb | 2 +- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb | 2 +- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 2 +- .../i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb | 2 +- .../easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb | 2 +- .../i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 2 +- .../i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 2 +- .../i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb | 2 +- .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb | 2 +- .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 2 +- .../i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb | 2 +- .../easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb | 2 +- .../i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb | 2 +- .../i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb | 2 +- .../impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb | 2 +- .../easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb | 2 +- .../impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb | 2 +- .../l/libcircle/libcircle-0.2.0-rc.1-goolf-1.4.10.eb | 2 +- .../l/libcircle/libcircle-0.2.0-rc.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb | 2 +- .../m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb | 2 +- .../easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb | 2 +- .../easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb | 2 +- .../easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb | 2 +- .../easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb | 2 +- .../OpenFOAM-Extend-1.6-goolf-1.4.10-20130711.eb | 2 +- .../OpenFOAM-Extend-1.6-ictce-4.1.13-20130711.eb | 2 +- .../OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb | 2 +- .../o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb | 2 +- .../o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb | 2 +- .../o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb | 2 +- easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb | 2 +- .../ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb | 2 +- .../p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb | 2 +- .../easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb | 2 +- .../easyconfigs/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb | 2 +- .../p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb | 2 +- .../p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb | 2 +- easybuild/easyconfigs/r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb | 2 +- easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb | 2 +- .../s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb | 2 +- .../s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb | 4 ++-- .../easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb | 4 ++-- .../easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/s/Silo/Silo-4.9.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/s/Silo/Silo-4.9.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb | 2 +- .../easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb | 2 +- 107 files changed, 113 insertions(+), 113 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb index 798d558246..6e29870586 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb @@ -12,7 +12,7 @@ version = "2.4.2" homepage = 'https://github.com/bedops/bedops' description = """ BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, - archiving, conversion and other management of genomic data of arbitrary scale.""" + archiving, conversion and other management of genomic data of arbitrary scale.""" # this application requires GCC-4.8.x or higher # be aware if you switch to a different toolchain diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb index 91498fff43..28fd6859e0 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb @@ -1,6 +1,6 @@ # Author: Pablo Escobar Lopez; Wiktor Jurkowski # Swiss Institute of Bioinformatics (SIB), Biozentrum - University of Basel -# Babraham Institute, UK +# Babraham Institute, UK easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb index 0c511d17e0..2493984594 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ # Author: Maxime Schmitt, University of Luxembourg -# +# # Based on the work of: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb index 0b9e9a4fe5..6997e33823 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb @@ -1,5 +1,5 @@ # Author: Maxime Schmitt, University of Luxembourg -# Author: Adam Huffman, The Francis Crick Institute +# Author: Adam Huffman, The Francis Crick Institute # # Based on the work of: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb index dd1aec5c92..3e92e22059 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb @@ -1,5 +1,5 @@ # Author: Maxime Schmitt, University of Luxembourg -# Author: Adam Huffman, The Francis Crick Institute +# Author: Adam Huffman, The Francis Crick Institute # # Based on the work of: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) diff --git a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-intel-2015a.eb b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-intel-2015a.eb index 1b091e506f..0f53e3f3c3 100644 --- a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-intel-2015a.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Benjamin P. Roberts # New Zealand eScience Infrastructure -# The University of Auckland, Auckland, New Zealand +# The University of Auckland, Auckland, New Zealand easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb index 5f300eb8ed..ea0ea19754 100644 --- a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Benjamin P. Roberts # New Zealand eScience Infrastructure -# The University of Auckland, Auckland, New Zealand +# The University of Auckland, Auckland, New Zealand easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb index 8327d3734b..fc4d027589 100644 --- a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb @@ -8,7 +8,7 @@ description = """IBM ILOG CPLEX Optimizer's mathematical programming technology toolchain = {'name': 'foss', 'version': '2015b'} -# the Academic Initiative version (as used in this file) can be downloaded as described on +# the Academic Initiative version (as used in this file) can be downloaded as described on # https://www.ibm.com/developerworks/community/blogs/jfp/entry/cplex_studio_in_ibm_academic_initiative?lang=en # a restricted "Community edition" version can be found on # https://www-01.ibm.com/software/websphere/products/optimization/cplex-studio-community-edition/ diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb index 50c119c61c..4e4589531c 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb index a72566ad44..cf00dd3653 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb index 2bc0ea310e..7f862017dd 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb @@ -20,7 +20,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('GLib', '2.34.3')] -# parallel build fails +# parallel build fails parallel = 1 sanity_check_paths = { diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb index 36527565d8..899422100c 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb @@ -20,7 +20,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('GLib', '2.34.3')] -# parallel build fails +# parallel build fails parallel = 1 sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-4.1.13-single.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-4.1.13-single.eb index 847312fb86..6d022e3132 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-4.1.13-single.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-4.1.13-single.eb @@ -17,7 +17,7 @@ source_urls = [homepage] ## single precision configopts = "--enable-sse --enable-single" -# the MPI opts from FFTW2 are valid options but unused until FFTW3.3 +# the MPI opts from FFTW2 are valid options but unused until FFTW3.3 configopts += " --enable-threads --enable-openmp --with-pic --enable-mpi" sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.2.0-single.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.2.0-single.eb index 8d6deb8033..15438c0430 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.2.0-single.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.2.0-single.eb @@ -17,7 +17,7 @@ source_urls = [homepage] ## single precision configopts = "--enable-sse --enable-single" -# the MPI opts from FFTW2 are valid options but unused until FFTW3.3 +# the MPI opts from FFTW2 are valid options but unused until FFTW3.3 configopts += " --enable-threads --enable-openmp --with-pic --enable-mpi" sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.3.0-single.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.3.0-single.eb index 4e798279db..1212e33f88 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.3.0-single.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.3.0-single.eb @@ -17,7 +17,7 @@ source_urls = [homepage] ## single precision configopts = "--enable-sse --enable-single" -# the MPI opts from FFTW2 are valid options but unused until FFTW3.3 +# the MPI opts from FFTW2 are valid options but unused until FFTW3.3 configopts += " --enable-threads --enable-openmp --with-pic --enable-mpi" sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb index cfa438bf8f..4bdecb5bb1 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb @@ -17,7 +17,7 @@ source_urls = [homepage] ## single precision configopts = "--enable-sse --enable-single" -# the MPI opts from FFTW2 are valid options but unused until FFTW3.3 +# the MPI opts from FFTW2 are valid options but unused until FFTW3.3 configopts += " --enable-threads --enable-openmp --with-pic --enable-mpi" preconfigopts = 'OMPI_MPICC=icc ' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb index a54077b4b3..63e63419b2 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb @@ -40,7 +40,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -# there is a bug in the build system causing the build with libtool to fail for the moment +# there is a bug in the build system causing the build with libtool to fail for the moment # (static library is also missing because of this) configopts += ' --without-libtool' diff --git a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb index 03a5996b54..9dd671125b 100644 --- a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb +++ b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb @@ -18,7 +18,7 @@ description = """ Next-generation sequencing platforms (Illumina/Solexa, ABI/SOL transform (BWT) have been implemented. The library core is written in C for maximum speed, with concise interfaces to higher-level programming languages like OCaml and Python. Many high-performance standalone programs (mapper, splice mapper, etc.) are provided along - with the library; in general, new algorithms and tools can be easily implemented on the top of it. """ + with the library; in general, new algorithms and tools can be easily implemented on the top of it. """ toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -28,7 +28,7 @@ sources = ['GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2'] # if core_i3 version doesn't work for you, try core_2 version below #sources = ['GEM-binaries-Linux-x86_64-core_2-20130406-045632.tbz2'] -# only Linux_x86-64 binaries are provided so we skip build_step. +# only Linux_x86-64 binaries are provided so we skip build_step. # We just use the MakeCp block to copy each file to the right destination folder (mainly the man files) skipsteps = ['build'] diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb index fefd3eeaab..e26ff137e5 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb @@ -4,7 +4,7 @@ name = 'glproto' version = '1.4.16' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" +description = "X protocol and ancillary headers" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb index 2c1515c3ee..a46e3dcda1 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb @@ -4,7 +4,7 @@ name = 'glproto' version = '1.4.16' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" +description = "X protocol and ancillary headers" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb index 1316bedb2a..172016aad3 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb @@ -4,7 +4,7 @@ name = 'glproto' version = '1.4.16' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" +description = "X protocol and ancillary headers" toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb index 282c406ca1..69cf5deb96 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb @@ -4,7 +4,7 @@ name = 'glproto' version = '1.4.16' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" +description = "X protocol and ancillary headers" toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb index efe43edfab..d770bc9878 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb @@ -4,7 +4,7 @@ name = 'glproto' version = '1.4.16' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" +description = "X protocol and ancillary headers" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index e0aa55d8e1..6a204cb330 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index ed9f544efd..4c78a146fe 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -20,6 +20,6 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic m32 = True # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb index cdfb37e60d..08072ed0ba 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb @@ -19,6 +19,6 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic m32 = True # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb index 05a3dcd524..511d688de0 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index 6a5c58b965..c44ccfe556 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb index 32c938b850..ed02f9aae2 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb @@ -19,6 +19,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb index c9a73b1fbd..74988d9060 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb @@ -19,6 +19,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 321fcf953c..001ee2403f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -19,6 +19,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb index 03f1826816..8fec794639 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb index 61d1d12258..1aa67b0e91 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 52c5610522..6178aa2f65 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb index 10206cc86f..99cabee972 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb index 14cfad4a95..c4adbe0ae3 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb index 5e54731d6a..2121a1a6d9 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 9d7dcdffc5..92c9a61b43 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb index 5b383c2276..3cd6a18055 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb index 2aeefc2cd9..22f0699649 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb index 6f91af21b3..6357cd5634 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 48ea7b9ce5..922aa79344 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index d88a37c91f..b7639d24d1 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb index 048251c331..21ed19633f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index 5843dfe200..da5a2ab9be 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 9e56e74b2d..9e61812d8f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb index 07bd2d77cd..9a3879ee53 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb index d3e34f99af..5e4968df60 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb index 54e5d17b0f..033aabd2c0 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index 23f4c48744..43cd007ba4 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb index 57ed02ab9a..28ece27457 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb index 107a4290a3..6f2bcda1cb 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb index 85451943cd..a9d198b99f 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb index 0272634c21..25f7950bae 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb index 0bd01e5fe2..df72fa53c0 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 7b891134eb..4b32c5dbb2 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb index baf8e132f9..c247bd8cc6 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb index 10fe208f63..362bb90b08 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb @@ -18,6 +18,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb index 3c0b578af0..9e343efe2e 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -17,6 +17,6 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = 'True' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.2.0-rc.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.2.0-rc.1-goolf-1.4.10.eb index 5c7402fd86..c1628b8313 100644 --- a/easybuild/easyconfigs/l/libcircle/libcircle-0.2.0-rc.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.2.0-rc.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ # With <3 for EasyBuild -# +# # EasyConfig for libcircle: # ---------------------------------------------------------------------------- # Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.2.0-rc.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.2.0-rc.1-ictce-5.3.0.eb index 0021c76f06..feda1f649b 100644 --- a/easybuild/easyconfigs/l/libcircle/libcircle-0.2.0-rc.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.2.0-rc.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ # With <3 for EasyBuild -# +# # EasyConfig for libcircle: # ---------------------------------------------------------------------------- # Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH diff --git a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb index ce172894c9..aa2cc82aa9 100644 --- a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb @@ -22,7 +22,7 @@ start_dir = "source" parallel = 1 -files_to_copy = ["../*"] +files_to_copy = ["../*"] sanity_check_paths = { 'files': ["bin/motevo", "bin/runUFE"], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb index 529c59d6ab..3b30e0e1d5 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb @@ -4,7 +4,7 @@ name = 'makedepend' version = '1.0.4' homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb index df5d7baa12..393090c994 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb @@ -4,7 +4,7 @@ name = 'makedepend' version = '1.0.4' homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb index 3d0c89f8f2..f5f634beae 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb @@ -4,7 +4,7 @@ name = 'makedepend' version = '1.0.4' homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb index fa3bc9877b..25ba8c0849 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb @@ -4,7 +4,7 @@ name = 'makedepend' version = '1.0.4' homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb index 3f3fa2cba5..858f7c2608 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb @@ -4,7 +4,7 @@ name = 'makedepend' version = '1.0.4' homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb index 653ce13c66..808282ac91 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb @@ -4,7 +4,7 @@ name = 'makedepend' version = '1.0.4' homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb index a42c1e4ac5..07b6b524bf 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb @@ -4,7 +4,7 @@ name = 'makedepend' version = '1.0.4' homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-1.6-goolf-1.4.10-20130711.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-1.6-goolf-1.4.10-20130711.eb index a8f00a37b1..4f3563d5d3 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-1.6-goolf-1.4.10-20130711.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-1.6-goolf-1.4.10-20130711.eb @@ -8,7 +8,7 @@ homepage = 'http://www.extend-project.de/' description = """OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, -to solid dynamics and electromagnetics.""" +to solid dynamics and electromagnetics.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-1.6-ictce-4.1.13-20130711.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-1.6-ictce-4.1.13-20130711.eb index 65508883f9..4426fd2e9c 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-1.6-ictce-4.1.13-20130711.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-1.6-ictce-4.1.13-20130711.eb @@ -8,7 +8,7 @@ homepage = 'http://www.extend-project.de/' description = """OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, -to solid dynamics and electromagnetics.""" +to solid dynamics and electromagnetics.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb index d7e99b5643..a8de03c3a1 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb @@ -8,7 +8,7 @@ homepage = 'http://www.extend-project.de/' description = """OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, -to solid dynamics and electromagnetics.""" +to solid dynamics and electromagnetics.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb index 79a66bc81f..1fe977591c 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb @@ -7,7 +7,7 @@ homepage = 'http://www.extend-project.de/' description = """OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, -to solid dynamics and electromagnetics.""" +to solid dynamics and electromagnetics.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb index 9ed9e874c8..d845c52d8f 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb @@ -7,7 +7,7 @@ homepage = 'http://www.extend-project.de/' description = """OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, -to solid dynamics and electromagnetics.""" +to solid dynamics and electromagnetics.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb index 8e980cbba3..e1a49bf5a0 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb @@ -7,7 +7,7 @@ homepage = 'http://www.extend-project.de/' description = """OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, -to solid dynamics and electromagnetics.""" +to solid dynamics and electromagnetics.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb index 9454cdc782..785161afd7 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb @@ -25,7 +25,7 @@ source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] dependencies = [('zlib', '1.2.8')] # plink makefile is a little bit tricky so we pass every options as arguments -# review plink original makefile for details +# review plink original makefile for details # if you want "new version check" change to WITH_WEBCHECK="1", but if your compute nodes # have no internet access better leave it as is buildopts = ' CXX_UNIX="$CXX $CXXFLAGS" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 ' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb index 1a6432b2aa..968d0aa66a 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -13,7 +13,7 @@ version = '4.8.0' homepage = 'http://trac.osgeo.org/proj/' description = """Program proj is a standard Unix filter function which converts -geographic longitude and latitude coordinates into cartesian coordinates""" +geographic longitude and latitude coordinates into cartesian coordinates""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb index 96e7b3b1b8..609a7355cc 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb @@ -45,7 +45,7 @@ configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOT #Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' #The ParaView server can be cranky, test downloads are quite often failing, especially in the case -#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the #first serial attempt would fail. prebuildopts = 'make VTKData ;' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb index a80a2bae48..e5a49a6762 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb @@ -44,7 +44,7 @@ configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOT #Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' #The ParaView server can be cranky, test downloads are quite often failing, especially in the case -#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the #first serial attempt would fail. prebuildopts = 'make VTKData ;' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb index 9449cd74f2..d675f99ad1 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb @@ -45,7 +45,7 @@ configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOT #Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' #The ParaView server can be cranky, test downloads are quite often failing, especially in the case -#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the #first serial attempt would fail. prebuildopts = 'make VTKData ;' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb index cb5acbbae9..63b92b07e5 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb @@ -44,7 +44,7 @@ configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOT #Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' #The ParaView server can be cranky, test downloads are quite often failing, especially in the case -#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the #first serial attempt would fail. prebuildopts = 'make VTKData ;' diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb index 3b392c874b..1450202b68 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] patches = ['old-libstdc++-hash_fun-map-set.patch'] -# Pasha's makefile is not suited for parallel execution +# Pasha's makefile is not suited for parallel execution parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb index e06bb5adee..9948217fd4 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb @@ -17,7 +17,7 @@ patches = [ 'Pasha_GCC-4.7.patch', ] -# Pasha's makefile is not suited for parallel execution +# Pasha's makefile is not suited for parallel execution parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb index c975074930..359a345c5b 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb @@ -18,7 +18,7 @@ patches = [ 'old-libstdc++-hash_fun-map-set.patch', ] -# Pasha's makefile is not suited for parallel execution +# Pasha's makefile is not suited for parallel execution parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb index 3ca4f9bfba..cf6204baea 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb @@ -19,7 +19,7 @@ patches = [ 'old-libstdc++-hash_fun-map-set.patch', ] -# Pasha's makefile is not suited for parallel execution +# Pasha's makefile is not suited for parallel execution parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb index bbafb52a0c..65d0ec04e7 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb @@ -20,7 +20,7 @@ patches = [ ] -# Pasha's makefile is not suited for parallel execution +# Pasha's makefile is not suited for parallel execution parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb index d956840f69..67dc78ccc9 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb @@ -21,7 +21,7 @@ patches = [ ] -# Pasha's makefile is not suited for parallel execution +# Pasha's makefile is not suited for parallel execution parallel = 1 moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb index ef867422c5..51aeabb7ca 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb @@ -7,7 +7,7 @@ name = 'PyQt' version = '4.11.3' homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' -description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb index 48c5bb750a..328b12d5a9 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb @@ -7,7 +7,7 @@ name = 'PyQt' version = '4.11.3' homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' -description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb index 97d67dd516..513e8a388c 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ # With <3 for EasyBuild -# +# # EasyConfig for Ruby 2.1: # ---------------------------------------------------------------------------- # Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb index 7acca63ee0..be5e8a2090 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb @@ -1,5 +1,5 @@ # With <3 for EasyBuild -# +# # EasyConfig for Ruby 2.1: # ---------------------------------------------------------------------------- # Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb index b2e22e2b13..8c87deb6f6 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb @@ -1,5 +1,5 @@ # With <3 for EasyBuild -# +# # EasyConfig for Ruby 2.1: # ---------------------------------------------------------------------------- # Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH diff --git a/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb b/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb index 5cf6c32e44..8bbd1d0d43 100644 --- a/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb +++ b/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://soap.genomics.org.cn/down/'] sources = ['soap%(version)srelease.tar.gz'] -# only Linux-x86_64 binaries are provided so we skip build step. +# only Linux-x86_64 binaries are provided so we skip build step. # We just use the MakeCp block to copy each file to the right destination folder skipsteps = ['build'] diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb index 9a31af40cd..195190a776 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb @@ -1,5 +1,5 @@ # With <3 for EasyBuild -# +# # EasyConfig for SOAPdenovo2: # ---------------------------------------------------------------------------- # Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH @@ -17,7 +17,7 @@ description = """SOAPdenovo is a novel short-read assembly method that can build de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. - SOAPdenovo2 is the successor of SOAPdenovo.""" + SOAPdenovo2 is the successor of SOAPdenovo.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb index 98fc2a7d48..c597bc0601 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb @@ -1,5 +1,5 @@ # With <3 for EasyBuild -# +# # EasyConfig for SOAPdenovo2: # ---------------------------------------------------------------------------- # Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH @@ -17,7 +17,7 @@ description = """SOAPdenovo is a novel short-read assembly method that can build de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. - SOAPdenovo2 is the successor of SOAPdenovo.""" + SOAPdenovo2 is the successor of SOAPdenovo.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb index 4f0d8353ab..003c593651 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb @@ -1,5 +1,5 @@ # With <3 for EasyBuild -# +# # EasyConfig for SOAPdenovo2: # ---------------------------------------------------------------------------- # Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH @@ -17,7 +17,7 @@ description = """SOAPdenovo is a novel short-read assembly method that can build de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. - SOAPdenovo2 is the successor of SOAPdenovo.""" + SOAPdenovo2 is the successor of SOAPdenovo.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb index 1761063fd7..16d7b49429 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb @@ -1,5 +1,5 @@ # With <3 for EasyBuild -# +# # EasyConfig for SOAPdenovo2: # ---------------------------------------------------------------------------- # Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH @@ -17,7 +17,7 @@ description = """SOAPdenovo is a novel short-read assembly method that can build de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. - SOAPdenovo2 is the successor of SOAPdenovo.""" + SOAPdenovo2 is the successor of SOAPdenovo.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb index 0df8fa5210..829511351f 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb @@ -1,5 +1,5 @@ # With <3 for EasyBuild -# +# # EasyConfig for SOAPdenovo2: # ---------------------------------------------------------------------------- # Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH @@ -17,7 +17,7 @@ description = """SOAPdenovo is a novel short-read assembly method that can build de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. - SOAPdenovo2 is the successor of SOAPdenovo.""" + SOAPdenovo2 is the successor of SOAPdenovo.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/s/Silo/Silo-4.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Silo/Silo-4.9.1-goolf-1.4.10.eb index 7bc12da16d..e71c024ff4 100644 --- a/easybuild/easyconfigs/s/Silo/Silo-4.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Silo/Silo-4.9.1-goolf-1.4.10.eb @@ -4,7 +4,7 @@ name = 'Silo' version = '4.9.1' homepage = 'https://wci.llnl.gov/codes/silo/' -description = """Silo is a library for reading and writing a wide variety of scientific data to binary, disk files""" +description = """Silo is a library for reading and writing a wide variety of scientific data to binary, disk files""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} diff --git a/easybuild/easyconfigs/s/Silo/Silo-4.9.1-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Silo/Silo-4.9.1-ictce-5.3.0.eb index 84c2cd61ba..e4c2903f0e 100644 --- a/easybuild/easyconfigs/s/Silo/Silo-4.9.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/Silo/Silo-4.9.1-ictce-5.3.0.eb @@ -4,7 +4,7 @@ name = 'Silo' version = '4.9.1' homepage = 'https://wci.llnl.gov/codes/silo/' -description = """Silo is a library for reading and writing a wide variety of scientific data to binary, disk files""" +description = """Silo is a library for reading and writing a wide variety of scientific data to binary, disk files""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb index c94ded9731..2ab7485885 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb @@ -4,7 +4,7 @@ name = 'snappy' version = '1.1.2' # snappy was migrated from code.google.com to github.com and this commit -# corresponds to release 1.1.2 (which they haven't tagged). +# corresponds to release 1.1.2 (which they haven't tagged). # see https://github.com/google/snappy/commit/1ff9be9 commit = '1ff9be9' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb index 901b001dcd..36e8b8b902 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb @@ -4,7 +4,7 @@ name = 'snappy' version = '1.1.3' # snappy was migrated from code.google.com to github.com and this commit -# corresponds to release 1.1.2 (which they haven't tagged). +# corresponds to release 1.1.2 (which they haven't tagged). # see https://github.com/google/snappy/commit/1ff9be9 commit = '1ff9be9' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb index 51a00b2812..0b9f7d0f3f 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb @@ -4,7 +4,7 @@ name = 'xproto' version = '7.0.23' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" +description = "X protocol and ancillary headers" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb index d17e8eb76f..e7dc372ce2 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb @@ -4,7 +4,7 @@ name = 'xproto' version = '7.0.23' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" +description = "X protocol and ancillary headers" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb index f34a19a932..4a07188aa9 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb @@ -4,7 +4,7 @@ name = 'xproto' version = '7.0.23' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" +description = "X protocol and ancillary headers" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb index fd2b06fd61..0b738cf50c 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb @@ -4,7 +4,7 @@ name = 'xproto' version = '7.0.23' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" +description = "X protocol and ancillary headers" toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb index dad31a77b4..90b584a81e 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb @@ -4,7 +4,7 @@ name = 'xproto' version = '7.0.23' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" +description = "X protocol and ancillary headers" toolchain = {'name': 'ictce', 'version': '5.3.0'} -- GitLab From ba6af2855b492c1ab8480c2f4c1dcf7d034a680b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 11:20:52 +0100 Subject: [PATCH 0264/2133] Style fixes with autopep8: a, d and j Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../ABINIT-7.0.3-x86_64_linux_gnu4.5.eb | 6 +-- .../ABINIT-7.0.5-x86_64_linux_gnu4.5.eb | 6 +-- .../ABINIT-7.2.1-x86_64_linux_gnu4.5.eb | 6 +-- ...-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 +-- .../ABySS-1.3.4-goolf-1.4.10-Python-2.7.3.eb | 6 +-- .../ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb | 6 +-- .../ABySS-1.3.4-ictce-5.3.0-Python-2.7.3.eb | 6 +-- .../a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb | 12 ++--- .../a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb | 12 ++--- .../a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb | 12 ++--- .../a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb | 12 ++--- easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb | 4 +- .../easyconfigs/a/ARB/ARB-5.5-goolf-1.4.10.eb | 2 +- .../easyconfigs/a/ARB/ARB-5.5-ictce-4.1.13.eb | 2 +- ...0.2515-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 10 ++-- ...SE-3.6.0.2515-goolf-1.4.10-Python-2.7.3.eb | 10 ++-- ...ASE-3.6.0.2515-ictce-4.0.6-Python-2.7.3.eb | 10 ++-- ...ASE-3.6.0.2515-ictce-5.3.0-Python-2.7.3.eb | 10 ++-- ....4-gompi-1.1.0-no-OFED-with-shared-libs.eb | 2 +- .../AutoDock_Vina-1.1.2_linux_x86.eb | 2 +- .../Autotools/Autotools-20150119-GCC-4.9.2.eb | 8 +-- .../Autotools/Autotools-20150215-GCC-4.7.2.eb | 6 +-- .../Autotools/Autotools-20150215-GCC-4.8.4.eb | 6 +-- .../Autotools/Autotools-20150215-GCC-4.9.2.eb | 6 +-- .../Autotools-20150215-GCC-4.9.3-2.25.eb | 6 +-- .../Autotools-20150215-GNU-4.9.2-2.25.eb | 6 +-- .../Autotools-20150215-GNU-4.9.3-2.25.eb | 6 +-- .../Autotools-20150215-GNU-5.1.0-2.25.eb | 6 +-- .../Autotools-20150215-foss-2015a.eb | 6 +-- .../Autotools-20150215-foss-2016a.eb | 6 +-- .../Autotools-20150215-intel-2015b.eb | 6 +-- .../Autotools-20150215-intel-2016a.eb | 6 +-- .../a/Autotools/Autotools-20150215.eb | 6 +-- .../a/argtable/argtable-2.13-goolf-1.4.10.eb | 2 +- .../aria2/aria2-1.15.1-goalf-1.1.0-no-OFED.eb | 6 +-- .../a/aria2/aria2-1.15.1-goolf-1.4.10.eb | 6 +-- .../a/aria2/aria2-1.15.1-ictce-4.0.6.eb | 6 +-- .../a/aria2/aria2-1.15.1-ictce-5.3.0.eb | 6 +-- .../DISCOVARdenovo-52488-foss-2015a.eb | 2 +- ...-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 50 +++++++++--------- .../DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 52 +++++++++---------- .../DOLFIN-1.0.0-ictce-4.0.6-Python-2.7.3.eb | 50 +++++++++--------- ...ndroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb | 6 +-- ...-0.9.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 +-- ...ocutils-0.9.1-goolf-1.4.10-Python-2.7.3.eb | 6 +-- ...Docutils-0.9.1-ictce-4.0.6-Python-2.7.3.eb | 6 +-- ...Docutils-0.9.1-ictce-5.3.0-Python-2.7.3.eb | 6 +-- .../j/JAGS/JAGS-3.4.0-goolf-1.4.10.eb | 1 - .../j/JAGS/JAGS-3.4.0-ictce-6.2.5.eb | 1 - .../j/JAGS/JAGS-3.4.0-intel-2014b.eb | 1 - easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 4 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 4 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 4 +- ...a2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 12 ++--- .../Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb | 12 ++--- .../Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb | 12 ++--- .../Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb | 12 ++--- 57 files changed, 246 insertions(+), 249 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb index a8e8be1611..9ff4e547c0 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb @@ -27,8 +27,8 @@ sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] source_urls = ['http://ftp.abinit.org/'] sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } + 'files': ["bin/abinit"], + 'dirs': [] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb index 083d321a07..b5b040ce63 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb @@ -29,8 +29,8 @@ sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] source_urls = ['http://ftp.abinit.org/'] sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } + 'files': ["bin/abinit"], + 'dirs': [] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb index 5ccd2f15a7..051d0927bf 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb @@ -30,8 +30,8 @@ sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] source_urls = ['http://ftp.abinit.org/'] sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } + 'files': ["bin/abinit"], + 'dirs': [] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 570c4b562c..c096f680fa 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -29,8 +29,8 @@ source_urls = ['http://www.bcgsc.ca/downloads/abyss/'] dependencies = [('Boost', '1.49.0', versionsuffix)] sanity_check_paths = { - 'files': ["bin/ABYSS", "bin/ABYSS-P"], - 'dirs': [] - } + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goolf-1.4.10-Python-2.7.3.eb index 893dbac4ab..6d7dc91575 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goolf-1.4.10-Python-2.7.3.eb @@ -29,8 +29,8 @@ source_urls = ['http://www.bcgsc.ca/downloads/abyss/'] dependencies = [('Boost', '1.49.0', versionsuffix)] sanity_check_paths = { - 'files': ["bin/ABYSS", "bin/ABYSS-P"], - 'dirs': [] - } + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb index 47d31cf715..935dda4340 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb @@ -29,8 +29,8 @@ source_urls = ['http://www.bcgsc.ca/downloads/abyss/'] dependencies = [('Boost', '1.49.0', versionsuffix)] sanity_check_paths = { - 'files': ["bin/ABYSS", "bin/ABYSS-P"], - 'dirs': [] - } + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-5.3.0-Python-2.7.3.eb index 8ce4ee39f1..f7709440c3 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-5.3.0-Python-2.7.3.eb @@ -29,8 +29,8 @@ source_urls = ['http://www.bcgsc.ca/downloads/abyss/'] dependencies = [('Boost', '1.49.0', versionsuffix)] sanity_check_paths = { - 'files': ["bin/ABYSS", "bin/ABYSS-P"], - 'dirs': [] - } + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb index 7204bb4bed..42399e1539 100644 --- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb @@ -25,14 +25,14 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')] dependencies = [ - ('expat', '2.1.0'), - ('MUMmer', '3.23'), - ] + ('expat', '2.1.0'), + ('MUMmer', '3.23'), +] sanity_check_paths = { - 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed' ], - 'dirs': [] - } + 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], + 'dirs': [] +} parallel = 1 # make crashes otherwise diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb index 67f7c8c305..e1a0148b75 100644 --- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb @@ -27,14 +27,14 @@ source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower patches = ['AMOS-3.1.0_GCC-4.7.patch'] dependencies = [ - ('expat', '2.1.0'), - ('MUMmer', '3.23'), - ] + ('expat', '2.1.0'), + ('MUMmer', '3.23'), +] sanity_check_paths = { - 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed' ], - 'dirs': [] - } + 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], + 'dirs': [] +} parallel = 1 # make crashes otherwise diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb index e18be68931..02a64a2c6f 100644 --- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb @@ -25,14 +25,14 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')] dependencies = [ - ('expat', '2.1.0'), - ('MUMmer', '3.23'), - ] + ('expat', '2.1.0'), + ('MUMmer', '3.23'), +] sanity_check_paths = { - 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed' ], - 'dirs': [] - } + 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], + 'dirs': [] +} parallel = 1 # make crashes otherwise diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb index 89797ac535..7fce76229e 100644 --- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb @@ -26,14 +26,14 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')] dependencies = [ - ('expat', '2.1.0'), - ('MUMmer', '3.23'), - ] + ('expat', '2.1.0'), + ('MUMmer', '3.23'), +] sanity_check_paths = { - 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed' ], - 'dirs': [] - } + 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], + 'dirs': [] +} parallel = 1 # make crashes otherwise diff --git a/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb b/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb index 5836d2ff45..673a19b69d 100644 --- a/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb +++ b/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb @@ -8,8 +8,8 @@ description = """ANSYS simulation software enables organizations to confidently toolchain = {'name': 'dummy', 'version': 'dummy'} -#create a zip file from the 3 install iso files. -#make sure all files of the iso's are in the same directory. +# create a zip file from the 3 install iso files. +# make sure all files of the iso's are in the same directory. sources = ['ANSYS-15.0.zip'] import os diff --git a/easybuild/easyconfigs/a/ARB/ARB-5.5-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ARB/ARB-5.5-goolf-1.4.10.eb index 5aa0f9160c..41b26e296f 100644 --- a/easybuild/easyconfigs/a/ARB/ARB-5.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ARB/ARB-5.5-goolf-1.4.10.eb @@ -24,7 +24,7 @@ dependencies = [ ('makedepend', '1.0.4'), ('imake', '1.0.5'), ('libXt', '1.1.4'), - ('motif', '2.3.4'), # libXm + ('motif', '2.3.4'), # libXm ('libXpm', '3.5.11'), ('libXaw', '1.0.12'), ('Perl', '5.16.3'), diff --git a/easybuild/easyconfigs/a/ARB/ARB-5.5-ictce-4.1.13.eb b/easybuild/easyconfigs/a/ARB/ARB-5.5-ictce-4.1.13.eb index 77b39fdaa5..7d9c072196 100644 --- a/easybuild/easyconfigs/a/ARB/ARB-5.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/a/ARB/ARB-5.5-ictce-4.1.13.eb @@ -24,7 +24,7 @@ dependencies = [ ('makedepend', '1.0.4'), ('imake', '1.0.5'), ('libXt', '1.1.4'), - ('motif', '2.3.4'), # libXm + ('motif', '2.3.4'), # libXm ('libXpm', '3.5.11'), ('libXaw', '1.0.12'), ('Perl', '5.16.3'), diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-goalf-1.1.0-no-OFED-Python-2.7.3.eb index d6c3ba40b8..bb52b4b69d 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -18,12 +18,12 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ] + (python, pythonver), +] sanity_check_paths = { - 'files': ['bin/ag', 'bin/ase', 'bin/ASE2ase.py', 'bin/testase.py'], - 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] - } + 'files': ['bin/ag', 'bin/ase', 'bin/ASE2ase.py', 'bin/testase.py'], + 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-goolf-1.4.10-Python-2.7.3.eb index eccf705edd..dbbc53352e 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-goolf-1.4.10-Python-2.7.3.eb @@ -18,12 +18,12 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ] + (python, pythonver), +] sanity_check_paths = { - 'files': ['bin/ag', 'bin/ase', 'bin/ASE2ase.py', 'bin/testase.py'], - 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] - } + 'files': ['bin/ag', 'bin/ase', 'bin/ASE2ase.py', 'bin/testase.py'], + 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-ictce-4.0.6-Python-2.7.3.eb index ea78c0bbca..3829980bc2 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-ictce-4.0.6-Python-2.7.3.eb @@ -18,12 +18,12 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ] + (python, pythonver), +] sanity_check_paths = { - 'files': ['bin/ag', 'bin/ase', 'bin/ASE2ase.py', 'bin/testase.py'], - 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] - } + 'files': ['bin/ag', 'bin/ase', 'bin/ASE2ase.py', 'bin/testase.py'], + 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-ictce-5.3.0-Python-2.7.3.eb index 290c09c81e..de265b05d3 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.6.0.2515-ictce-5.3.0-Python-2.7.3.eb @@ -19,12 +19,12 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ] + (python, pythonver), +] sanity_check_paths = { - 'files': ['bin/ag', 'bin/ase', 'bin/ASE2ase.py', 'bin/testase.py'], - 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] - } + 'files': ['bin/ag', 'bin/ase', 'bin/ASE2ase.py', 'bin/testase.py'], + 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb index 308e6f6035..a05c00d082 100644 --- a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb +++ b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb @@ -16,7 +16,7 @@ source_urls = [('http://sourceforge.net/projects/math-atlas/files/Stable/%s' % v patches = ['ATLAS-3.8.4_illegal-instruction-fix.patch', 'ATLAS-3.8.4_make-install-shared.patch' - ] + ] # fix for http://math-atlas.sourceforge.net/errata.html#sharedProbe configopts = "-Ss f77lib '-L${EBROOTGCC}/lib64 -lgfortran'" diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb index a27cf3bd19..98f8c2275a 100644 --- a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb +++ b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb @@ -15,7 +15,7 @@ description = """ AutoDock Vina is an open-source program for doing molecular do toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://vina.scripps.edu/download/'] -sources = ['%s_%s%s.tgz' % (name.lower(), version.replace('.','_'), versionsuffix)] +sources = ['%s_%s%s.tgz' % (name.lower(), version.replace('.', '_'), versionsuffix)] sanity_check_paths = { 'files': ["bin/vina_split", "bin/vina"], diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb index 067ccdbe63..66216b2e54 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'Autotools' -version = '20150119' # date of the most recent change +version = '20150119' # date of the most recent change homepage = 'http://autotools.io' description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'GCC', 'version': '4.9.2'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.5'), # 20150119 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.5'), # 20150119 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.7.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.7.2.eb index 7f04debe9c..d72ed94ae6 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.7.2.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'GCC', 'version': '4.7.2'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.8.4.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.8.4.eb index 357867c586..cdbc438429 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.8.4.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'GCC', 'version': '4.8.4'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb index 9fe586bfbb..2b3b95424e 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.2.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'GCC', 'version': '4.9.2'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.3-2.25.eb index 8870d76965..b735d846ba 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-4.9.3-2.25.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb index 25b293c3c4..f3b0354178 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.3-2.25.eb index 80fa06d91b..c1363ba804 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.3-2.25.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb index 0d6c26a78c..cac7fe9cde 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015a.eb index 6a68f164a9..474b894ca2 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015a.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015a.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'foss', 'version': '2015a'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016a.eb index a07bbf4e25..b640e29fa5 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016a.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016a.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'foss', 'version': '2016a'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015b.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015b.eb index 7677218c94..82ab19bc93 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015b.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015b.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'intel', 'version': '2015b'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016a.eb index 0810dfe536..caa4818cd6 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016a.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016a.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'intel', 'version': '2016a'} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb index 6763feae56..af33b5e023 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb @@ -9,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'dummy', 'version': ''} dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.6'), # 20150215 + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb index d2502b1343..5b65e6e0a5 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb @@ -15,7 +15,7 @@ description = """ Argtable is an ANSI C library for parsing GNU style toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%s%s.tar.gz' % (name, version.replace('.','-'))] +sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] sanity_check_paths = { 'files': ['lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.la'], diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goalf-1.1.0-no-OFED.eb index ebcf12ae1b..118bf6fc3b 100644 --- a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goalf-1.1.0-no-OFED.eb @@ -21,8 +21,8 @@ source_urls = ['http://sourceforge.net/projects/aria2/files', 'download'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/aria2c'], - 'dirs': [] - } + 'files': ['bin/aria2c'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goolf-1.4.10.eb b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goolf-1.4.10.eb index cb532e1ea2..7d1302187b 100644 --- a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goolf-1.4.10.eb @@ -21,8 +21,8 @@ source_urls = ['http://sourceforge.net/projects/aria2/files', 'download'] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['bin/aria2c'], - 'dirs': [] - } + 'files': ['bin/aria2c'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-4.0.6.eb b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-4.0.6.eb index 1e9c1ad980..b6ba853506 100644 --- a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-4.0.6.eb @@ -21,8 +21,8 @@ source_urls = ['http://sourceforge.net/projects/aria2/files', 'download'] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/aria2c'], - 'dirs': [] - } + 'files': ['bin/aria2c'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-5.3.0.eb b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-5.3.0.eb index 3da57c79d8..f4d08974f2 100644 --- a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-5.3.0.eb @@ -22,8 +22,8 @@ source_urls = ['http://sourceforge.net/projects/aria2/files', 'download'] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/aria2c'], - 'dirs': [] - } + 'files': ['bin/aria2c'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb b/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb index 5f9ea822ee..1fc6b8de78 100644 --- a/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb +++ b/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb @@ -19,7 +19,7 @@ dependencies = [ sanity_check_paths = { 'files': ["bin/AffineAlign"], - 'dirs': ["bin","share"], + 'dirs': ["bin", "share"], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 64119b5667..4de16cc800 100644 --- a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -18,9 +18,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://launchpad.net/%s/%s.x/%s/+download' % (name.lower(), majver, version)] patches = [ - 'wl_pkg_linkflags.patch', - 'petsc-slepc-libs.patch' - ] + 'wl_pkg_linkflags.patch', + 'petsc-slepc-libs.patch' +] builddependencies = [('CMake', '2.8.4')] @@ -29,27 +29,27 @@ python_version = '2.7.3' versionsuffix = '-%s-%s' % (python, python_version) dependencies = [ - (python, python_version), - ('Boost', '1.49.0', versionsuffix), - ('UFC', '2.0.5', versionsuffix), - ('SWIG', '2.0.4', versionsuffix), - ('FFC', '1.0.0', versionsuffix), - ('FIAT', '1.0.0', versionsuffix), - ('Instant', '1.0.0', versionsuffix), - ('Viper', '1.0.0', versionsuffix), - ('UFL', '1.0.0', versionsuffix), - ('SCOTCH', '5.1.12b_esmumps'), - ('Armadillo', '2.4.4', versionsuffix), - ('ParMETIS', '4.0.2'), - ('SuiteSparse', '3.7.0', '-withparmetis'), - ('CGAL', '4.0', versionsuffix), - ('PETSc', '3.3-p2', versionsuffix), - ('SLEPc', '3.3-p1', versionsuffix), - ('MTL4', '4.0.8878', '', True), - ('Trilinos', '10.12.2', versionsuffix), - ('Sphinx', '1.1.3', versionsuffix), - ('zlib', '1.2.7'), - ('libxml2', '2.8.0') - ] + (python, python_version), + ('Boost', '1.49.0', versionsuffix), + ('UFC', '2.0.5', versionsuffix), + ('SWIG', '2.0.4', versionsuffix), + ('FFC', '1.0.0', versionsuffix), + ('FIAT', '1.0.0', versionsuffix), + ('Instant', '1.0.0', versionsuffix), + ('Viper', '1.0.0', versionsuffix), + ('UFL', '1.0.0', versionsuffix), + ('SCOTCH', '5.1.12b_esmumps'), + ('Armadillo', '2.4.4', versionsuffix), + ('ParMETIS', '4.0.2'), + ('SuiteSparse', '3.7.0', '-withparmetis'), + ('CGAL', '4.0', versionsuffix), + ('PETSc', '3.3-p2', versionsuffix), + ('SLEPc', '3.3-p1', versionsuffix), + ('MTL4', '4.0.8878', '', True), + ('Trilinos', '10.12.2', versionsuffix), + ('Sphinx', '1.1.3', versionsuffix), + ('zlib', '1.2.7'), + ('libxml2', '2.8.0') +] moduleclass = 'math' diff --git a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb index dcf7a43c08..77e43460d5 100644 --- a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -18,10 +18,10 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://launchpad.net/%s/%s.x/%s/+download' % (name.lower(), majver, version)] patches = [ - 'wl_pkg_linkflags.patch', - 'petsc-slepc-libs.patch', - 'DOLFIN-1.0.0_GCC-4.7.patch', - ] + 'wl_pkg_linkflags.patch', + 'petsc-slepc-libs.patch', + 'DOLFIN-1.0.0_GCC-4.7.patch', +] builddependencies = [('CMake', '2.8.4')] @@ -30,27 +30,27 @@ python_version = '2.7.3' versionsuffix = '-%s-%s' % (python, python_version) dependencies = [ - (python, python_version), - ('Boost', '1.49.0', versionsuffix), - ('UFC', '2.0.5', versionsuffix), - ('SWIG', '2.0.4', versionsuffix), - ('FFC', '1.0.0', versionsuffix), - ('FIAT', '1.0.0', versionsuffix), - ('Instant', '1.0.0', versionsuffix), - ('Viper', '1.0.0', versionsuffix), - ('UFL', '1.0.0', versionsuffix), - ('SCOTCH', '5.1.12b_esmumps'), - ('Armadillo', '2.4.4', versionsuffix), - ('ParMETIS', '4.0.2'), - ('SuiteSparse', '3.7.0', '-withparmetis'), - ('CGAL', '4.0', versionsuffix), - ('PETSc', '3.3-p2', versionsuffix), - ('SLEPc', '3.3-p1', versionsuffix), - ('MTL4', '4.0.8878', '', True), - ('Trilinos', '10.12.2', versionsuffix), - ('Sphinx', '1.1.3', versionsuffix), - ('zlib', '1.2.7'), - ('libxml2', '2.8.0') - ] + (python, python_version), + ('Boost', '1.49.0', versionsuffix), + ('UFC', '2.0.5', versionsuffix), + ('SWIG', '2.0.4', versionsuffix), + ('FFC', '1.0.0', versionsuffix), + ('FIAT', '1.0.0', versionsuffix), + ('Instant', '1.0.0', versionsuffix), + ('Viper', '1.0.0', versionsuffix), + ('UFL', '1.0.0', versionsuffix), + ('SCOTCH', '5.1.12b_esmumps'), + ('Armadillo', '2.4.4', versionsuffix), + ('ParMETIS', '4.0.2'), + ('SuiteSparse', '3.7.0', '-withparmetis'), + ('CGAL', '4.0', versionsuffix), + ('PETSc', '3.3-p2', versionsuffix), + ('SLEPc', '3.3-p1', versionsuffix), + ('MTL4', '4.0.8878', '', True), + ('Trilinos', '10.12.2', versionsuffix), + ('Sphinx', '1.1.3', versionsuffix), + ('zlib', '1.2.7'), + ('libxml2', '2.8.0') +] moduleclass = 'math' diff --git a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-ictce-4.0.6-Python-2.7.3.eb index 7391205922..ac6c64cf00 100644 --- a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-ictce-4.0.6-Python-2.7.3.eb @@ -18,9 +18,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://launchpad.net/%s/%s.x/%s/+download' % (name.lower(), majver, version)] patches = [ - 'wl_pkg_linkflags.patch', - 'petsc-slepc-libs.patch' - ] + 'wl_pkg_linkflags.patch', + 'petsc-slepc-libs.patch' +] builddependencies = [('CMake', '2.8.4')] @@ -29,27 +29,27 @@ python_version = '2.7.3' versionsuffix = '-%s-%s' % (python, python_version) dependencies = [ - (python, python_version), - ('Boost', '1.49.0', versionsuffix), - ('UFC', '2.0.5', versionsuffix), - ('SWIG', '2.0.4', versionsuffix), - ('FFC', '1.0.0', versionsuffix), - ('FIAT', '1.0.0', versionsuffix), - ('Instant', '1.0.0', versionsuffix), - ('Viper', '1.0.0', versionsuffix), - ('UFL', '1.0.0', versionsuffix), - ('SCOTCH', '5.1.12b_esmumps'), - ('Armadillo', '2.4.4', versionsuffix), - ('ParMETIS', '4.0.2'), - ('SuiteSparse', '3.7.0', '-withparmetis'), - ('CGAL', '4.0', versionsuffix), - ('PETSc', '3.3-p2', versionsuffix), - ('SLEPc', '3.3-p1', versionsuffix), - ('MTL4', '4.0.8878', '', True), - ('Trilinos', '10.12.2', versionsuffix), - ('Sphinx', '1.1.3', versionsuffix), - ('zlib', '1.2.7'), - ('libxml2', '2.8.0') - ] + (python, python_version), + ('Boost', '1.49.0', versionsuffix), + ('UFC', '2.0.5', versionsuffix), + ('SWIG', '2.0.4', versionsuffix), + ('FFC', '1.0.0', versionsuffix), + ('FIAT', '1.0.0', versionsuffix), + ('Instant', '1.0.0', versionsuffix), + ('Viper', '1.0.0', versionsuffix), + ('UFL', '1.0.0', versionsuffix), + ('SCOTCH', '5.1.12b_esmumps'), + ('Armadillo', '2.4.4', versionsuffix), + ('ParMETIS', '4.0.2'), + ('SuiteSparse', '3.7.0', '-withparmetis'), + ('CGAL', '4.0', versionsuffix), + ('PETSc', '3.3-p2', versionsuffix), + ('SLEPc', '3.3-p1', versionsuffix), + ('MTL4', '4.0.8878', '', True), + ('Trilinos', '10.12.2', versionsuffix), + ('Sphinx', '1.1.3', versionsuffix), + ('zlib', '1.2.7'), + ('libxml2', '2.8.0') +] moduleclass = 'math' diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb index 2734b69ecf..7d7b15088e 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -#This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou @@ -31,8 +31,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py', - 'bin/sumtrees.py','bin/strict_consensus_merge.py'], + 'files': ['bin/cattrees.py', 'bin/long_branch_symmdiff.py', 'bin/sumlabels.py', + 'bin/sumtrees.py', 'bin/strict_consensus_merge.py'], 'dirs': [], } diff --git a/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 67c0828444..05f82d3b1d 100644 --- a/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -24,8 +24,8 @@ dependencies = [(python, pythonversion)] pylibdir = "lib/python%s/site-packages/%s" % (".".join(pythonversion.split(".")[0:2]), name.lower()) sanity_check_paths = { - 'files': [], - 'dirs': ["bin", pylibdir] - } + 'files': [], + 'dirs': ["bin", pylibdir] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-goolf-1.4.10-Python-2.7.3.eb index 53a00b7cbb..b16e3ee2f0 100644 --- a/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-goolf-1.4.10-Python-2.7.3.eb @@ -24,8 +24,8 @@ dependencies = [(python, pythonversion)] pylibdir = "lib/python%s/site-packages/%s" % (".".join(pythonversion.split(".")[0:2]), name.lower()) sanity_check_paths = { - 'files': [], - 'dirs': ["bin", pylibdir] - } + 'files': [], + 'dirs': ["bin", pylibdir] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-ictce-4.0.6-Python-2.7.3.eb index bcb77c2818..e54119ec9b 100644 --- a/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-ictce-4.0.6-Python-2.7.3.eb @@ -24,8 +24,8 @@ dependencies = [(python, pythonversion)] pylibdir = "lib/python%s/site-packages/%s" % (".".join(pythonversion.split(".")[0:2]), name.lower()) sanity_check_paths = { - 'files': [], - 'dirs': ["bin", pylibdir] - } + 'files': [], + 'dirs': ["bin", pylibdir] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-ictce-5.3.0-Python-2.7.3.eb index 63105571a8..9fcadcde27 100644 --- a/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/Docutils/Docutils-0.9.1-ictce-5.3.0-Python-2.7.3.eb @@ -25,8 +25,8 @@ dependencies = [(python, pythonversion)] pylibdir = "lib/python%s/site-packages/%s" % (".".join(pythonversion.split(".")[0:2]), name.lower()) sanity_check_paths = { - 'files': [], - 'dirs': ["bin", pylibdir] - } + 'files': [], + 'dirs': ["bin", pylibdir] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-goolf-1.4.10.eb index c85a8270b1..d0c1108872 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-goolf-1.4.10.eb @@ -30,4 +30,3 @@ modextrapaths = { } moduleclass = 'math' - diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-ictce-6.2.5.eb b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-ictce-6.2.5.eb index 4b9b0d8456..9e1ed006d5 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-ictce-6.2.5.eb @@ -30,4 +30,3 @@ modextrapaths = { } moduleclass = 'math' - diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-intel-2014b.eb b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-intel-2014b.eb index e57e27043b..76755f474c 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-intel-2014b.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-intel-2014b.eb @@ -30,4 +30,3 @@ modextrapaths = { } moduleclass = 'math' - diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index 903be570eb..9ff6f83aaf 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -16,8 +16,8 @@ checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] options = {'modulename': 'jube2'} sanity_check_paths = { - 'files': ['bin/jube'], - 'dirs': [] + 'files': ['bin/jube'], + 'dirs': [] } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index 545b5785ea..6a73bae83a 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -16,8 +16,8 @@ checksums = ['96a7946d38d678b25ba4bbd539482a14'] options = {'modulename': 'jube2'} sanity_check_paths = { - 'files': ['bin/jube'], - 'dirs': [] + 'files': ['bin/jube'], + 'dirs': [] } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index b270f53d57..0d36653ae0 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -16,8 +16,8 @@ checksums = ['f506e9f39898af3d7456890ba219ab90'] options = {'modulename': 'jube2'} sanity_check_paths = { - 'files': ['bin/jube'], - 'dirs': [] + 'files': ['bin/jube'], + 'dirs': [] } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 46c4f977e8..5d9c1fff84 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -18,16 +18,16 @@ pythonversion = "2.7.3" versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('setuptools', '0.6c11', versionsuffix) - ] + (python, pythonversion), + ('setuptools', '0.6c11', versionsuffix) +] py_short_ver = ".".join(pythonversion.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': [], - 'dirs': ["%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)] - } + 'files': [], + 'dirs': ["%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb index e37ffbc4e2..2e7f9bf582 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb @@ -17,16 +17,16 @@ pythonversion = "2.7.3" versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('setuptools', '0.6c11', versionsuffix) - ] + (python, pythonversion), + ('setuptools', '0.6c11', versionsuffix) +] py_short_ver = ".".join(pythonversion.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': [], - 'dirs': ["%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)] - } + 'files': [], + 'dirs': ["%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb index 191856a900..6ac06a966d 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb @@ -18,16 +18,16 @@ pythonversion = "2.7.3" versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('setuptools', '0.6c11', versionsuffix) - ] + (python, pythonversion), + ('setuptools', '0.6c11', versionsuffix) +] py_short_ver = ".".join(pythonversion.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': [], - 'dirs': ["%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)] - } + 'files': [], + 'dirs': ["%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb index 9711dba080..64c7c6c244 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb @@ -18,16 +18,16 @@ pythonversion = "2.7.3" versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('setuptools', '0.6c11', versionsuffix) - ] + (python, pythonversion), + ('setuptools', '0.6c11', versionsuffix) +] py_short_ver = ".".join(pythonversion.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': [], - 'dirs': ["%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)] - } + 'files': [], + 'dirs': ["%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)] +} moduleclass = 'devel' -- GitLab From 0ef9e51a9c654cfa3fc26f6c9b639a6ac2008f27 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 11:23:32 +0100 Subject: [PATCH 0265/2133] Style fixes with autopep8: b Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb | 6 +++--- .../BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb | 2 +- .../BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb | 2 +- .../BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb | 2 +- .../BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb | 2 +- .../b/BEDTools/BEDTools-2.22.0-intel-2014b.eb | 2 +- .../BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 2 +- .../b/BEDTools/BEDTools-2.23.0-intel-2015a.eb | 2 +- .../b/BEDTools/BEDTools-2.25.0-foss-2015a.eb | 2 +- .../BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb | 2 +- .../BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb | 6 +++--- .../b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb | 6 +++--- .../b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb | 6 +++--- .../b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb | 6 +++--- .../b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb | 6 +++--- .../BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb | 1 - .../b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb | 1 - .../b/BLAST/BLAST-2.2.26-Linux_x86_64.eb | 2 +- .../BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb | 5 ++--- .../b/BOINC/BOINC-7.2.42-GCC-4.8.2-client.eb | 19 +++++++++---------- .../BOINC/BOINC-7.2.42-ictce-5.5.0-client.eb | 19 +++++++++---------- .../b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb | 16 ++++++++-------- .../b/BamTools/BamTools-2.4.0-foss-2015b.eb | 2 +- .../b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/b/Bash/Bash-4.3-GCC-4.9.2.eb | 14 +++++++------- .../b/BayesTraits/BayesTraits-1.0-linux32.eb | 2 +- .../BayesTraits-2.0-Beta-Linux64.eb | 2 +- easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb | 5 ++--- ...iopython-1.61-goolf-1.4.10-Python-2.7.3.eb | 6 +++--- ...Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb | 6 +++--- .../b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 8 ++++---- .../b/Bison/Bison-2.7-iccifort-2011.13.367.eb | 4 ++-- .../b/Bison/Bison-2.7-ictce-4.1.13.eb | 4 ++-- .../b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb | 6 +++--- .../Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb | 6 +++--- .../b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb | 6 +++--- .../b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb | 7 +++---- .../b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb | 7 +++---- .../b/Boost/Boost-1.47.0-goolf-1.4.10.eb | 2 +- ...1.49.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../Boost-1.49.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Boost-1.49.0-goolf-1.4.10-Python-2.7.5.eb | 2 +- .../Boost-1.49.0-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../Boost-1.49.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb | 4 ++-- ...1.51.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../Boost/Boost-1.51.0-goalf-1.1.0-no-OFED.eb | 2 +- .../Boost-1.51.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../b/Boost/Boost-1.51.0-goolf-1.4.10.eb | 2 +- .../Boost-1.51.0-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../b/Boost/Boost-1.51.0-ictce-4.0.6.eb | 2 +- .../b/Boost/Boost-1.51.0-ictce-4.1.13.eb | 2 +- .../b/Boost/Boost-1.51.0-ictce-5.2.0.eb | 2 +- .../Boost-1.51.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../b/Boost/Boost-1.51.0-ictce-5.3.0.eb | 2 +- ....53.0-goalf-1.5.12-no-OFED-Python-2.7.5.eb | 2 +- .../b/Boost/Boost-1.53.0-goolf-1.4.10.eb | 2 +- .../Boost-1.53.0-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../b/Boost/Boost-1.53.0-ictce-4.1.13.eb | 2 +- .../b/Boost/Boost-1.53.0-ictce-5.2.0.eb | 2 +- .../Boost-1.53.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../Boost-1.53.0-ictce-5.3.0-Python-2.7.5.eb | 2 +- .../b/Boost/Boost-1.53.0-ictce-5.3.0.eb | 2 +- .../Boost-1.53.0-ictce-5.5.0-Python-2.7.5.eb | 2 +- .../b/Boost/Boost-1.53.0-ictce-6.2.5.eb | 2 +- .../Boost-1.55.0-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb | 2 +- easybuild/easyconfigs/b/Boost/Boost-1.55.0.eb | 2 +- .../b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb | 6 +++--- .../b/Bowtie/Bowtie-1.1.2-foss-2015b.eb | 6 +++--- .../b/Bowtie/Bowtie-1.1.2-intel-2015a.eb | 7 +++---- .../b/Bowtie/Bowtie-1.1.2-intel-2015b.eb | 7 +++---- .../b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 4 ++-- .../b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 2 +- .../b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 4 ++-- .../b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 4 ++-- .../b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb | 4 ++-- .../b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb | 2 +- .../b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb | 2 +- .../b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb | 2 +- .../b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb | 2 +- .../b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb | 2 +- .../bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb | 6 +++--- .../b/bbFTP/bbFTP-3.2.0-goolf-1.4.10.eb | 6 +++--- .../bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb | 1 - .../bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb | 8 ++++---- .../b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb | 8 ++++---- .../b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb | 2 +- .../easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb | 8 ++++---- ...beagle-lib-20120124-goalf-1.1.0-no-OFED.eb | 4 ++-- .../beagle-lib-20120124-goolf-1.4.10.eb | 4 ++-- .../beagle-lib-20120124-ictce-4.0.6.eb | 4 ++-- .../beagle-lib-20120124-ictce-5.3.0.eb | 4 ++-- .../beagle-lib-20141202-intel-2015a.eb | 6 +++--- .../binutils-2.22-goalf-1.1.0-no-OFED.eb | 2 +- .../binutils-2.22-gompi-1.4.12-no-OFED.eb | 2 +- .../b/binutils/binutils-2.22-goolf-1.4.10.eb | 2 +- .../b/binutils/binutils-2.22-goolf-1.5.14.eb | 2 +- .../b/binutils/binutils-2.24-foss-2014b.eb | 2 +- .../b/binutils/binutils-2.24-intel-2014b.eb | 2 +- .../binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 2 +- .../binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3.eb | 2 +- .../binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25.1.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25.eb | 2 +- .../byacc-20120526-goalf-1.1.0-no-OFED.eb | 6 +++--- .../b/byacc/byacc-20120526-goolf-1.4.10.eb | 6 +++--- .../b/byacc/byacc-20120526-ictce-4.0.6.eb | 8 ++++---- .../b/byacc/byacc-20120526-ictce-5.3.0.eb | 6 +++--- 112 files changed, 212 insertions(+), 223 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb index 6e29870586..ffd5f8b8e6 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb @@ -28,9 +28,9 @@ parallel = 1 files_to_copy = ["bin"] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed" , "sort-bed", - "starchcat", "vcf2bed", "wig2bed", - "gtf2bed", "bedops", "wig2bed"]], + 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed", "sort-bed", + "starchcat", "vcf2bed", "wig2bed", + "gtf2bed", "bedops", "wig2bed"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb index ba457aaa3a..0c8d3ca6a1 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb @@ -18,7 +18,7 @@ buildopts = 'CXX="$CXX"' files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.rst'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test'], } diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb index e21399a897..dc8e5c74f1 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb @@ -18,7 +18,7 @@ buildopts = 'CXX="$CXX"' files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.rst'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test'], } diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb index 3d93f1ffe1..f0c69050e7 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb @@ -22,7 +22,7 @@ buildopts = 'CXX="$CXX"' files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.rst'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test'], } diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb index 28fd6859e0..f644a66576 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb @@ -20,7 +20,7 @@ sources = ['v%(version)s.tar.gz'] files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.md'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test'], } diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb index 92af179960..7133a6b8a4 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb @@ -22,7 +22,7 @@ buildopts = 'CXX="$CXX"' files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.md'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test'], } diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb index 2493984594..2f9e862e72 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -25,7 +25,7 @@ buildopts = 'CXX="$CXX"' files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], 'dirs': files_to_copy, } diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb index 6160ea7421..185d7a2d1a 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb @@ -22,7 +22,7 @@ buildopts = 'CXX="$CXX"' files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], } diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb index 6997e33823..bcb3a9de52 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015a.eb @@ -26,7 +26,7 @@ buildopts = 'CXX="$CXX"' files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], 'dirs': files_to_copy, } diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb index 3e92e22059..a4e3ce1eb7 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb @@ -26,7 +26,7 @@ buildopts = 'CXX="$CXX"' files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], 'dirs': files_to_copy, } diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb index 8129083a06..3d76340994 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb @@ -30,8 +30,8 @@ dependencies = [('Boost', '1.51.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' sanity_check_paths = { - 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], - 'dirs': [] - } + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb index e7772ac728..d441a3b6be 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb @@ -30,8 +30,8 @@ dependencies = [('Boost', '1.51.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' sanity_check_paths = { - 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], - 'dirs': [] - } + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb index 3800356ed9..5d3bf84644 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb @@ -32,8 +32,8 @@ dependencies = [('Boost', '1.51.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' sanity_check_paths = { - 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], - 'dirs': [] - } + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb index d52c0aba66..0da49b06b6 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb @@ -30,8 +30,8 @@ dependencies = [('Boost', '1.51.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' sanity_check_paths = { - 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], - 'dirs': [] - } + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb index adcf957193..9a1f3c0269 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb @@ -32,8 +32,8 @@ dependencies = [('Boost', '1.51.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' sanity_check_paths = { - 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], - 'dirs': [] - } + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb index 37178f8aa5..8c97b6b7aa 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb @@ -38,4 +38,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb index 505c849588..5daf7c4b33 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb @@ -37,4 +37,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb index 7b97564a4d..22babb46e9 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb @@ -20,7 +20,7 @@ source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/release/%(version) sources = ['%(namelower)s-%(version)s-x64-linux.tar.gz'] sanity_check_paths = { - 'files': ["bin/blastall", "bin/impala", "bin/blastpgp" ], + 'files': ["bin/blastall", "bin/impala", "bin/blastpgp"], 'dirs': [] } diff --git a/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb b/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb index ba1d06a7ff..5d421fbcca 100644 --- a/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb +++ b/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb @@ -16,8 +16,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_BZ2] dependencies = [ - ('OpenSSL','1.0.1f'), - ('cURL','7.29.0'), + ('OpenSSL', '1.0.1f'), + ('cURL', '7.29.0'), ] with_configure = True @@ -34,4 +34,3 @@ sanity_check_paths = { } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-GCC-4.8.2-client.eb b/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-GCC-4.8.2-client.eb index 599b616ab9..20337ea09b 100644 --- a/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-GCC-4.8.2-client.eb +++ b/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-GCC-4.8.2-client.eb @@ -16,17 +16,17 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_BZ2] dependencies = [ - ('OpenSSL','1.0.1f'), - ('cURL','7.34.0'), + ('OpenSSL', '1.0.1f'), + ('cURL', '7.34.0'), ] builddependencies = [ - ('libtool','2.4.2'), - ('make','3.82'), - ('pkg-config','0.28'), - ('M4','1.4.16'), - ('Autoconf','2.69'), - ('Automake','1.14.1') + ('libtool', '2.4.2'), + ('make', '3.82'), + ('pkg-config', '0.28'), + ('M4', '1.4.16'), + ('Autoconf', '2.69'), + ('Automake', '1.14.1') ] prebuildopts = "./_autosetup && ./configure --disable-server --disable-manager --enable-client &&" @@ -35,9 +35,8 @@ files_to_copy = [(['client/boinc', 'client/boinccmd'], 'bin')] # make sure the binary are available after installation sanity_check_paths = { - 'files': ["bin/boinc",], + 'files': ["bin/boinc", ], 'dirs': [], } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-ictce-5.5.0-client.eb b/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-ictce-5.5.0-client.eb index bc81b334de..1915ed43fc 100644 --- a/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-ictce-5.5.0-client.eb +++ b/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-ictce-5.5.0-client.eb @@ -16,17 +16,17 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_BZ2] dependencies = [ - ('OpenSSL','1.0.1f'), - ('cURL','7.34.0'), + ('OpenSSL', '1.0.1f'), + ('cURL', '7.34.0'), ] builddependencies = [ - ('libtool','2.4.2'), - ('make','3.82'), - ('pkg-config','0.28'), - ('M4','1.4.16'), - ('Autoconf','2.69'), - ('Automake','1.14') + ('libtool', '2.4.2'), + ('make', '3.82'), + ('pkg-config', '0.28'), + ('M4', '1.4.16'), + ('Autoconf', '2.69'), + ('Automake', '1.14') ] prebuildopts = "./_autosetup && ./configure --disable-server --disable-manager --enable-client &&" @@ -35,9 +35,8 @@ files_to_copy = [(['client/boinc', 'client/boinccmd'], 'bin')] # make sure the binary are available after installation sanity_check_paths = { - 'files': ["bin/boinc",], + 'files': ["bin/boinc", ], 'dirs': [], } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb index d31fc0a136..400f14ed06 100644 --- a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb @@ -16,20 +16,20 @@ skipsteps = ['configure'] installopts = "DESTDIR=%(installdir)s" patches = [ - 'BSMAP-2.74_makefile-modif.patch', - 'BSMAP-2.74_parameters-cpp.patch', - 'BSMAP-2.74_samtools-deps.patch', + 'BSMAP-2.74_makefile-modif.patch', + 'BSMAP-2.74_parameters-cpp.patch', + 'BSMAP-2.74_samtools-deps.patch', ] dependencies = [ - ('ncurses', '5.9'), - ('zlib', '1.2.7'), - ('SAMtools', '0.1.18'), + ('ncurses', '5.9'), + ('zlib', '1.2.7'), + ('SAMtools', '0.1.18'), ] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bsmap", "methratio.py", "sam2bam.sh"]], - 'dirs': [], + 'files': ["bin/%s" % x for x in ["bsmap", "methratio.py", "sam2bam.sh"]], + 'dirs': [], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2015b.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2015b.eb index c4a843674b..9e9c2961a5 100644 --- a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2015b.eb @@ -22,7 +22,7 @@ builddependencies = [('CMake', '3.4.1')] files_to_copy = ["bin", "lib", "include", "docs", "LICENSE", "README"] -sanity_check_paths = { +sanity_check_paths = { 'files': ["bin/bamtools", "include/shared/bamtools_global.h", "lib/libbamtools.a", "lib/libbamtools.so", "lib/libbamtools-utils.a", "lib/libjsoncpp.a"], 'dirs': ["include/api", "docs"] diff --git a/easybuild/easyconfigs/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb index b2a23aa149..57dbb97a1a 100644 --- a/easybuild/easyconfigs/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb @@ -20,7 +20,7 @@ description = """Bash is an sh-compatible command language interpreter that exec read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).""" -toolchain = {'name' : 'goalf', 'version' : '1.1.0-no-OFED'} +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/b/Bash/Bash-4.3-GCC-4.9.2.eb b/easybuild/easyconfigs/b/Bash/Bash-4.3-GCC-4.9.2.eb index d02188852b..3d11d3fad4 100644 --- a/easybuild/easyconfigs/b/Bash/Bash-4.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/Bash/Bash-4.3-GCC-4.9.2.eb @@ -1,13 +1,13 @@ ## -## This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild ## -## Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -## Authors:: Valentin Plugaru -## License:: MIT/GPL -## $Id$ +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ ## -## This work implements a part of the HPCBIOS project and is a component of the policy: -## http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html ### # easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb index 49c78aa1c4..8d561cd81b 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb @@ -27,6 +27,6 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = {'PATH':''} +modextrapaths = {'PATH': ''} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb index 159ed9b248..29cb55f251 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb @@ -28,6 +28,6 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = {'PATH':''} +modextrapaths = {'PATH': ''} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb b/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb index b396cebf89..16f5b548ac 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb @@ -25,13 +25,12 @@ dependencies = [ # this is not mandatory but beagle-lib is recommended by developers # beagle-lib will also load the required java dependency # if you remove this you should add the java dependency - ('beagle-lib', '20120124', '',('goolf', '1.4.10')), + ('beagle-lib', '20120124', '', ('goolf', '1.4.10')), ] sanity_check_paths = { - 'files': ["bin/beast" ], + 'files': ["bin/beast"], 'dirs': [] } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb index baf247c07d..45922449e6 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb @@ -36,9 +36,9 @@ dependencies = [ sanity_check_paths = { 'files': [], 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, - 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ - pyshortver), - 'lib/python%s/site-packages/BioSQL' % pyshortver] + 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version, + pyshortver), + 'lib/python%s/site-packages/BioSQL' % pyshortver] } options = {'modulename': 'Bio'} diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb index 96eae4f635..cdbf5d2851 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb @@ -36,9 +36,9 @@ dependencies = [ sanity_check_paths = { 'files': [], 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, - 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ - pyshortver), - 'lib/python%s/site-packages/BioSQL' % pyshortver] + 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version, + pyshortver), + 'lib/python%s/site-packages/BioSQL' % pyshortver] } options = {'modulename': 'Bio'} diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb index 07dcfa192d..9fe13b94a1 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -18,14 +18,14 @@ determine cytosine methylation states""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["http://www.bioinformatics.babraham.ac.uk/projects/bismark/"] -sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] +sources = ['%s_v%s.tar.gz' % (name.lower(), version)] dependencies = [('Bowtie2', '2.0.2')] sanity_check_paths = { - 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", - "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], - 'dirs': [], + 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", + "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-iccifort-2011.13.367.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-iccifort-2011.13.367.eb index 6f79524592..0971fbca29 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-iccifort-2011.13.367.eb @@ -15,8 +15,8 @@ source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] sanity_check_paths = { - 'files':["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs':[], + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb index 1345612aec..a47f4cfdd8 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb @@ -15,8 +15,8 @@ source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] sanity_check_paths = { - 'files':["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs':[], + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb index 28b4adc0bd..5a270ebc00 100644 --- a/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb @@ -23,9 +23,9 @@ sources = [SOURCE_TAR_GZ] # put here the list of generated executables when compiling list_of_executables = ["convertSamples", "estimateDE", "estimateExpression", "estimateHyperPar", - "estimateVBExpression", "extractSamples", "getFoldChange", "getGeneExpression", - "getPPLR", "getVariance", "getWithinGeneExpression", "parseAlignment", - "transposeLargeFile", "getCounts.py", "extractTranscriptInfo.py"] + "estimateVBExpression", "extractSamples", "getFoldChange", "getGeneExpression", + "getPPLR", "getVariance", "getWithinGeneExpression", "parseAlignment", + "transposeLargeFile", "getCounts.py", "extractTranscriptInfo.py"] # this is the real EasyBuild line to copy all the executables to "bin" files_to_copy = [(list_of_executables, "bin")] diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb index 41a9f3fdef..8bcb1abedd 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb @@ -21,8 +21,8 @@ source_urls = ['http://www.coker.com.au/bonnie++/'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['sbin/bonnie++'], - 'dirs': [] - } + 'files': ['sbin/bonnie++'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb index 28f31121d6..fd432782eb 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb @@ -21,8 +21,8 @@ source_urls = ['http://www.coker.com.au/bonnie++/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['sbin/bonnie++'], - 'dirs': [] - } + 'files': ['sbin/bonnie++'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb index 7b2aca1bc7..f4e01e36bd 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb @@ -21,9 +21,8 @@ source_urls = ['http://www.coker.com.au/bonnie++/'] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['sbin/bonnie++'], - 'dirs': [] - } + 'files': ['sbin/bonnie++'], + 'dirs': [] +} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb index 80cfb940af..c663871a9c 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb @@ -22,9 +22,8 @@ source_urls = ['http://www.coker.com.au/bonnie++/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['sbin/bonnie++'], - 'dirs': [] - } + 'files': ['sbin/bonnie++'], + 'dirs': [] +} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.47.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.47.0-goolf-1.4.10.eb index 93386e296d..3a571ac328 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.47.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.47.0-goolf-1.4.10.eb @@ -19,6 +19,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 3a7a111835..38cca32ea7 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -21,6 +21,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.3.eb index c961d98fd8..26f6bca712 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.3.eb @@ -21,6 +21,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.5.eb index 99ad6a98dc..a28c67be70 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.5.eb @@ -21,6 +21,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-ictce-4.0.6-Python-2.7.3.eb index 7e087bb042..f6191d854f 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-ictce-4.0.6-Python-2.7.3.eb @@ -23,6 +23,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-ictce-5.3.0-Python-2.7.3.eb index 3988e42a3d..ea0b132e92 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-ictce-5.3.0-Python-2.7.3.eb @@ -23,6 +23,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb index 6d898a6437..4d9a1a23d1 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] -#maxparallel=1 +osdependencies = [('zlib-devel', 'zlib1g-dev')] +# maxparallel=1 moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index d48b1c70a1..26a0348c88 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -21,6 +21,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED.eb index cb53c502fc..5841132659 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goolf-1.4.10-Python-2.7.3.eb index 313d9d65c4..95d230ca9d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goolf-1.4.10-Python-2.7.3.eb @@ -21,6 +21,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goolf-1.4.10.eb index f5cc38969b..fe0aacf8dd 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goolf-1.4.10.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6-Python-2.7.3.eb index b323695956..7d098018b7 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6-Python-2.7.3.eb @@ -23,6 +23,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6.eb index 709900a2b0..20af60928b 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.1.13.eb index edcf74cbec..9b9c1f416c 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.1.13.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.2.0.eb index 97d8361b7a..078df28545 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.2.0.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.3.0-Python-2.7.3.eb index 13e799e076..c0d9d3958e 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.3.0-Python-2.7.3.eb @@ -23,6 +23,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.3.0.eb index b49e9e58e9..016ded779d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-5.3.0.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goalf-1.5.12-no-OFED-Python-2.7.5.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goalf-1.5.12-no-OFED-Python-2.7.5.eb index 403498d6f4..8177dfdfc7 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goalf-1.5.12-no-OFED-Python-2.7.5.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goalf-1.5.12-no-OFED-Python-2.7.5.eb @@ -21,6 +21,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goolf-1.4.10.eb index 6e295b56b6..90c4f9d0e5 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goolf-1.4.10.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13-Python-2.7.3.eb index 354f0c7260..15ca81dd99 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13-Python-2.7.3.eb @@ -23,6 +23,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13.eb index fad7f26ba9..e59984e8e7 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.2.0.eb index 472f8aa41f..6c8ec824c0 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.2.0.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.3.eb index b82fa3aec4..79d1f85483 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.3.eb @@ -23,6 +23,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.5.eb index e55911ea59..0ed130e7a2 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.5.eb @@ -21,6 +21,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0.eb index a7526a054e..125204c6c1 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.5.0-Python-2.7.5.eb index c3ef017964..d634055e62 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.5.0-Python-2.7.5.eb @@ -23,6 +23,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-6.2.5.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-6.2.5.eb index 5d078f7526..2d3562ccc9 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-6.2.5.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-5.5.0-Python-2.7.6.eb index 87a7b60a53..6436848a16 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-5.5.0-Python-2.7.6.eb @@ -23,6 +23,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb index d29dcc1cda..005df0b624 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb @@ -23,6 +23,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0.eb index fb5ddf0185..9e85b84df7 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0.eb @@ -16,6 +16,6 @@ configopts = '--without-libraries=python' toolset = 'gcc' -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb index 0240ff0e2c..b0b3446182 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb @@ -1,6 +1,6 @@ -#Modified from existing version by: -#Robert Schmidt -#Ottawa Hospital Research Institute - Bioinformatics Team +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team name = 'Bowtie' version = '1.1.1' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2015b.eb index 74828669ae..b83380f7c8 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2015b.eb @@ -1,6 +1,6 @@ -#Modified from existing version by: -#Robert Schmidt -#Ottawa Hospital Research Institute - Bioinformatics Team +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team name = 'Bowtie' version = '1.1.2' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb index 8837567287..6eb22c637f 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb @@ -1,6 +1,6 @@ -#Modified from existing version by: -#Robert Schmidt -#Ottawa Hospital Research Institute - Bioinformatics Team +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team name = 'Bowtie' version = '1.1.2' @@ -18,4 +18,3 @@ source_urls = ['http://download.sourceforge.net/bowtie-bio/'] patches = ['int64typedef.patch'] moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015b.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015b.eb index 63be2bee21..e8fb12a0cf 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015b.eb @@ -1,6 +1,6 @@ -#Modified from existing version by: -#Robert Schmidt -#Ottawa Hospital Research Institute - Bioinformatics Team +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team name = 'Bowtie' version = '1.1.2' @@ -18,4 +18,3 @@ source_urls = ['http://download.sourceforge.net/bowtie-bio/'] patches = ['int64typedef.patch'] moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index ae75b8cebd..dc88165bd7 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'Bowtie2' version = '2.0.5' @@ -22,7 +22,7 @@ source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/ files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), - "doc", "example", "scripts",] + "doc", "example", "scripts", ] sanity_check_paths = { 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index 640a7f6d83..f0363a6b44 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'Bowtie2' version = '2.0.6' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index 93890f908f..9de79dd21c 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'Bowtie2' version = '2.1.0' @@ -22,7 +22,7 @@ source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/ files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), - "doc", "example","scripts"] + "doc", "example", "scripts"] sanity_check_paths = { 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index 6dbb873164..19af7a159b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'Bowtie2' version = '2.2.0' @@ -22,7 +22,7 @@ source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/ files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "doc", "example", "scripts"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb index 83794c9d53..cc0a728014 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'Bowtie2' version = '2.2.2' @@ -22,7 +22,7 @@ source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/ files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb index 1a8d964de1..d2d24de2f8 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb @@ -24,7 +24,7 @@ source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/ files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb index 30dfc18960..3f05bda0e8 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb @@ -24,7 +24,7 @@ source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/ files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb index cc4bd53b3a..d7856c8fa2 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb @@ -24,7 +24,7 @@ source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/ files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb index 9b9219de67..a342fa3e4d 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb @@ -24,7 +24,7 @@ source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/ files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb index 7fc6a11c7d..3901df0ef7 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb @@ -24,7 +24,7 @@ source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/ files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb index 523b1ad59c..e14fa5b01a 100644 --- a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb @@ -32,8 +32,8 @@ start_dir = 'bbftpc' buildopts = "CC=$CC" sanity_check_paths = { - 'files': ['bin/bbftp'], - 'dirs': [] - } + 'files': ['bin/bbftp'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goolf-1.4.10.eb index b3183258a9..b334202a6e 100644 --- a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goolf-1.4.10.eb @@ -32,8 +32,8 @@ start_dir = 'bbftpc' buildopts = "CC=$CC" sanity_check_paths = { - 'files': ['bin/bbftp'], - 'dirs': [] - } + 'files': ['bin/bbftp'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb b/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb index 81abdbbdb7..17f6d6b14b 100644 --- a/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb +++ b/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb @@ -35,4 +35,3 @@ sanity_check_paths = { } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb index ead21fe6c8..eae65e841f 100644 --- a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb @@ -24,13 +24,13 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCE_TAR_BZ2] source_urls = ['http://bbftppro.myftp.org/'] -unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball +unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball start_dir = 'bbftpc' sanity_check_paths = { - 'files': ['bin/bbftp'], - 'dirs': [] - } + 'files': ['bin/bbftp'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb index 944cb25b8b..29c92454a6 100644 --- a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb @@ -24,13 +24,13 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_BZ2] source_urls = ['http://bbftppro.myftp.org/'] -unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball +unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball start_dir = 'bbftpc' sanity_check_paths = { - 'files': ['bin/bbftp'], - 'dirs': [] - } + 'files': ['bin/bbftp'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb index 8cff88ba26..21a811ccbf 100644 --- a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_BZ2] source_urls = ['http://bbftppro.myftp.org/'] -unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball +unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball start_dir = 'bbftpc' diff --git a/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb b/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb index 1d80e71dae..3755390098 100644 --- a/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb @@ -17,12 +17,12 @@ sources = [SOURCELOWER_TAR_BZ2] toolchain = {'name': 'GCC', 'version': '4.8.2'} dependencies = [ - ('libreadline','6.3'), - ('flex','2.5.38'), - ('Bison','3.0.2'), + ('libreadline', '6.3'), + ('flex', '2.5.38'), + ('Bison', '3.0.2'), ] builddependencies = [ - ('texinfo','5.2'), + ('texinfo', '5.2'), ] configopts = ['--with-readline'] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb index 8cc9ec017e..0165eeb653 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile for includefile in ["beagle.h", "platform.h"]] + ["lib/libhmsbeagle%s.so" % libfile - for libfile in ["-cpu", "-cpu-sse", "-jni" ,""]], - 'dirs' : [] + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] } moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb index 6ce8bc4c64..f54d71284a 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb @@ -27,8 +27,8 @@ sanity_check_paths = { 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile for includefile in ["beagle.h", "platform.h"]] + ["lib/libhmsbeagle%s.so" % libfile - for libfile in ["-cpu", "-cpu-sse", "-jni" ,""]], - 'dirs' : [] + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] } moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb index 1a9b8e86f1..55504df755 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb @@ -23,8 +23,8 @@ sanity_check_paths = { 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile for includefile in ["beagle.h", "platform.h"]] + ["lib/libhmsbeagle%s.so" % libfile - for libfile in ["-cpu", "-cpu-sse", "-jni" ,""]], - 'dirs' : [] + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] } moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb index 971aefa649..d4fc0c8fee 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb @@ -23,8 +23,8 @@ sanity_check_paths = { 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile for includefile in ["beagle.h", "platform.h"]] + ["lib/libhmsbeagle%s.so" % libfile - for libfile in ["-cpu", "-cpu-sse", "-jni" ,""]], - 'dirs' : [] + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] } moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb index 6958ac7224..cc7febf444 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'beagle-lib' -#revision r1261 +# revision r1261 version = '20141202' homepage = 'http://code.google.com/p/beagle-lib/' @@ -29,8 +29,8 @@ sanity_check_paths = { 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile for includefile in ["beagle.h", "platform.h"]] + ["lib/libhmsbeagle%s.so" % libfile - for libfile in ["-cpu", "-cpu-sse", "-jni" ,""]], - 'dirs' : [] + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] } moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index 89688dc6f1..bfc339020f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -28,7 +28,7 @@ source_urls = [GNU_SOURCE] configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index fc3ab9230d..437f04c2a6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -28,7 +28,7 @@ source_urls = [GNU_SOURCE] configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index 10612dc973..5f76d89a06 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -27,7 +27,7 @@ source_urls = [GNU_SOURCE] configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb index f0f82557eb..5dae8ebe27 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -25,7 +25,7 @@ sources = ['binutils-%(version)s.tar.bz2'] source_urls = [GNU_SOURCE] binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb index f289f62f1b..3d49fdcf03 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb @@ -19,7 +19,7 @@ dependencies = [ configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 90ee55811f..77fb03962b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -22,7 +22,7 @@ configopts = '--with-sysroot=/' buildopts = 'CFLAGS="$CFLAGS -wd175"' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 9ceff3cb2c..608c44a155 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -29,7 +29,7 @@ prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index f62c14d803..17ecd5c190 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -28,7 +28,7 @@ prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 6d5e96c3f7..61254037e0 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -29,7 +29,7 @@ prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index 36bd18b1ae..0007322f1f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -28,7 +28,7 @@ prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index e24f90d2ed..e6f5a84c78 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -29,7 +29,7 @@ prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 77644355ad..5fcc8fc6b3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -29,7 +29,7 @@ prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index 6e4fce3123..b6d188a41b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -29,7 +29,7 @@ prebuildopts = preconfigopts configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 12add4fe48..3a95cee4b6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -29,7 +29,7 @@ prebuildopts = preconfigopts configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb index 42ae4e574e..17776b5889 100644 --- a/easybuild/easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb @@ -13,8 +13,8 @@ sources = [SOURCELOWER_TGZ] source_urls = ['ftp://invisible-island.net/byacc'] sanity_check_paths = { - 'files': ["bin/yacc"], - 'dirs': [] - } + 'files': ["bin/yacc"], + 'dirs': [] +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/byacc/byacc-20120526-goolf-1.4.10.eb b/easybuild/easyconfigs/b/byacc/byacc-20120526-goolf-1.4.10.eb index f53938591a..9a479b92a1 100644 --- a/easybuild/easyconfigs/b/byacc/byacc-20120526-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/byacc/byacc-20120526-goolf-1.4.10.eb @@ -13,8 +13,8 @@ sources = [SOURCELOWER_TGZ] source_urls = ['ftp://invisible-island.net/byacc'] sanity_check_paths = { - 'files': ["bin/yacc"], - 'dirs': [] - } + 'files': ["bin/yacc"], + 'dirs': [] +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb b/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb index b2e4ab6e24..5112bff567 100644 --- a/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb @@ -7,14 +7,14 @@ homepage = 'http://invisible-island.net/byacc/byacc.html' description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.""" -toolchain = {'name': 'ictce', 'version' : '4.0.6'} +toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = [SOURCELOWER_TGZ] source_urls = ['ftp://invisible-island.net/byacc'] sanity_check_paths = { - 'files': ["bin/yacc"], - 'dirs': [] - } + 'files': ["bin/yacc"], + 'dirs': [] +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-5.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-5.3.0.eb index 39def10fe5..2dcca844dd 100644 --- a/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-5.3.0.eb @@ -14,8 +14,8 @@ sources = [SOURCELOWER_TGZ] source_urls = ['ftp://invisible-island.net/byacc'] sanity_check_paths = { - 'files': ["bin/yacc"], - 'dirs': [] - } + 'files': ["bin/yacc"], + 'dirs': [] +} moduleclass = 'lang' -- GitLab From bd64ddba02efe71576b39eb5d961a3970337148a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 11:40:39 +0100 Subject: [PATCH 0266/2133] Style fixes with autopep8: e, k, q, w, y and z Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../ECore-1.5.2-ictce-5.5.0-clusterapps.eb | 8 +++---- .../e/ECore/ECore-1.5.2-ictce-5.5.0.eb | 2 +- .../e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb | 4 ++-- .../e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb | 4 ++-- .../ELinks-0.12pre5-goalf-1.1.0-no-OFED.eb | 6 ++--- .../e/ELinks/ELinks-0.12pre5-goolf-1.4.10.eb | 6 ++--- .../e/ELinks/ELinks-0.12pre5-ictce-4.0.6.eb | 6 ++--- .../e/ELinks/ELinks-0.12pre5-ictce-5.3.0.eb | 6 ++--- ...esSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb | 12 +++++----- ...PResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb | 12 +++++----- .../ESPResSo-3.1.1-goolf-1.4.10-parallel.eb | 10 ++++----- .../ESPResSo-3.1.1-goolf-1.4.10-serial.eb | 10 ++++----- .../ESPResSo-3.1.1-ictce-4.0.6-parallel.eb | 12 +++++----- .../ESPResSo-3.1.1-ictce-4.0.6-serial.eb | 12 +++++----- .../ESPResSo-3.1.1-ictce-5.3.0-parallel.eb | 10 ++++----- .../ESPResSo-3.1.1-ictce-5.3.0-serial.eb | 10 ++++----- .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 2 +- .../e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb | 2 +- .../e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb | 4 ++-- .../e/eudev/eudev-3.0-intel-2014b.eb | 4 ++-- .../e/eudev/eudev-3.0-intel-2015a.eb | 4 ++-- .../e/eudev/eudev-3.1.2-intel-2015b.eb | 4 ++-- .../e/eudev/eudev-3.1.5-intel-2015b.eb | 4 ++-- .../Kerberos_V5-1.12.2-intel-2014b.eb | 2 +- .../QLogicMPI-2.9-926.1005_rhel5_qlc.eb | 12 +++++----- .../easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb | 2 +- .../QuantumESPRESSO-4.2-ictce-5.3.0.eb | 2 +- .../QuantumESPRESSO-4.2-ictce-5.5.0.eb | 2 +- .../WIEN2k/WIEN2k-12.1-goalf-1.1.0-no-OFED.eb | 22 +++++++++---------- .../w/WIEN2k/WIEN2k-12.1-goolf-1.4.10.eb | 2 +- .../w/WIEN2k/WIEN2k-12.1-ictce-4.0.6.eb | 22 +++++++++---------- .../w/WIEN2k/WIEN2k-14.1-intel-2014b.eb | 8 +++---- .../w/WIEN2k/WIEN2k-14.1-intel-2015a.eb | 8 +++---- .../w/WIEN2k/WIEN2k-14.2-intel-2015a.eb | 8 +++---- .../w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb | 2 +- .../w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb | 2 +- ...-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 8 +++---- ...2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb | 2 +- ...i2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb | 8 +++---- ...YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb | 2 +- ...YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb | 2 +- .../YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb | 2 +- .../y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb | 6 ++--- .../y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb | 6 ++--- .../y/Yasm/Yasm-1.2.0-ictce-5.3.0.eb | 6 ++--- .../z/zsh/zsh-5.0.2-goolf-1.4.10.eb | 2 +- .../z/zsh/zsh-5.0.2-ictce-4.1.13.eb | 2 +- .../zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb | 6 ++--- .../z/zsync/zsync-0.6.2-ictce-4.0.6.eb | 6 ++--- .../z/zsync/zsync-0.6.2-ictce-5.3.0.eb | 6 ++--- 53 files changed, 160 insertions(+), 160 deletions(-) diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb index ca072da66b..fafcf623a0 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb @@ -18,10 +18,10 @@ patches = ['ecore-license-var.patch'] dependencies = [('OpenMPI', '1.4.5')] sanity_check_paths = { - 'files': ['arch/linux-rh5-x86_64/bin/%s' % x for x in ['absperm', 'FormationFactor', 'nmr', - 'orterun', 'packer', 'randomwalkffmpi', - 'unpacker']] + \ - ['absperm.sh', 'formationfactor.sh', 'nmr.sh', 'rw_formationfactor.sh'], + 'files': ['arch/linux-rh5-x86_64/bin/%s' % x for x in ['absperm', 'FormationFactor', 'nmr', + 'orterun', 'packer', 'randomwalkffmpi', + 'unpacker']] + + ['absperm.sh', 'formationfactor.sh', 'nmr.sh', 'rw_formationfactor.sh'], 'dirs': [], } diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb index 7c028041b8..d93540e9b8 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb @@ -16,7 +16,7 @@ patches = ['ecore-license-var.patch'] dependencies = [('OpenMPI', '1.4.5')] sanity_check_paths = { - 'files': ["ecore.sh", 'noarch/launch.sh'] + \ + 'files': ["ecore.sh", 'noarch/launch.sh'] + ['arch/linux-rh5-x86_64/bin/%s' % x for x in ['diagenesismodeller', 'ecore', 'packer', 'PorenetworkExtraction', 'Poresim', 'unpacker']], 'dirs': [], diff --git a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb index 5403f1fde9..8ac9aea768 100644 --- a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'ELPH' version = '1.0.1' @@ -26,7 +26,7 @@ buildopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ (["elph"], "bin"), "COPYRIGHT", "LICENSE", "Readme.ELPH", "VERSION" ] +files_to_copy = [(["elph"], "bin"), "COPYRIGHT", "LICENSE", "Readme.ELPH", "VERSION"] sanity_check_paths = { 'files': ["bin/elph"], diff --git a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb index 8986e97200..ba2c506ee5 100644 --- a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'ELPH' version = '1.0.1' @@ -26,7 +26,7 @@ buildopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ (["elph"], "bin"), "COPYRIGHT", "LICENSE", "Readme.ELPH", "VERSION" ] +files_to_copy = [(["elph"], "bin"), "COPYRIGHT", "LICENSE", "Readme.ELPH", "VERSION"] sanity_check_paths = { 'files': ["bin/elph"], diff --git a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goalf-1.1.0-no-OFED.eb index 740d133cb4..6e775a095b 100644 --- a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goalf-1.1.0-no-OFED.eb @@ -21,8 +21,8 @@ source_urls = ['http://elinks.or.cz/download/'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/elinks'], - 'dirs': [] - } + 'files': ['bin/elinks'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goolf-1.4.10.eb index 098e55a84e..ee65cc074e 100644 --- a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goolf-1.4.10.eb @@ -21,8 +21,8 @@ source_urls = ['http://elinks.or.cz/download/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['bin/elinks'], - 'dirs': [] - } + 'files': ['bin/elinks'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-4.0.6.eb b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-4.0.6.eb index 3298a3a17d..413650f9a5 100644 --- a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-4.0.6.eb @@ -21,8 +21,8 @@ source_urls = ['http://elinks.or.cz/download/'] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/elinks'], - 'dirs': [] - } + 'files': ['bin/elinks'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-5.3.0.eb index 1dbae1bd2f..176ffcb6bd 100644 --- a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-5.3.0.eb @@ -22,8 +22,8 @@ source_urls = ['http://elinks.or.cz/download/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/elinks'], - 'dirs': [] - } + 'files': ['bin/elinks'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb index dac20cc956..5ef397df32 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb @@ -10,8 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-80.html ## -name = 'ESPResSo' -version = '3.1.1' +name = 'ESPResSo' +version = '3.1.1' versionsuffix = '-parallel' homepage = 'http://espressomd.org/' @@ -20,15 +20,15 @@ description = """ESPResSo is a highly versatile software package for performing of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology.""" -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -configopts = '--with-mpi' +configopts = '--with-mpi' sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://download.savannah.gnu.org/releases/espressomd/')] dependencies = [ - ('Tcl', '8.5.12'), - ] + ('Tcl', '8.5.12'), +] moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb index fbac405214..dc0eba6edb 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb @@ -10,8 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-80.html ## -name = 'ESPResSo' -version = '3.1.1' +name = 'ESPResSo' +version = '3.1.1' versionsuffix = '-serial' homepage = 'http://espressomd.org/' @@ -20,15 +20,15 @@ description = """ESPResSo is a highly versatile software package for performing of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology.""" -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -configopts = '' # Modify this line to add or change espresso config options +configopts = '' # Modify this line to add or change espresso config options sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://download.savannah.gnu.org/releases/espressomd/')] dependencies = [ - ('Tcl', '8.5.12'), - ] + ('Tcl', '8.5.12'), +] moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-parallel.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-parallel.eb index 39f5667ba5..209b0e8d81 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-parallel.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-parallel.eb @@ -10,8 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-80.html ## -name = 'ESPResSo' -version = '3.1.1' +name = 'ESPResSo' +version = '3.1.1' versionsuffix = '-parallel' homepage = 'http://espressomd.org/' @@ -22,13 +22,13 @@ description = """ESPResSo is a highly versatile software package for performing toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -configopts = '--with-mpi' +configopts = '--with-mpi' sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://download.savannah.gnu.org/releases/espressomd/')] dependencies = [ - ('Tcl', '8.5.12'), - ] + ('Tcl', '8.5.12'), +] moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-serial.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-serial.eb index 79d7c26962..80ab0978a1 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-serial.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-serial.eb @@ -10,8 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-80.html ## -name = 'ESPResSo' -version = '3.1.1' +name = 'ESPResSo' +version = '3.1.1' versionsuffix = '-serial' homepage = 'http://espressomd.org/' @@ -22,13 +22,13 @@ description = """ESPResSo is a highly versatile software package for performing toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -configopts = '' # Modify this line to add or change espresso config options +configopts = '' # Modify this line to add or change espresso config options sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://download.savannah.gnu.org/releases/espressomd/')] dependencies = [ - ('Tcl', '8.5.12'), - ] + ('Tcl', '8.5.12'), +] moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb index 0d5009ded4..5b960cc12d 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb @@ -10,8 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-80.html ## -name = 'ESPResSo' -version = '3.1.1' +name = 'ESPResSo' +version = '3.1.1' versionsuffix = '-parallel' homepage = 'http://espressomd.org/' @@ -20,15 +20,15 @@ description = """ESPResSo is a highly versatile software package for performing of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology.""" -toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -configopts = '--with-mpi' +configopts = '--with-mpi' sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://download.savannah.gnu.org/releases/espressomd/')] dependencies = [ - ('Tcl', '8.5.12'), - ] + ('Tcl', '8.5.12'), +] moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb index 638f30315a..21dd493eb1 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb @@ -10,8 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-80.html ## -name = 'ESPResSo' -version = '3.1.1' +name = 'ESPResSo' +version = '3.1.1' versionsuffix = '-serial' homepage = 'http://espressomd.org/' @@ -20,15 +20,15 @@ description = """ESPResSo is a highly versatile software package for performing of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology.""" -toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -configopts = '--with-mpi' +configopts = '--with-mpi' sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://download.savannah.gnu.org/releases/espressomd/')] dependencies = [ - ('Tcl', '8.5.12'), - ] + ('Tcl', '8.5.12'), +] moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-parallel.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-parallel.eb index 890278722c..9ad3efca4c 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-parallel.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-parallel.eb @@ -10,8 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-80.html ## -name = 'ESPResSo' -version = '3.1.1' +name = 'ESPResSo' +version = '3.1.1' versionsuffix = '-parallel' homepage = 'http://espressomd.org/' @@ -23,13 +23,13 @@ description = """ESPResSo is a highly versatile software package for performing toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -configopts = '--with-mpi' +configopts = '--with-mpi' sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://download.savannah.gnu.org/releases/espressomd/')] dependencies = [ - ('Tcl', '8.5.12'), - ] + ('Tcl', '8.5.12'), +] moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-serial.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-serial.eb index dd73e5835e..525e2ebf3e 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-serial.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-serial.eb @@ -10,8 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-80.html ## -name = 'ESPResSo' -version = '3.1.1' +name = 'ESPResSo' +version = '3.1.1' versionsuffix = '-serial' homepage = 'http://espressomd.org/' @@ -23,13 +23,13 @@ description = """ESPResSo is a highly versatile software package for performing toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -configopts = '--with-mpi' +configopts = '--with-mpi' sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://download.savannah.gnu.org/releases/espressomd/')] dependencies = [ - ('Tcl', '8.5.12'), - ] + ('Tcl', '8.5.12'), +] moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb index 9ec46d296f..17f0b9d160 100644 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -24,7 +24,7 @@ configopts = "--with-netcdf-prefix=$EBROOTNETCDF " configopts += "--with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' " configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include'" -dependencies = [ ('netCDF', '4.1.3') ] +dependencies = [('netCDF', '4.1.3')] sanity_check_paths = { 'files': ["bin/etsf_io"], diff --git a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb index 9f3aa94ef1..3968d910aa 100644 --- a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = ['otp_src_%(version)s.tar.gz'] source_urls = ['http://www.erlang.org/download'] -builddependencies = [('Java','1.7.0_45','',True)] +builddependencies = [('Java', '1.7.0_45', '', True)] configopts = '--with-javac ' diff --git a/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb index eb6680d2d6..037dcd8185 100644 --- a/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('Boost', '1.51.0'), # Boost-1.53.0 not working? + ('Boost', '1.51.0'), # Boost-1.53.0 not working? ('gperftools', '2.1'), ('protobuf', '2.5.0') ] diff --git a/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb index 361605cda9..b0dc02f6dd 100644 --- a/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb @@ -12,8 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] sanity_check_paths = { - 'files' : ['bin/ed'], - 'dirs' : [], + 'files': ['bin/ed'], + 'dirs': [], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb index babb529111..48f5d0b7b4 100644 --- a/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb @@ -12,8 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/%(name)s/'] sanity_check_paths = { - 'files' : ['bin/ed'], - 'dirs' : [], + 'files': ['bin/ed'], + 'dirs': [], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb index a1c5928f0b..464dcb0125 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb @@ -26,8 +26,8 @@ configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpag runtest = 'check' sanity_check_paths = { - 'files' : ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], - 'dirs' : [], + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], } moduleclass = 'system' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb index 5108981bdd..245048609d 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb @@ -26,8 +26,8 @@ configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpag runtest = 'check' sanity_check_paths = { - 'files' : ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], - 'dirs' : [], + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], } moduleclass = 'system' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.1.2-intel-2015b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.2-intel-2015b.eb index b06feacb05..da7d5f4069 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.1.2-intel-2015b.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.2-intel-2015b.eb @@ -26,8 +26,8 @@ configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpag runtest = 'check' sanity_check_paths = { - 'files' : ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], - 'dirs' : [], + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], } moduleclass = 'system' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-intel-2015b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-intel-2015b.eb index cd53df3296..b58e614820 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-intel-2015b.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-intel-2015b.eb @@ -26,8 +26,8 @@ configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpag runtest = 'check' sanity_check_paths = { - 'files' : ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], - 'dirs' : [], + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], } moduleclass = 'system' diff --git a/easybuild/easyconfigs/k/Kerberos_V5/Kerberos_V5-1.12.2-intel-2014b.eb b/easybuild/easyconfigs/k/Kerberos_V5/Kerberos_V5-1.12.2-intel-2014b.eb index d8151b8cd7..7e7833875f 100644 --- a/easybuild/easyconfigs/k/Kerberos_V5/Kerberos_V5-1.12.2-intel-2014b.eb +++ b/easybuild/easyconfigs/k/Kerberos_V5/Kerberos_V5-1.12.2-intel-2014b.eb @@ -26,7 +26,7 @@ sanity_check_paths = { 'sbin/kdb5_util', 'sbin/gss-server', 'sbin/kadmind', 'lib/libkrb5.%s' % SHLIB_EXT, 'lib/libgssapi_krb5.%s' % SHLIB_EXT, 'lib/libkadm5clnt.%s' % SHLIB_EXT, 'lib/libkadm5srv.%s' % SHLIB_EXT, 'lib/libkdb5.%s' % SHLIB_EXT, 'lib/libk5crypto.%s' % SHLIB_EXT, - ], + ], 'dirs': ['lib/krb5'] } diff --git a/easybuild/easyconfigs/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb b/easybuild/easyconfigs/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb index f21ebd8d63..20ed128824 100644 --- a/easybuild/easyconfigs/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb +++ b/easybuild/easyconfigs/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb @@ -15,12 +15,12 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # download the rpm directly or get it from the .bin file and extract it with ./nameoffile.bin -x and type yes sources = [ - 'mpi-benchmark-%s.x86_64.rpm' % version, - 'mpi-libs-%s.x86_64.rpm' % version, - 'mpi-frontend-%s.i386.rpm' % version, - 'qlogic-mpi-register-0.1.0-926.1005_rhel5_qlc.noarch.rpm', - 'mpi-devel-%s.noarch.rpm'%version - ] + 'mpi-benchmark-%s.x86_64.rpm' % version, + 'mpi-libs-%s.x86_64.rpm' % version, + 'mpi-frontend-%s.i386.rpm' % version, + 'qlogic-mpi-register-0.1.0-926.1005_rhel5_qlc.noarch.rpm', + 'mpi-devel-%s.noarch.rpm' % version +] makesymlinks = ['usr/lib', 'usr/lib64', 'usr/include', 'usr/bin'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb index 5406e997c6..feb87dfbe1 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb @@ -14,7 +14,7 @@ sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] -configopts="-confirm-license -opensource -silent" +configopts = "-confirm-license -opensource -silent" sanity_check_paths = { 'files': ['lib/libQtCore.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb index c5c6c8344b..1d7ae2908b 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb @@ -14,7 +14,7 @@ sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] -configopts="-confirm-license -opensource -silent" +configopts = "-confirm-license -opensource -silent" sanity_check_paths = { 'files': ['lib/libQtCore.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb index 37bdd94912..09c9e0166c 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb @@ -15,7 +15,7 @@ sources = [ 'wannier90-1.2.tar.gz', 'want-2.3.0.tar.gz', 'yambo-3.2.1-r.448.tar.gz', - ] +] source_urls = [ 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0.eb index 6b0604d138..e7e19c0343 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0.eb @@ -15,7 +15,7 @@ sources = [ 'wannier90-1.2.tar.gz', 'want-2.3.0.tar.gz', 'yambo-3.2.1-r.448.tar.gz', - ] +] source_urls = [ 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-goalf-1.1.0-no-OFED.eb index 77cc5a82b0..c324b952c6 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-goalf-1.1.0-no-OFED.eb @@ -16,16 +16,16 @@ patches = ['WIEN2k-12.1_fix-range-array-constructor.patch'] osdependencies = ['libpthread.a'] # delivered by glibc-static or glibc-devel tests = [ - # test case 1: NaCl - ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), - # test case 2: TiO2 - ('TiO2', - '-b -numk 1000 -rkmax 7.5', - '-in1ef -cc 0.00001 -fc 0.5 -i 100', - [r'^:ENE.*-4018.0761', - r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', - r'^:FGL002.*14.63.*total forces' - ]) - ] + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [r'^:ENE.*-4018.0761', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces' + ]) +] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-goolf-1.4.10.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-goolf-1.4.10.eb index 244607e4e4..074aab4b4c 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-goolf-1.4.10.eb @@ -25,7 +25,7 @@ tests = [ [r'^:ENE.*-4018.0761', r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', r'^:FGL002.*14.63.*total forces' - ]), + ]), ] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-ictce-4.0.6.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-ictce-4.0.6.eb index 924f23b3b4..233776585c 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-ictce-4.0.6.eb @@ -18,16 +18,16 @@ dependencies = [('FFTW', '3.3.1')] osdependencies = ['libpthread.a'] # delivered by glibc-static or glibc-devel tests = [ - # test case 1: NaCl - ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), - # test case 2: TiO2 - ('TiO2', - '-b -numk 1000 -rkmax 7.5', - '-in1ef -cc 0.00001 -fc 0.5 -i 100', - [r'^:ENE.*-4018.0761', - r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', - r'^:FGL002.*14.63.*total forces' - ]) - ] + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [r'^:ENE.*-4018.0761', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces' + ]) +] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb index 9a8f71d9ca..d99b5a04c8 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb @@ -37,10 +37,10 @@ tests = [ '-b -numk 1000 -rkmax 7.5', '-in1ef -cc 0.00001 -fc 0.5 -i 100', [ - r'^:ENE.*-4018.07', - r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', - r'^:FGL002.*14.63.*total forces', - ]), + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), ] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb index a5d641a90f..4fc60981dc 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb @@ -37,10 +37,10 @@ tests = [ '-b -numk 1000 -rkmax 7.5', '-in1ef -cc 0.00001 -fc 0.5 -i 100', [ - r'^:ENE.*-4018.07', - r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', - r'^:FGL002.*14.63.*total forces', - ]), + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), ] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb index 5149928839..2e1d5ab15d 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb @@ -31,10 +31,10 @@ tests = [ '-b -numk 1000 -rkmax 7.5', '-in1ef -cc 0.00001 -fc 0.5 -i 100', [ - r'^:ENE.*-4018.07', - r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', - r'^:FGL002.*14.63.*total forces', - ]), + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), ] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb index 8e3d2604d5..e43733e3f6 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb @@ -25,7 +25,7 @@ dependencies = [ ('netCDF', '4.2.1.1'), ('netCDF-Fortran', '4.2'), ('libpng', '1.5.14'), - ('JasPer','1.900.1'), + ('JasPer', '1.900.1'), ] moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb index 7d70493e14..3a831bedc4 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb @@ -25,7 +25,7 @@ dependencies = [ ('netCDF', '4.2.1.1'), ('netCDF-Fortran', '4.2'), ('libpng', '1.5.14'), - ('JasPer','1.900.1'), + ('JasPer', '1.900.1'), ] moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 12cf06119f..dabd647780 100644 --- a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} # eg. http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5/wiki2beamer-0.9.5.zip/download sources = ['wiki2beamer-0.9.5.zip'] -source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5','download'] +source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5', 'download'] python = 'Python' pyver = '2.7.3' @@ -37,8 +37,8 @@ start_dir = 'code' options = {'modulename': False} sanity_check_paths = { - 'files': ["bin/wiki2beamer"], - 'dirs': ["."] - } + 'files': ["bin/wiki2beamer"], + 'dirs': ["."] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb index e59097b639..330c38528f 100644 --- a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} # eg. http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5/wiki2beamer-0.9.5.zip/download sources = ['wiki2beamer-0.9.5.zip'] -source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5','download'] +source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5', 'download'] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb index 37b9d91c99..d475ee038e 100644 --- a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} # eg. http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5/wiki2beamer-0.9.5.zip/download sources = ['wiki2beamer-0.9.5.zip'] -source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5','download'] +source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5', 'download'] python = 'Python' pyver = '2.7.3' @@ -37,8 +37,8 @@ start_dir = 'code' options = {'modulename': False} sanity_check_paths = { - 'files': ["bin/wiki2beamer"], - 'dirs': ["."] - } + 'files': ["bin/wiki2beamer"], + 'dirs': ["."] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb index b409a46b6b..04fcdaad37 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb @@ -24,7 +24,7 @@ sources = [SOURCE_TAR_GZ] perl = 'Perl' perlver = '5.16.3' perlverextra = '' -versionsuffix = '-%s-%s%s' % (perl, perlver,perlverextra) +versionsuffix = '-%s-%s%s' % (perl, perlver, perlverextra) dependencies = [ (perl, perlver, perlverextra), diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb index fa45b910fb..814139aaa0 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb @@ -24,7 +24,7 @@ sources = [SOURCE_TAR_GZ] perl = 'Perl' perlver = '5.16.3' perlverextra = '' -versionsuffix = '-%s-%s%s' % (perl, perlver,perlverextra) +versionsuffix = '-%s-%s%s' % (perl, perlver, perlverextra) dependencies = [ (perl, perlver, perlverextra), diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb index f2c952182b..4816f11ffd 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb @@ -24,7 +24,7 @@ sources = [SOURCE_TAR_GZ] perl = 'Perl' perlver = '5.16.3' perlverextra = '' -versionsuffix = '-%s-%s%s' % (perl, perlver,perlverextra) +versionsuffix = '-%s-%s%s' % (perl, perlver, perlverextra) dependencies = [ (perl, perlver, perlverextra), diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb index 44f8a5205c..e2bfa1c5fb 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb @@ -24,8 +24,8 @@ source_urls = ['http://www.tortall.net/projects/yasm/releases/'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/yasm'], - 'dirs': [] - } + 'files': ['bin/yasm'], + 'dirs': [] +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb index 592b6f2117..5b66cf87a7 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb @@ -24,8 +24,8 @@ source_urls = ['http://www.tortall.net/projects/yasm/releases/'] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/yasm'], - 'dirs': [] - } + 'files': ['bin/yasm'], + 'dirs': [] +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-5.3.0.eb index ab7055fa1c..a98dbc5915 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-5.3.0.eb @@ -25,8 +25,8 @@ source_urls = ['http://www.tortall.net/projects/yasm/releases/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/yasm'], - 'dirs': [] - } + 'files': ['bin/yasm'], + 'dirs': [] +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/z/zsh/zsh-5.0.2-goolf-1.4.10.eb index f585c174c3..1b0f601684 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.0.2-goolf-1.4.10.eb @@ -6,7 +6,7 @@ version = '5.0.2' homepage = 'http://www.zsh.org/' description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language." -toolchain = {'name':'goolf', 'version': '1.4.10'} +toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-4.1.13.eb b/easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-4.1.13.eb index 72db46c65f..14216f2009 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-4.1.13.eb @@ -6,7 +6,7 @@ version = '5.0.2' homepage = 'http://www.zsh.org/' description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language." -toolchain = {'name':'ictce', 'version': '4.1.13'} +toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] diff --git a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb index 35d2652e62..b70a682d96 100644 --- a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb @@ -24,8 +24,8 @@ source_urls = ['http://zsync.moria.org.uk/download/'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/zsync'], - 'dirs': [] - } + 'files': ['bin/zsync'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-4.0.6.eb index 406951135b..9a77005cb5 100644 --- a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-4.0.6.eb @@ -24,8 +24,8 @@ source_urls = ['http://zsync.moria.org.uk/download/'] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/zsync'], - 'dirs': [] - } + 'files': ['bin/zsync'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-5.3.0.eb index d72b794ff1..960ac2460a 100644 --- a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-5.3.0.eb @@ -25,8 +25,8 @@ source_urls = ['http://zsync.moria.org.uk/download/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/zsync'], - 'dirs': [] - } + 'files': ['bin/zsync'], + 'dirs': [] +} moduleclass = 'tools' -- GitLab From 9e9e4d74b22e3c734d8960b480f853bd168c4c2d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 13:08:01 +0100 Subject: [PATCH 0267/2133] Style fixes with autopep8: f Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb | 6 ++--- .../f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb | 6 ++--- ...TX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb | 26 +++++++++---------- .../FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb | 26 +++++++++---------- .../FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb | 26 +++++++++---------- .../FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb | 26 +++++++++---------- .../FASTX-Toolkit-0.0.14-foss-2015b.eb | 10 +++---- .../FASTX-Toolkit-0.0.14-goolf-1.4.10.eb | 12 ++++----- .../FASTX-Toolkit-0.0.14-intel-2015a.eb | 12 ++++----- .../easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb | 2 +- ...-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 18 ++++++------- .../FFC-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 18 ++++++------- .../FFC/FFC-1.0.0-ictce-4.0.6-Python-2.7.3.eb | 18 ++++++------- .../FFC/FFC-1.0.0-ictce-5.3.0-Python-2.7.3.eb | 18 ++++++------- .../f/FFTW/FFTW-2.1.5-gompi-1.1.0-no-OFED.eb | 3 ++- .../f/FFTW/FFTW-2.1.5-ictce-5.3.0.eb | 3 ++- .../f/FFTW/FFTW-2.1.5-ictce-5.5.0.eb | 3 ++- .../f/FFTW/FFTW-3.3.1-gompi-1.1.0-no-OFED.eb | 4 +-- .../f/FFTW/FFTW-3.3.2-gmvapich2-1.7.9a2.eb | 4 +-- .../f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb | 4 +-- .../f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12.eb | 4 +-- .../f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12rc1.eb | 8 +++--- .../f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb | 8 +++--- .../f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb | 4 +-- .../f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb | 4 +-- .../f/FFTW/FFTW-3.3.3-gompi-1.5.12-no-OFED.eb | 4 +-- .../f/FFTW/FFTW-3.3.3-gompi-1.5.12.eb | 4 +-- .../f/FFTW/FFTW-3.3.3-gompi-1.6.10.eb | 4 +-- .../f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb | 4 +-- .../f/FFTW/FFTW-3.3.3-ictce-4.1.13-single.eb | 2 +- .../f/FFTW/FFTW-3.3.3-ictce-5.2.0-single.eb | 2 +- .../f/FFTW/FFTW-3.3.3-ictce-5.3.0-single.eb | 2 +- .../f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb | 2 +- .../f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb | 4 +-- .../f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb | 4 +-- .../f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb | 4 +-- .../f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb | 4 +-- .../f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb | 2 -- .../FIAT/FIAT-1.1-ictce-5.2.0-Python-2.7.3.eb | 3 ++- .../FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../FIAT/FIAT-1.1-intel-2014b-Python-2.7.8.eb | 3 ++- .../f/FLTK/FLTK-1.3.2-foss-2014b.eb | 2 +- .../f/FLTK/FLTK-1.3.2-goolf-1.4.10.eb | 4 +-- .../f/FLTK/FLTK-1.3.2-ictce-5.3.0.eb | 2 +- .../f/FLTK/FLTK-1.3.2-intel-2014b.eb | 2 +- .../f/FSL/FSL-4.1.9-ictce-4.0.6.eb | 6 ++--- .../f/FSL/FSL-4.1.9-ictce-5.3.0.eb | 6 ++--- .../f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb | 2 +- .../f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb | 2 +- .../f/ffmpeg/ffmpeg-2.4-intel-2014b.eb | 2 +- .../f/ffmpeg/ffmpeg-2.8-intel-2015b.eb | 2 +- .../fontconfig-2.11.1-foss-2014b.eb | 2 +- .../fontconfig-2.11.1-goolf-1.7.20.eb | 2 +- .../fontconfig-2.11.1-intel-2014b.eb | 2 +- .../fontconfig-2.11.94-goolf-1.7.20.eb | 2 +- .../fontsproto-2.1.3-intel-2015a.eb | 4 +-- .../fontsproto-2.1.3-intel-2015b.eb | 4 +-- 57 files changed, 187 insertions(+), 183 deletions(-) diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb index f7530e1017..c1501d5c82 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb @@ -6,7 +6,7 @@ # License:: MIT/GPL # ## -easyblock='MakeCp' +easyblock = 'MakeCp' name = "FASTA" version = "36.3.5e" @@ -28,8 +28,8 @@ files_to_copy = ["bin", "conf", "data", "doc", "FASTA_LIST", "misc", "README", " sanity_check_paths = { 'files': ["FASTA_LIST", "README"] + ['bin/%s' % x for x in ['lav2svg', 'lav2ps', 'map_db']] + ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', - 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', - 'ssearch', 'tfastm', 'tfastx']], + 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', + 'ssearch', 'tfastm', 'tfastx']], 'dirs': ["conf", "data", "doc", "misc", "seq", "sql", "test"] } diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb index 8f61866180..6b9a39e112 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb @@ -6,7 +6,7 @@ # License:: MIT/GPL # ## -easyblock='MakeCp' +easyblock = 'MakeCp' name = "FASTA" version = "36.3.5e" @@ -28,8 +28,8 @@ files_to_copy = ["bin", "conf", "data", "doc", "FASTA_LIST", "misc", "README", " sanity_check_paths = { 'files': ["FASTA_LIST", "README"] + ['bin/%s' % x for x in ['lav2svg', 'lav2ps', 'map_db']] + ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', - 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', - 'ssearch', 'tfastm', 'tfastx']], + 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', + 'ssearch', 'tfastm', 'tfastx']], 'dirs': ["conf", "data", "doc", "misc", "seq", "sql", "test"] } diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb index 2fa88fc7e0..cc92c2f5a3 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb @@ -26,20 +26,20 @@ altname = '_'.join(name.split('-')).lower() sources = ['%s-%s.tar.bz2' % (altname, version)] source_urls = ['http://hannonlab.cshl.edu/%s' % altname] -dependencies = [('libgtextutils', '0.6.1')]; +dependencies = [('libgtextutils', '0.6.1')] sanity_check_paths = { - 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', - 'artifacts_filter', 'reverse_complement', - 'collapser', 'uncollapser', 'renamer', - 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', - 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', - 'to_fasta', 'quality_filter', 'quality_trimmer', - 'masker']], - 'dirs': ['.'] - } + 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', + 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', + 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', + 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', + 'to_fasta', 'quality_filter', 'quality_trimmer', + 'masker']], + 'dirs': ['.'] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb index b2711aa2a6..98cc1b1ac3 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb @@ -26,20 +26,20 @@ altname = '_'.join(name.split('-')).lower() sources = ['%s-%s.tar.bz2' % (altname, version)] source_urls = ['http://hannonlab.cshl.edu/%s' % altname] -dependencies = [('libgtextutils', '0.6.1')]; +dependencies = [('libgtextutils', '0.6.1')] sanity_check_paths = { - 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', - 'artifacts_filter', 'reverse_complement', - 'collapser', 'uncollapser', 'renamer', - 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', - 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', - 'to_fasta', 'quality_filter', 'quality_trimmer', - 'masker']], - 'dirs': ['.'] - } + 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', + 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', + 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', + 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', + 'to_fasta', 'quality_filter', 'quality_trimmer', + 'masker']], + 'dirs': ['.'] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb index aaddc8190a..01f7d5e8e2 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb @@ -26,22 +26,22 @@ altname = '_'.join(name.split('-')).lower() sources = ['%s-%s.tar.bz2' % (altname, version)] source_urls = ['http://hannonlab.cshl.edu/%s' % altname] -dependencies = [('libgtextutils', '0.6.1')]; +dependencies = [('libgtextutils', '0.6.1')] configopts = '--disable-wall' # avoid use of -Werror sanity_check_paths = { - 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', - 'artifacts_filter', 'reverse_complement', - 'collapser', 'uncollapser', 'renamer', - 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', - 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', - 'to_fasta', 'quality_filter', 'quality_trimmer', - 'masker']], - 'dirs': ['.'] - } + 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', + 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', + 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', + 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', + 'to_fasta', 'quality_filter', 'quality_trimmer', + 'masker']], + 'dirs': ['.'] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb index 02992118cc..0af3bc5808 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb @@ -27,22 +27,22 @@ altname = '_'.join(name.split('-')).lower() sources = ['%s-%s.tar.bz2' % (altname, version)] source_urls = ['http://hannonlab.cshl.edu/%s' % altname] -dependencies = [('libgtextutils', '0.6.1')]; +dependencies = [('libgtextutils', '0.6.1')] configopts = '--disable-wall' # avoid use of -Werror sanity_check_paths = { - 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', - 'artifacts_filter', 'reverse_complement', - 'collapser', 'uncollapser', 'renamer', - 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', - 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', - 'to_fasta', 'quality_filter', 'quality_trimmer', - 'masker']], - 'dirs': ['.'] - } + 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', + 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', + 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', + 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', + 'to_fasta', 'quality_filter', 'quality_trimmer', + 'masker']], + 'dirs': ['.'] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb index 46d174be2c..000e1a89b7 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb @@ -25,20 +25,20 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] sources = ['fastx_toolkit-%(version)s.tar.bz2'] -builddependencies = [('libgtextutils', '0.7')]; +builddependencies = [('libgtextutils', '0.7')] sanity_check_paths = { 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', - 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', - 'quality_trimmer', 'masker']], + 'quality_trimmer', 'masker']], 'dirs': ['.'] - } +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb index 16426d6788..1b0419e8b8 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb @@ -22,24 +22,24 @@ description = """The FASTX-Toolkit is a collection of command line tools for toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -altname = name.lower().replace('-','_') +altname = name.lower().replace('-', '_') source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] sources = ['%s-%%(version)s.tar.bz2' % altname] -dependencies = [('libgtextutils', '0.6.1')]; +dependencies = [('libgtextutils', '0.6.1')] sanity_check_paths = { 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', - 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', - 'quality_trimmer', 'masker']], + 'quality_trimmer', 'masker']], 'dirs': ['.'] - } +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb index 18c56837a0..88eedbe248 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb @@ -22,24 +22,24 @@ description = """The FASTX-Toolkit is a collection of command line tools for toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} -altname = name.lower().replace('-','_') +altname = name.lower().replace('-', '_') source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] sources = ['%s-%%(version)s.tar.bz2' % altname] -dependencies = [('libgtextutils', '0.6.1')]; +dependencies = [('libgtextutils', '0.6.1')] sanity_check_paths = { 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', - 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', - 'quality_trimmer', 'masker']], + 'quality_trimmer', 'masker']], 'dirs': ['.'] - } +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb index f0c7225183..a1ceee68c9 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb @@ -16,7 +16,7 @@ sources = ['FDS_6.0.1-SMV_6.1.5_linux64.tar.gz'] dependencies = [('OpenMPI', '1.6.5-GCC-4.8.2-no-OFED')] -skipsteps= ['configure', 'build'] +skipsteps = ['configure', 'build'] sanity_check_paths = { 'files': ['bin/fds', 'bin/fds_mpi'], diff --git a/easybuild/easyconfigs/f/FFC/FFC-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/f/FFC/FFC-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index e65ba501f9..6a8af569fc 100644 --- a/easybuild/easyconfigs/f/FFC/FFC-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/f/FFC/FFC-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -20,16 +20,16 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('UFL', '1.0.0', versionsuffix), - ('FIAT', '1.0.0', versionsuffix), - ('UFC', '2.0.5', versionsuffix), - ('Viper', '1.0.0', versionsuffix), - ] + (python, pythonversion), + ('UFL', '1.0.0', versionsuffix), + ('FIAT', '1.0.0', versionsuffix), + ('UFC', '2.0.5', versionsuffix), + ('Viper', '1.0.0', versionsuffix), +] sanity_check_paths = { - 'files': ['bin/ffc'], - 'dirs': ['lib/python%s/site-packages/ffc' % pythonshortversion] - } + 'files': ['bin/ffc'], + 'dirs': ['lib/python%s/site-packages/ffc' % pythonshortversion] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FFC/FFC-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/f/FFC/FFC-1.0.0-goolf-1.4.10-Python-2.7.3.eb index f26919582f..f3d91879f4 100644 --- a/easybuild/easyconfigs/f/FFC/FFC-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/f/FFC/FFC-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -20,16 +20,16 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('UFL', '1.0.0', versionsuffix), - ('FIAT', '1.0.0', versionsuffix), - ('UFC', '2.0.5', versionsuffix), - ('Viper', '1.0.0', versionsuffix), - ] + (python, pythonversion), + ('UFL', '1.0.0', versionsuffix), + ('FIAT', '1.0.0', versionsuffix), + ('UFC', '2.0.5', versionsuffix), + ('Viper', '1.0.0', versionsuffix), +] sanity_check_paths = { - 'files': ['bin/ffc'], - 'dirs': ['lib/python%s/site-packages/ffc' % pythonshortversion] - } + 'files': ['bin/ffc'], + 'dirs': ['lib/python%s/site-packages/ffc' % pythonshortversion] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FFC/FFC-1.0.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/f/FFC/FFC-1.0.0-ictce-4.0.6-Python-2.7.3.eb index 97fb1dceaa..aff35de683 100644 --- a/easybuild/easyconfigs/f/FFC/FFC-1.0.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/f/FFC/FFC-1.0.0-ictce-4.0.6-Python-2.7.3.eb @@ -20,16 +20,16 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('UFL', '1.0.0', versionsuffix), - ('FIAT', '1.0.0', versionsuffix), - ('UFC', '2.0.5', versionsuffix), - ('Viper', '1.0.0', versionsuffix), - ] + (python, pythonversion), + ('UFL', '1.0.0', versionsuffix), + ('FIAT', '1.0.0', versionsuffix), + ('UFC', '2.0.5', versionsuffix), + ('Viper', '1.0.0', versionsuffix), +] sanity_check_paths = { - 'files': ['bin/ffc'], - 'dirs': ['lib/python%s/site-packages/ffc' % pythonshortversion] - } + 'files': ['bin/ffc'], + 'dirs': ['lib/python%s/site-packages/ffc' % pythonshortversion] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FFC/FFC-1.0.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/f/FFC/FFC-1.0.0-ictce-5.3.0-Python-2.7.3.eb index fbc743734d..646f52f874 100644 --- a/easybuild/easyconfigs/f/FFC/FFC-1.0.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/f/FFC/FFC-1.0.0-ictce-5.3.0-Python-2.7.3.eb @@ -21,16 +21,16 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('UFL', '1.0.0', versionsuffix), - ('FIAT', '1.0.0', versionsuffix), - ('UFC', '2.0.5', versionsuffix), - ('Viper', '1.0.0', versionsuffix), - ] + (python, pythonversion), + ('UFL', '1.0.0', versionsuffix), + ('FIAT', '1.0.0', versionsuffix), + ('UFC', '2.0.5', versionsuffix), + ('Viper', '1.0.0', versionsuffix), +] sanity_check_paths = { - 'files': ['bin/ffc'], - 'dirs': ['lib/python%s/site-packages/ffc' % pythonshortversion] - } + 'files': ['bin/ffc'], + 'dirs': ['lib/python%s/site-packages/ffc' % pythonshortversion] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-gompi-1.1.0-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-gompi-1.1.0-no-OFED.eb index 207690907c..2e1dfdd8af 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-gompi-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-gompi-1.1.0-no-OFED.eb @@ -23,7 +23,8 @@ configopts = [ sanity_check_paths = { 'files': ['include/%sfftw%s.h' % (x, y) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']] + ['lib/lib%sfftw%s.a' % (x, y) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']] + - ['lib/lib%sfftw%s.%s' % (x, y, SHLIB_EXT) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']], + ['lib/lib%sfftw%s.%s' % (x, y, SHLIB_EXT) for x in ['d', 'dr', 's', 'sr'] + for y in ['', '_mpi', '_threads']], 'dirs': [], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-ictce-5.3.0.eb index 27849ede43..4dafd1540f 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-ictce-5.3.0.eb @@ -23,7 +23,8 @@ configopts = [ sanity_check_paths = { 'files': ['include/%sfftw%s.h' % (x, y) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']] + ['lib/lib%sfftw%s.a' % (x, y) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']] + - ['lib/lib%sfftw%s.%s' % (x, y, SHLIB_EXT) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']], + ['lib/lib%sfftw%s.%s' % (x, y, SHLIB_EXT) for x in ['d', 'dr', 's', 'sr'] + for y in ['', '_mpi', '_threads']], 'dirs': [], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-ictce-5.5.0.eb index a551eedc1d..e665c5c101 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-ictce-5.5.0.eb @@ -23,7 +23,8 @@ configopts = [ sanity_check_paths = { 'files': ['include/%sfftw%s.h' % (x, y) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']] + ['lib/lib%sfftw%s.a' % (x, y) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']] + - ['lib/lib%sfftw%s.%s' % (x, y, SHLIB_EXT) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']], + ['lib/lib%sfftw%s.%s' % (x, y, SHLIB_EXT) for x in ['d', 'dr', 's', 'sr'] + for y in ['', '_mpi', '_threads']], 'dirs': [], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.1-gompi-1.1.0-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.1-gompi-1.1.0-no-OFED.eb index df746888b8..ebce2cd9e3 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.1-gompi-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.1-gompi-1.1.0-no-OFED.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.2-gmvapich2-1.7.9a2.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.2-gmvapich2-1.7.9a2.eb index f3605b7205..47f16bc4a3 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.2-gmvapich2-1.7.9a2.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.2-gmvapich2-1.7.9a2.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb index 34bdcce1b8..228133848f 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12.eb index dbbb079aaf..7348b00826 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12rc1.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12rc1.eb index 7c08b5de11..d5647435f6 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12rc1.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12rc1.eb @@ -25,10 +25,10 @@ configopts = [ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb index b7323c4cfc..8f61ad3268 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb @@ -25,10 +25,10 @@ configopts = [ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb index b4a9a90a01..0d10db3dc0 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb index bc93d09c52..0d03ca311a 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12-no-OFED.eb index 6ce64fb09e..6d9e48f885 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12-no-OFED.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12.eb index a07a8a5b7a..7e3372ad72 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.10.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.10.eb index 9273c85cd6..361d76b7d2 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.10.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.10.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb index 23271fb82e..83140eb85e 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-4.1.13-single.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-4.1.13-single.eb index 6d022e3132..b4152bae55 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-4.1.13-single.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-4.1.13-single.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -## single precision +# single precision configopts = "--enable-sse --enable-single" # the MPI opts from FFTW2 are valid options but unused until FFTW3.3 diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.2.0-single.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.2.0-single.eb index 15438c0430..c3d56eb83c 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.2.0-single.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.2.0-single.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -## single precision +# single precision configopts = "--enable-sse --enable-single" # the MPI opts from FFTW2 are valid options but unused until FFTW3.3 diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.3.0-single.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.3.0-single.eb index 1212e33f88..5755a3492e 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.3.0-single.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.3.0-single.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -## single precision +# single precision configopts = "--enable-sse --enable-single" # the MPI opts from FFTW2 are valid options but unused until FFTW3.3 diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb index 4bdecb5bb1..614cce8c96 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -## single precision +# single precision configopts = "--enable-sse --enable-single" # the MPI opts from FFTW2 are valid options but unused until FFTW3.3 diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb index 7a9d4c279e..93a27c610b 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb index 128daff670..9cf62510e7 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb index 31bdfdd956..52ec320554 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb index 6ae444ae02..13413d4abc 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb index cb01772a4f..14eb6c4917 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb @@ -22,7 +22,6 @@ configopts = [ ] - sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', @@ -33,4 +32,3 @@ sanity_check_paths = { } moduleclass = 'numlib' - diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.2.0-Python-2.7.3.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.2.0-Python-2.7.3.eb index 38a7cbfbd8..acfceb386c 100644 --- a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.2.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.2.0-Python-2.7.3.eb @@ -10,7 +10,8 @@ arbitrary order instances of Jacobi-type quadrature rules on the same element sh toolchain = {'name': 'ictce', 'version': '5.2.0'} -source_urls = ['https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/'] +source_urls = [ + 'https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/'] sources = [SOURCELOWER_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb index c1e3ad55f7..25b886e5b9 100644 --- a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb @@ -10,7 +10,8 @@ arbitrary order instances of Jacobi-type quadrature rules on the same element sh toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/'] +source_urls = [ + 'https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/'] sources = [SOURCELOWER_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-intel-2014b-Python-2.7.8.eb index 1d1b0eda5c..cc9dc901e8 100644 --- a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-intel-2014b-Python-2.7.8.eb @@ -10,7 +10,8 @@ arbitrary order instances of Jacobi-type quadrature rules on the same element sh toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/'] +source_urls = [ + 'https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/'] sources = [SOURCELOWER_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-foss-2014b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-foss-2014b.eb index 0bc1badf5f..5a7bfc53c3 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-foss-2014b.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-foss-2014b.eb @@ -23,7 +23,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/fltk-config','bin/fluid'], + 'files': ['bin/fltk-config', 'bin/fluid'], 'dirs': ['lib'], } diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-goolf-1.4.10.eb index 9b7f1917c4..8918226221 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-goolf-1.4.10.eb @@ -11,7 +11,7 @@ description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.""" -toolchain = {'name': 'goolf' , 'version': '1.4.10'} +toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] @@ -22,7 +22,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/fltk-config','bin/fluid'], + 'files': ['bin/fltk-config', 'bin/fluid'], 'dirs': ['lib'], } diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-ictce-5.3.0.eb index 11bcbb2f83..cdb8c79111 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-ictce-5.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/fltk-config','bin/fluid'], + 'files': ['bin/fltk-config', 'bin/fluid'], 'dirs': ['lib'], } diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-intel-2014b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-intel-2014b.eb index 5bc592de5f..a70eaf3871 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-intel-2014b.eb @@ -23,7 +23,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/fltk-config','bin/fluid'], + 'files': ['bin/fltk-config', 'bin/fluid'], 'dirs': ['lib'], } diff --git a/easybuild/easyconfigs/f/FSL/FSL-4.1.9-ictce-4.0.6.eb b/easybuild/easyconfigs/f/FSL/FSL-4.1.9-ictce-4.0.6.eb index f58cfc0a32..087f9525ef 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-4.1.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-4.1.9-ictce-4.0.6.eb @@ -10,9 +10,9 @@ source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] sources = ['%s-%s-sources.tar.gz' % (name.lower(), version)] patches = [ - 'FSL_makefile_fixes.patch', - 'FSL_icc_nan-inf_fix.patch' - ] + 'FSL_makefile_fixes.patch', + 'FSL_icc_nan-inf_fix.patch' +] # libX11-devel is required for X11/Xlib.h, required by tk build osdependencies = ['libX11-devel'] diff --git a/easybuild/easyconfigs/f/FSL/FSL-4.1.9-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FSL/FSL-4.1.9-ictce-5.3.0.eb index e20f5d2a08..af52a65745 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-4.1.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-4.1.9-ictce-5.3.0.eb @@ -10,9 +10,9 @@ source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] sources = ['%s-%s-sources.tar.gz' % (name.lower(), version)] patches = [ - 'FSL_makefile_fixes.patch', - 'FSL_icc_nan-inf_fix.patch' - ] + 'FSL_makefile_fixes.patch', + 'FSL_icc_nan-inf_fix.patch' +] # libX11-devel is required for X11/Xlib.h, required by tk build osdependencies = ['libX11-devel'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb index 41209b695a..4bf3f06a01 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb @@ -31,7 +31,7 @@ install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc" sanity_check_paths = { 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.32.jar"], + "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.32.jar"], 'dirs': ["Contaminants", "Help", "Templates", "uk"], } diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb index 4abf658ad6..b774c4ad40 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb +++ b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb @@ -19,7 +19,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb index 4461759fe7..d79e616065 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb +++ b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb @@ -19,7 +19,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb index 9493af88c9..12db25bb17 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb +++ b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb @@ -21,7 +21,7 @@ configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enab configopts += '--enable-libx264' sanity_check_paths = { - 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-foss-2014b.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-foss-2014b.eb index 4cd5e51c8c..c1ab6dd32f 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-foss-2014b.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-foss-2014b.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('expat', '2.1.0'), - ('freetype','2.5.3'), + ('freetype', '2.5.3'), ] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb index e77da2e1fe..51c9c97afb 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('expat', '2.1.0'), - ('freetype','2.5.3'), + ('freetype', '2.5.3'), ] configopts = '--disable-docs ' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2014b.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2014b.eb index 1d43a6c1f3..0cbc9d1200 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2014b.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2014b.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('expat', '2.1.0'), - ('freetype','2.5.3'), + ('freetype', '2.5.3'), ] configopts = '--disable-docs ' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-goolf-1.7.20.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-goolf-1.7.20.eb index 8fdfa9a81b..6e68a31103 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-goolf-1.7.20.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('expat', '2.1.0'), - ('freetype','2.6'), + ('freetype', '2.6'), ] configopts = '--disable-docs ' diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb index 7e4853de2f..6c5ce99387 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : [], - 'dirs' : ['include/X11/fonts'], + 'files': [], + 'dirs': ['include/X11/fonts'], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb index 5c120f5dd2..5c83a62b97 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : [], - 'dirs' : ['include/X11/fonts'], + 'files': [], + 'dirs': ['include/X11/fonts'], } moduleclass = 'devel' -- GitLab From d3466d43c41f2f7a6a2c5c126e928c31b94bd5c0 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 13:11:06 +0100 Subject: [PATCH 0268/2133] Style fixes with autopep8: h Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs.eb | 2 +- .../easyconfigs/h/HDF5/HDF5-1.8.10-intel-2014b-gpfs.eb | 2 +- easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.2.0.eb | 4 ++-- .../h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb | 6 +++--- .../h/HH-suite/HH-suite-2.0.16-goolf-1.4.10.eb | 6 +++--- .../h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb | 6 +++--- .../easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-4.0.6.eb | 6 +++--- easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb | 6 +++--- .../easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb | 2 +- .../easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb | 2 +- .../easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb | 2 +- .../easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb | 2 +- .../HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb | 6 +++--- .../HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb | 6 +++--- .../HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb | 2 +- .../HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb | 2 +- .../HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb | 1 - .../h/HarfBuzz/HarfBuzz-0.9.35-intel-2014b.eb | 4 ++-- .../h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb | 4 ++-- .../h/HarfBuzz/HarfBuzz-1.1.0-intel-2015b.eb | 4 ++-- .../h/Hypre/Hypre-2.8.0b-goalf-1.1.0-no-OFED.eb | 6 +++--- .../easyconfigs/h/Hypre/Hypre-2.8.0b-goolf-1.4.10.eb | 6 +++--- .../easyconfigs/h/Hypre/Hypre-2.8.0b-ictce-4.0.6.eb | 6 +++--- .../easyconfigs/h/Hypre/Hypre-2.8.0b-ictce-5.3.0.eb | 6 +++--- .../h/h5py/h5py-2.2.1-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../h/h5py/h5py-2.2.1-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../h/h5utils/h5utils-1.12.1-goalf-1.1.0-no-OFED.eb | 10 +++++----- .../h/h5utils/h5utils-1.12.1-goolf-1.4.10.eb | 10 +++++----- .../h/h5utils/h5utils-1.12.1-ictce-4.0.6.eb | 10 +++++----- .../h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb | 10 +++++----- .../hwloc-1.10.0-iccifort-2015.1.133-GCC-4.9.2.eb | 1 - .../hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb | 1 - .../easyconfigs/h/hwloc/hwloc-1.11.1-GCC-4.9.3.eb | 1 - .../hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 1 - .../easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb | 2 +- .../h/hwloc/hwloc-1.9-iccifort-2013_sp1.4.211.eb | 1 - 38 files changed, 78 insertions(+), 84 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs.eb index 031479c2f3..ec1b30de69 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs.eb @@ -19,7 +19,7 @@ patches = [ dependencies = [ ('zlib', '1.2.7'), - ('Szip','2.1'), + ('Szip', '2.1'), ] configopts = "--enable-gpfs" diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-intel-2014b-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-intel-2014b-gpfs.eb index 62eff2e443..fa45e3d80d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-intel-2014b-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-intel-2014b-gpfs.eb @@ -19,7 +19,7 @@ patches = [ dependencies = [ ('zlib', '1.2.8'), - ('Szip','2.1'), + ('Szip', '2.1'), ] configopts = "--enable-gpfs" diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.2.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.2.0.eb index 0166822809..7cd6cdf595 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.2.0.eb @@ -18,8 +18,8 @@ patches = [ ] dependencies = [ - ('zlib','1.2.7'), - ('Szip','2.1'), + ('zlib', '1.2.7'), + ('Szip', '2.1'), ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb index c29c1cc257..9bc25a5071 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb @@ -28,8 +28,8 @@ skipsteps = ['configure'] installopts = "INSTALL_DIR=%(installdir)s" sanity_check_paths = { - 'files': ["bin/hhalign", "bin/hhblits", "bin/hhconsensus", "bin/hhfilter", "bin/hhmake", "bin/hhsearch"], - 'dirs': [] - } + 'files': ["bin/hhalign", "bin/hhblits", "bin/hhconsensus", "bin/hhfilter", "bin/hhmake", "bin/hhsearch"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goolf-1.4.10.eb index 6fd5c2e8bf..562e595557 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goolf-1.4.10.eb @@ -28,8 +28,8 @@ skipsteps = ['configure'] installopts = "INSTALL_DIR=%(installdir)s" sanity_check_paths = { - 'files': ["bin/hhalign", "bin/hhblits", "bin/hhconsensus", "bin/hhfilter", "bin/hhmake", "bin/hhsearch"], - 'dirs': [] - } + 'files': ["bin/hhalign", "bin/hhblits", "bin/hhconsensus", "bin/hhfilter", "bin/hhmake", "bin/hhsearch"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb index 3879fe81ad..9f844f7f8c 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb @@ -33,8 +33,8 @@ sources = ['hmmer-%s-linux-intel-x86_64.tar.gz' % version] source_urls = ['http://selab.janelia.org/software/%s/%s/' % (versiondir, version)] sanity_check_paths = { - 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], - 'dirs': [] - } + 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb index 2c24669f8f..ac2ff916ef 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb @@ -32,8 +32,8 @@ sources = ['hmmer-%s-linux-intel-x86_64.tar.gz' % version] source_urls = ['http://selab.janelia.org/software/%s/%s/' % (versiondir, version)] sanity_check_paths = { - 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], - 'dirs': [] - } + 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-4.0.6.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-4.0.6.eb index 43301b81dc..4f2f846bc8 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-4.0.6.eb @@ -33,8 +33,8 @@ sources = ['hmmer-%s-linux-intel-x86_64.tar.gz' % version] source_urls = ['http://selab.janelia.org/software/%s/%s/' % (versiondir, version)] sanity_check_paths = { - 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], - 'dirs': [] - } + 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb index 11e40f315c..52d1571680 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb @@ -34,8 +34,8 @@ sources = ['hmmer-%s-linux-intel-x86_64.tar.gz' % version] source_urls = ['http://selab.janelia.org/software/%s/%s/' % (versiondir, version)] sanity_check_paths = { - 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], - 'dirs': [] - } + 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb index 35d93e8b65..7b6ea628da 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb @@ -35,7 +35,7 @@ installopts = ' && cd easel && make install' sanity_check_paths = { 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", - "esl-alimap", "esl-cluster", "esl-mask"]], + "esl-alimap", "esl-cluster", "esl-mask"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb index 6b7248a777..65bc990310 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb @@ -35,7 +35,7 @@ installopts = ' && cd easel && make install' sanity_check_paths = { 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", - "esl-alimap", "esl-cluster", "esl-mask"]], + "esl-alimap", "esl-cluster", "esl-mask"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb index b56baf902e..9a8eaafde6 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb @@ -35,7 +35,7 @@ installopts = ' && cd easel && make install' sanity_check_paths = { 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", - "esl-alimap", "esl-cluster", "esl-mask"]], + "esl-alimap", "esl-cluster", "esl-mask"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index 5255f85ddc..36707aa8fe 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -34,7 +34,7 @@ installopts = ' && cd easel && make install' sanity_check_paths = { 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", - "esl-alimap", "esl-cluster", "esl-mask"]], + "esl-alimap", "esl-cluster", "esl-mask"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb index b103b8110e..05c50b39b9 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb @@ -19,7 +19,7 @@ homepage = 'http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html' description = """Bioinformatics & Computational Biology productivity environment includes a set of HPC tools, which are needed for scientific computing and visualization in the respective domain. """ -toolchain = {'name': 'goolf', 'version': '1.4.10'} # ie. build against the GNU compilers & OpenMPI stack +toolchain = {'name': 'goolf', 'version': '1.4.10'} # ie. build against the GNU compilers & OpenMPI stack dependencies = [ ('ALLPATHS-LG', '46968'), @@ -33,7 +33,7 @@ dependencies = [ ('Bowtie2', '2.0.2'), ('bam2fastq', '1.1.0'), ('biodeps', '1.6'), -# ('CD-HIT', '4.5.4', '-2011-03-07'), + # ('CD-HIT', '4.5.4', '-2011-03-07'), ('ClustalW2', '2.1'), ('Cufflinks', '2.0.2'), ('EMBOSS', '6.5.7'), @@ -57,7 +57,7 @@ dependencies = [ ('NEURON', '7.2'), ('Oases', '0.2.08'), ('PAML', '4.7'), -# ('PLINK', '1.07'), + # ('PLINK', '1.07'), ('Pasha', '1.0.3'), ('Primer3', '2.3.0'), ('RAxML', '7.7.5', '-hybrid-sse3'), diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb index e1d3fd7aa1..a420531cae 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb @@ -19,10 +19,10 @@ homepage = 'http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html' description = """Bioinformatics & Computational Biology productivity environment includes a set of HPC tools, which are needed for scientific computing and visualization in the respective domain. """ -toolchain = {'name': 'ictce', 'version': '5.3.0'} # ie. build against the INTEL compilers & MPI stack / March 2013 +toolchain = {'name': 'ictce', 'version': '5.3.0'} # ie. build against the INTEL compilers & MPI stack / March 2013 dependencies = [ -# ('ALLPATHS-LG', '46968'), + # ('ALLPATHS-LG', '46968'), ('AMOS', '3.1.0'), ('BFAST', '0.7.0a'), ('BLAST+', '2.2.28', '-Python-2.7.3'), @@ -43,7 +43,7 @@ dependencies = [ ('GLIMMER', '3.02b'), ('GROMACS', '4.6.1', '-hybrid'), ('HMMER', '3.0'), -# ('HH-suite', '2.0.16'), + # ('HH-suite', '2.0.16'), ('Infernal', '1.1rc1'), ('libgtextutils', '0.6.1'), ('libharu', '2.2.0'), diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb index 3925d65933..ac9bda6d5d 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb @@ -31,7 +31,7 @@ dependencies = [ ('HMMER', '3.0'), ('MrBayes', '3.1.2'), ('mpiBLAST', '1.6.0'), -# ('Rosetta', '3.5'), + # ('Rosetta', '3.5'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb index fc1b20fc8e..a4a4c517a0 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb @@ -31,7 +31,7 @@ dependencies = [ ('HMMER', '3.0'), ('MrBayes', '3.1.2'), ('mpiBLAST', '1.6.0'), -# ('Rosetta', '3.5'), + # ('Rosetta', '3.5'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb index b2b1287193..53cb50514f 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb @@ -23,9 +23,9 @@ description = """Common Set of Open Source Math Libraries includes a set of HPC toolchain = {'name': 'ictce', 'version': '5.3.0'} dependencies = [ - ('PETSc', '3.3-p2', '-Python-2.7.3'), - ('GSL', '1.15'), - ('SPRNG', '2.0b'), + ('PETSc', '3.3-p2', '-Python-2.7.3'), + ('GSL', '1.15'), + ('SPRNG', '2.0b'), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb index 0ad29d6c94..96acd93725 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb @@ -15,4 +15,3 @@ source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] patches = ['HPL_parallel-make.patch'] moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.35-intel-2014b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.35-intel-2014b.eb index da1d4ca30f..473cec461a 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.35-intel-2014b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.35-intel-2014b.eb @@ -12,8 +12,8 @@ source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] dependencies = [ - ('cairo', '1.12.18'), - ('GObject-Introspection', '1.42.0'), + ('cairo', '1.12.18'), + ('GObject-Introspection', '1.42.0'), ] patches = ['HarfBuzz-%(version)s_config.patch'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb index 816c289c55..8537af8ca5 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb @@ -12,8 +12,8 @@ source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] dependencies = [ - ('cairo', '1.14.2'), - ('GObject-Introspection', '1.44.0'), + ('cairo', '1.14.2'), + ('GObject-Introspection', '1.44.0'), ] configopts = '--with-gobject --enable-introspection=yes ' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.0-intel-2015b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.0-intel-2015b.eb index 15e2c94d10..4669cfc27f 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.0-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.0-intel-2015b.eb @@ -12,8 +12,8 @@ source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] dependencies = [ - ('cairo', '1.14.4'), - ('GObject-Introspection', '1.47.1'), + ('cairo', '1.14.4'), + ('GObject-Introspection', '1.47.1'), ] configopts = '--with-gobject --enable-introspection=yes ' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-goalf-1.1.0-no-OFED.eb index 964e73f35c..8348598dca 100644 --- a/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-goalf-1.1.0-no-OFED.eb @@ -15,8 +15,8 @@ sources = [SOURCELOWER_TAR_GZ] start_dir = "src" sanity_check_paths = { - 'files': ['lib/libHYPRE.a'], - 'dirs': ['include'] - } + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-goolf-1.4.10.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-goolf-1.4.10.eb index 57e599416b..8022f1e636 100644 --- a/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-goolf-1.4.10.eb @@ -14,8 +14,8 @@ sources = [SOURCELOWER_TAR_GZ] start_dir = "src" sanity_check_paths = { - 'files': ['lib/libHYPRE.a'], - 'dirs': ['include'] - } + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-ictce-4.0.6.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-ictce-4.0.6.eb index 1e62113c7c..4d7372a276 100644 --- a/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-ictce-4.0.6.eb @@ -15,8 +15,8 @@ sources = [SOURCELOWER_TAR_GZ] start_dir = "src" sanity_check_paths = { - 'files': ['lib/libHYPRE.a'], - 'dirs': ['include'] - } + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-ictce-5.3.0.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-ictce-5.3.0.eb index c7c83dd59e..a01d7fbee8 100644 --- a/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.8.0b-ictce-5.3.0.eb @@ -16,8 +16,8 @@ sources = [SOURCELOWER_TAR_GZ] start_dir = "src" sanity_check_paths = { - 'files': ['lib/libHYPRE.a'], - 'dirs': ['include'] - } + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-goolf-1.4.10-Python-2.7.3.eb index 9852693c15..c9f750bf70 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-goolf-1.4.10-Python-2.7.3.eb @@ -26,7 +26,7 @@ dependencies = [ (python, pythonver), ('HDF5', '1.8.12', '-zlib-1.2.7'), ('mpi4py', '1.3', versionsuffix), # required for MPI support - ('Cython', '0.19.1', versionsuffix), # required to build h5py with MPI support + ('Cython', '0.19.1', versionsuffix), # required to build h5py with MPI support ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-4.1.13-Python-2.7.3.eb index 7f4bdd782b..eb868b185c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-4.1.13-Python-2.7.3.eb @@ -26,7 +26,7 @@ dependencies = [ (python, pythonver), ('HDF5', '1.8.12', '-zlib-1.2.7'), ('mpi4py', '1.3', versionsuffix), # required for MPI support - ('Cython', '0.19.1', versionsuffix), # required to build h5py with MPI support + ('Cython', '0.19.1', versionsuffix), # required to build h5py with MPI support ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-goalf-1.1.0-no-OFED.eb index c8bbf3c141..a9fe70521e 100644 --- a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-goalf-1.1.0-no-OFED.eb @@ -18,11 +18,11 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'usempi': True} dependencies = [ - ('zlib', '1.2.7'), - ('libpng', '1.5.11'), - ('libmatheval', '1.1.8'), - ('HDF5', '1.8.7'), - ] + ('zlib', '1.2.7'), + ('libpng', '1.5.11'), + ('libmatheval', '1.1.8'), + ('HDF5', '1.8.7'), +] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-goolf-1.4.10.eb index 2c3932e7b7..2efbe0acab 100644 --- a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-goolf-1.4.10.eb @@ -16,11 +16,11 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} dependencies = [ - ('zlib', '1.2.7'), - ('libpng', '1.5.11'), - ('libmatheval', '1.1.8'), - ('HDF5', '1.8.7'), - ] + ('zlib', '1.2.7'), + ('libpng', '1.5.11'), + ('libmatheval', '1.1.8'), + ('HDF5', '1.8.7'), +] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-4.0.6.eb b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-4.0.6.eb index ed7d1cacaa..a75aef9437 100644 --- a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-4.0.6.eb @@ -17,11 +17,11 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'usempi': True} dependencies = [ - ('zlib', '1.2.7'), - ('libpng', '1.5.11'), - ('libmatheval', '1.1.8'), - ('HDF5', '1.8.7'), - ] + ('zlib', '1.2.7'), + ('libpng', '1.5.11'), + ('libmatheval', '1.1.8'), + ('HDF5', '1.8.7'), +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['h5fromtxt', 'h5math', 'h5topng', 'h5totxt', 'h5tovtk']], diff --git a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb index 975690f50f..09424f6b1b 100644 --- a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb @@ -18,11 +18,11 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} dependencies = [ - ('zlib', '1.2.7'), - ('libpng', '1.5.11'), - ('libmatheval', '1.1.8'), - ('HDF5', '1.8.7'), - ] + ('zlib', '1.2.7'), + ('libpng', '1.5.11'), + ('libmatheval', '1.1.8'), + ('HDF5', '1.8.7'), +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['h5fromtxt', 'h5math', 'h5topng', 'h5totxt', 'h5tovtk']], diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.1.133-GCC-4.9.2.eb index 6adec23e71..3ecf13cb7d 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.1.133-GCC-4.9.2.eb @@ -17,4 +17,3 @@ source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/ sources = [SOURCE_TAR_GZ] moduleclass = 'system' - diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb index 6a875c1d32..c0454d9632 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb @@ -17,4 +17,3 @@ source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/ sources = [SOURCE_TAR_GZ] moduleclass = 'system' - diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-GCC-4.9.3.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-GCC-4.9.3.eb index a63d6bae6e..4d49031a3a 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-GCC-4.9.3.eb @@ -21,4 +21,3 @@ dependencies = [('numactl', '2.0.11')] configopts = "--enable-libnuma=$EBROOTNUMACTL" moduleclass = 'system' - diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 50bcad92f3..d803930b96 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -21,4 +21,3 @@ source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/ sources = [SOURCE_TAR_GZ] moduleclass = 'system' - diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb index dd384c19f8..0af84a15f7 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.9-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.9-iccifort-2013_sp1.4.211.eb index 528befdb9a..c4ebd968ce 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.9-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.9-iccifort-2013_sp1.4.211.eb @@ -17,4 +17,3 @@ source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/ sources = [SOURCE_TAR_GZ] moduleclass = 'system' - -- GitLab From f671ff366c7cf04eae4c648476645caa27e8e349 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 13:09:19 +0100 Subject: [PATCH 0269/2133] Style fixes with autopep8: g Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../g/GATE/GATE-7.0-intel-2015a.eb | 2 +- .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 4 ++-- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 6 +++--- .../easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 6 +++--- .../easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 6 +++--- .../easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 6 +++--- .../easyconfigs/g/GCCcore/GCCcore-4.9.3.eb | 3 ++- .../g/GDAL/GDAL-1.9.2-ictce-4.1.13.eb | 2 +- .../g/GDAL/GDAL-1.9.2-iqacml-3.7.3.eb | 2 +- ...30406-045632_pre-release-3_Linux-x86_64.eb | 2 +- .../g/GHC/GHC-7.6.2-goalf-1.1.0-no-OFED.eb | 2 +- .../g/GHC/GHC-7.6.2-goolf-1.4.10.eb | 2 +- .../g/GHC/GHC-7.8.3-goalf-1.1.0-no-OFED.eb | 2 +- .../g/GHC/GHC-7.8.3-goolf-1.4.10.eb | 2 +- .../g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb | 2 +- .../g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb | 2 +- .../g/GLib/GLib-2.41.2-intel-2014b.eb | 2 +- .../GLib-2.44.1-intel-2015a-Python-2.7.10.eb | 4 ++-- .../GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb | 1 - .../g/GMP/GMP-6.0.0a-intel-2015b.eb | 1 - ...0.8965-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 12 +++++------ ...AW-0.9.0.8965-goolf-1.4.10-Python-2.7.3.eb | 12 +++++------ ...PAW-0.9.0.8965-ictce-4.0.6-Python-2.7.3.eb | 14 ++++++------- ...PAW-0.9.0.8965-ictce-5.3.0-Python-2.7.3.eb | 12 +++++------ .../g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb | 2 +- .../g/GTS/GTS-0.7.6-intel-2014b.eb | 2 +- .../GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb | 2 +- .../g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb | 2 +- .../Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb | 2 +- .../g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb | 2 +- ...GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 2 +- .../g/Graphviz/Graphviz-2.38.0-intel-2014b.eb | 4 ++-- ...aphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 4 ++-- .../g/git/git-1.7.12-ictce-5.3.0.eb | 6 +++--- .../glproto-1.4.16-goalf-1.1.0-no-OFED.eb | 8 ++++---- .../g/glproto/glproto-1.4.16-goolf-1.4.10.eb | 8 ++++---- .../g/glproto/glproto-1.4.16-ictce-4.0.6.eb | 8 ++++---- .../g/glproto/glproto-1.4.16-ictce-5.3.0.eb | 8 ++++---- .../gnuplot-4.6.0-goalf-1.1.0-no-OFED.eb | 6 +++--- .../g/gnuplot/gnuplot-4.6.0-goolf-1.4.10.eb | 6 +++--- .../g/gnuplot/gnuplot-4.6.0-ictce-4.0.6.eb | 6 +++--- .../g/gnuplot/gnuplot-4.6.0-ictce-5.3.0.eb | 6 +++--- .../gnutls-3.1.8-goalf-1.1.0-no-OFED.eb | 18 ++++++++--------- .../g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb | 18 ++++++++--------- .../g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb | 4 ++-- .../gperf/gperf-3.0.4-goalf-1.1.0-no-OFED.eb | 6 +++--- .../g/gperf/gperf-3.0.4-goolf-1.4.10.eb | 6 +++--- .../g/gperf/gperf-3.0.4-ictce-4.0.6.eb | 6 +++--- .../g/gperf/gperf-3.0.4-ictce-5.3.0.eb | 6 +++--- .../easyconfigs/g/gpsmpi/gpsmpi-2014.12.eb | 3 +-- .../easyconfigs/g/gpsolf/gpsolf-2014.12.eb | 1 - .../grib_api-1.9.18-goalf-1.1.0-no-OFED.eb | 4 ++-- .../grib_api/grib_api-1.9.18-goolf-1.4.10.eb | 4 ++-- .../grib_api/grib_api-1.9.18-ictce-4.1.13.eb | 4 ++-- .../g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb | 4 ++-- .../g/gtest/gtest-1.6.0-intel-2014b.eb | 2 +- .../guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb | 20 +++++++++---------- .../g/guile/guile-1.8.8-goolf-1.4.10.eb | 20 +++++++++---------- .../g/guile/guile-1.8.8-ictce-4.0.6.eb | 20 +++++++++---------- 59 files changed, 168 insertions(+), 171 deletions(-) diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb index 55757f7ccc..e93ce79175 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb @@ -8,7 +8,7 @@ description = """GATE is an advanced opensource software developed by the intern toolchain = {'name': 'intel', 'version': '2015a'} -sources = [('%(namelower)s_v%(version)s.tar_.gz' , "tar xfvz %s")] +sources = [('%(namelower)s_v%(version)s.tar_.gz', "tar xfvz %s")] source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/'] patches = [ diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index 8bb06bd90a..3b725d6c3c 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -100,8 +100,8 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver, 'lib6 full_sanity_check = True sanity_check_paths = { - 'files': ['bin/gc3utils'], - 'dirs': ['lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg/gc3libs' % {'pyver': pyshortver}], + 'files': ['bin/gc3utils'], + 'dirs': ['lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg/gc3libs' % {'pyver': pyshortver}], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 6fee6c35e8..662fb134c2 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -101,9 +101,9 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index 8a1d9386f8..b08b112eb7 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -101,9 +101,9 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index b62aa2387d..92f6d885db 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -101,9 +101,9 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index e73e2257cc..e5720c5610 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -101,9 +101,9 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index 2027c9fa8e..2e4f04adbb 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -13,7 +13,8 @@ mpfr_version = '3.1.2' gcc_name = 'GCC' source_urls = [ - 'http://ftpmirror.gnu.org/%s/%s-%s' % (gcc_name.lower(), gcc_name.lower(), version), # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/%s/%s-%s' % (gcc_name.lower(), gcc_name.lower(), + version), # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-4.1.13.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-4.1.13.eb index 94cef6458d..4eded30be6 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """GDAL is a translator library for raster geospatial data formats Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.""" - + toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = ['http://download.osgeo.org/gdal/'] diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-iqacml-3.7.3.eb index 83b2c99400..670cd7dbd4 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-iqacml-3.7.3.eb @@ -8,7 +8,7 @@ description = """GDAL is a translator library for raster geospatial data formats Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.""" - + toolchain = {'name': 'iqacml', 'version': '3.7.3'} source_urls = ['http://download.osgeo.org/gdal/'] diff --git a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb index 9dd671125b..009df93cd7 100644 --- a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb +++ b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb @@ -35,7 +35,7 @@ skipsteps = ['build'] # glob support in MakeCp easyblock is required so EasyBuild-1.12 or higher is required easybuild_version = '1.12.0' -files_to_copy = [ (["man/*"], 'man/man1/'), "bin" ] +files_to_copy = [(["man/*"], 'man/man1/'), "bin"] sanity_check_paths = { 'files': ["bin/gem-indexer", "bin/gem-mapper", "bin/gem-rna-mapper"], diff --git a/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goalf-1.1.0-no-OFED.eb index 9a068844e1..ab5b8f6d40 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goalf-1.1.0-no-OFED.eb @@ -7,7 +7,7 @@ description = """GHC is the Glasgow Haskell Compiler.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = ['%s-%s-src.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goolf-1.4.10.eb index 36f3fcc67a..a2a6d5433e 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goolf-1.4.10.eb @@ -6,7 +6,7 @@ description = """GHC is the Glasgow Haskell Compiler.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%s-%s-src.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goalf-1.1.0-no-OFED.eb index 8fecfa9a31..52ae11225d 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goalf-1.1.0-no-OFED.eb @@ -6,7 +6,7 @@ description = """GHC is the Glasgow Haskell Compiler.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = ['%s-%s-src.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goolf-1.4.10.eb index ea5b087cdd..b6feb9a68c 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goolf-1.4.10.eb @@ -6,7 +6,7 @@ description = """GHC is the Glasgow Haskell Compiler.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%s-%s-src.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb index 5079733d91..8ad521809b 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb @@ -6,7 +6,7 @@ # License:: MIT/GPL # ## -easyblock='MakeCp' +easyblock = 'MakeCp' name = "GLIMMER" version = "3.02b" diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb index 7722b501dd..e4aa1f5c2e 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb @@ -6,7 +6,7 @@ # License:: MIT/GPL # ## -easyblock='MakeCp' +easyblock = 'MakeCp' name = "GLIMMER" version = "3.02b" diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb index 207b74b508..c44d4a669f 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -5,7 +5,7 @@ version = '2.41.2' homepage = 'http://www.gtk.org/' description = """GLib is one of the base libraries of the GTK+ project""" -toolchain = {'name': 'intel', 'version': '2014b'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) +toolchain = {'name': 'intel', 'version': '2014b'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb index cf36332497..9f4e52261e 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb @@ -16,9 +16,9 @@ dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), ] -python= 'Python' +python = 'Python' pyver = '2.7.10' -versionsuffix = '-%s-%s' % (python, pyver) +versionsuffix = '-%s-%s' % (python, pyver) builddependencies = [(python, pyver)] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb index d83527abe3..6189b95fa0 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb @@ -35,4 +35,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb index 1497e83746..c2785aa4a7 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015b.eb @@ -28,4 +28,3 @@ sanity_check_paths = { } moduleclass = 'math' - diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-goalf-1.1.0-no-OFED-Python-2.7.3.eb index ed849d076b..4eac8c213d 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -21,13 +21,13 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('ASE', '3.6.0.2515', versionsuffix) - ] + (python, pythonver), + ('ASE', '3.6.0.2515', versionsuffix) +] sanity_check_paths = { - 'files': ['bin/gpaw%s' % x for x in ['', '-basis', '-mpisim', '-python', '-setup', '-test']], - 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] - } + 'files': ['bin/gpaw%s' % x for x in ['', '-basis', '-mpisim', '-python', '-setup', '-test']], + 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-goolf-1.4.10-Python-2.7.3.eb index b74ab76176..c7f6453945 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-goolf-1.4.10-Python-2.7.3.eb @@ -20,13 +20,13 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('ASE', '3.6.0.2515', versionsuffix) - ] + (python, pythonver), + ('ASE', '3.6.0.2515', versionsuffix) +] sanity_check_paths = { - 'files': ['bin/gpaw%s' % x for x in ['', '-basis', '-mpisim', '-python', '-setup', '-test']], - 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] - } + 'files': ['bin/gpaw%s' % x for x in ['', '-basis', '-mpisim', '-python', '-setup', '-test']], + 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-ictce-4.0.6-Python-2.7.3.eb index b784121754..d4915b51fb 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-ictce-4.0.6-Python-2.7.3.eb @@ -7,7 +7,7 @@ homepage = 'https://wiki.fysik.dtu.dk/gpaw/' description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.""" - + toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ['https://wiki.fysik.dtu.dk/gpaw-files/'] @@ -21,13 +21,13 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('ASE', '3.6.0.2515', versionsuffix) - ] + (python, pythonver), + ('ASE', '3.6.0.2515', versionsuffix) +] sanity_check_paths = { - 'files': ['bin/gpaw%s' % x for x in ['', '-basis', '-mpisim', '-python', '-setup', '-test']], - 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] - } + 'files': ['bin/gpaw%s' % x for x in ['', '-basis', '-mpisim', '-python', '-setup', '-test']], + 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-ictce-5.3.0-Python-2.7.3.eb index ed0f7d5368..5403b3585f 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-ictce-5.3.0-Python-2.7.3.eb @@ -22,13 +22,13 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('ASE', '3.6.0.2515', versionsuffix) - ] + (python, pythonver), + ('ASE', '3.6.0.2515', versionsuffix) +] sanity_check_paths = { - 'files': ['bin/gpaw%s' % x for x in ['', '-basis', '-mpisim', '-python', '-setup', '-test']], - 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] - } + 'files': ['bin/gpaw%s' % x for x in ['', '-basis', '-mpisim', '-python', '-setup', '-test']], + 'dirs': ['lib/python%s/site-packages/%s' % (pythonshortver, name.lower())] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb index f600de3146..3d384db2d6 100644 --- a/easybuild/easyconfigs/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb @@ -27,7 +27,7 @@ dependencies = [('PnMPI', '1.2.0')] builddependencies = [('CMake', '2.8.10.2')] -configopts = '-DCMAKE_BUILD_TYPE=Release -DPnMPI_INSTALL_PREFIX=${EBROOTPNMPI}' +configopts = '-DCMAKE_BUILD_TYPE=Release -DPnMPI_INSTALL_PREFIX=${EBROOTPNMPI}' buildopts = 'CXXFLAGS="$CXXFLAGS -fpermissive"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2014b.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2014b.eb index 20a9adba50..5c0a28293c 100644 --- a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2014b.eb @@ -14,7 +14,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('GLib', '2.40.0'), + ('GLib', '2.40.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb index 540cb54071..4aff5dab8a 100644 --- a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb @@ -18,7 +18,7 @@ glibver = '2.44.1' versionsuffix = '-%s-%s' % (glib, glibver) dependencies = [ - (glib, glibver), + (glib, glibver), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb index 32054f56b5..dd53f85088 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb @@ -6,7 +6,7 @@ description = """Geant4 is a toolkit for the simulation of the passage of partic Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.""" -toolchain = {'name': 'ictce', 'version':'4.0.6'} +toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ['http://geant4.cern.ch/support/source'] sources = ['%(namelower)s.%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb index b6f358819f..fbf3b03c0b 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb @@ -6,7 +6,7 @@ description = """Geant4 is a toolkit for the simulation of the passage of partic Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.""" -toolchain = {'name': 'goalf', 'version':'1.1.0-no-OFED'} +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['http://geant4.cern.ch/support/source'] sources = ['%(namelower)s.%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb index d2acaf5f1d..8eb3941ded 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb @@ -6,7 +6,7 @@ description = """Geant4 is a toolkit for the simulation of the passage of partic Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.""" -toolchain = {'name': 'ictce', 'version':'4.0.6'} +toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ['http://geant4.cern.ch/support/source'] sources = ['%(namelower)s.%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 0fa0ab2a82..df30b5f05b 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -15,7 +15,7 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] -sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] +sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz'] checksums = ['0a7b041efdd7a5d7ced0ae48eb4a9e06'] diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb index fdd14fa479..aee7aa31e0 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb @@ -42,8 +42,8 @@ builddependencies = [ ] patches = [ - 'Graphviz-2.38.0_icc_vmalloc.patch', - 'Graphviz-2.38.0_icc_sfio.patch', + 'Graphviz-2.38.0_icc_vmalloc.patch', + 'Graphviz-2.38.0_icc_sfio.patch', ] configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index f2c3631ad0..231a5ddb6f 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -44,8 +44,8 @@ builddependencies = [ ] patches = [ - 'Graphviz-2.38.0_icc_vmalloc.patch', - 'Graphviz-2.38.0_icc_sfio.patch', + 'Graphviz-2.38.0_icc_vmalloc.patch', + 'Graphviz-2.38.0_icc_sfio.patch', ] configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' diff --git a/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb b/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb index 75c6bb092f..4c4de49303 100644 --- a/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb @@ -30,8 +30,8 @@ dependencies = [('gettext', '0.18.2')] configopts = "--enable-pthreads='-lpthread'" sanity_check_paths = { - 'files': ["bin/git"], - 'dirs': [] - } + 'files': ["bin/git"], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb index e26ff137e5..a111fa37d7 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb @@ -13,9 +13,9 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], - 'dirs': [] - } + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', + 'glxtokens', 'internal/glcore']], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb index a46e3dcda1..824d2e05e3 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb @@ -12,9 +12,9 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], - 'dirs': [] - } + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', + 'glxtokens', 'internal/glcore']], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb index 172016aad3..fbc9e27321 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb @@ -13,9 +13,9 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], - 'dirs': [] - } + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', + 'glxtokens', 'internal/glcore']], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb index d770bc9878..99f5e68e02 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb @@ -14,9 +14,9 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], - 'dirs': [] - } + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', + 'glxtokens', 'internal/glcore']], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goalf-1.1.0-no-OFED.eb index 81a026fc55..bd0bbb0ca0 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goalf-1.1.0-no-OFED.eb @@ -24,8 +24,8 @@ source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/gnuplot'], - 'dirs': [] - } + 'files': ['bin/gnuplot'], + 'dirs': [] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goolf-1.4.10.eb index 9c6317ae8b..3d45dffc3f 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goolf-1.4.10.eb @@ -23,8 +23,8 @@ source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['bin/gnuplot'], - 'dirs': [] - } + 'files': ['bin/gnuplot'], + 'dirs': [] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-4.0.6.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-4.0.6.eb index a473b4546f..23b0d23f05 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-4.0.6.eb @@ -24,8 +24,8 @@ source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/gnuplot'], - 'dirs': [] - } + 'files': ['bin/gnuplot'], + 'dirs': [] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-5.3.0.eb index c4db96bf96..b95685cff8 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-5.3.0.eb @@ -25,8 +25,8 @@ source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/gnuplot'], - 'dirs': [] - } + 'files': ['bin/gnuplot'], + 'dirs': [] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb index 9315e9e792..989ba1dc22 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb @@ -12,18 +12,18 @@ source_urls = ['ftp://ftp.gnutls.org/pub/gnutls/'] sources = [SOURCE_TAR_XZ] dependencies = [ - ('GMP', '5.0.5'), - ('nettle', '2.6'), - ('guile', '1.8.8'), - ] + ('GMP', '5.0.5'), + ('nettle', '2.6'), + ('guile', '1.8.8'), +] configopts = "--with-guile-site-dir=$EBROOTGUILE" sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['certtool', 'danetool', 'gnutls-cli', 'gnutls-cli-debug', - 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + - ['lib/libgnutls%s' % x for x in ['.a', 'xx.a', '-xssl.a', '-openssl.a']], - 'dirs': ['include/gnutls'], - } + 'files': ['bin/%s' % x for x in ['certtool', 'danetool', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.a', 'xx.a', '-xssl.a', '-openssl.a']], + 'dirs': ['include/gnutls'], +} moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb index 0fc5d46401..24da5d4615 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb @@ -11,18 +11,18 @@ source_urls = ['ftp://ftp.gnutls.org/pub/gnutls/'] sources = [SOURCE_TAR_XZ] dependencies = [ - ('GMP', '5.0.5'), - ('nettle', '2.6'), - ('guile', '1.8.8'), - ] + ('GMP', '5.0.5'), + ('nettle', '2.6'), + ('guile', '1.8.8'), +] configopts = "--with-guile-site-dir=$EBROOTGUILE" sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['certtool', 'danetool', 'gnutls-cli', 'gnutls-cli-debug', - 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + - ['lib/libgnutls%s' % x for x in ['.a', 'xx.a', '-xssl.a', '-openssl.a']], - 'dirs': ['include/gnutls'], - } + 'files': ['bin/%s' % x for x in ['certtool', 'danetool', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.a', 'xx.a', '-xssl.a', '-openssl.a']], + 'dirs': ['include/gnutls'], +} moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb index d883037773..28416d4ec1 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb @@ -32,8 +32,8 @@ configopts = "--with-guile-site-dir=$EBROOTGUILE --enable-openssl-compatibility sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'crywrap', 'gnutls-cli', 'gnutls-cli-debug', 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + - ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]] + - ['lib/guile/%s/guile-gnutls-v-2.so' % guileshortver], + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]] + + ['lib/guile/%s/guile-gnutls-v-2.so' % guileshortver], 'dirs': ['include/gnutls'], } diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goalf-1.1.0-no-OFED.eb index a5318892cf..62b829ab9b 100644 --- a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goalf-1.1.0-no-OFED.eb @@ -15,8 +15,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/gperf'], - 'dirs': [] - } + 'files': ['bin/gperf'], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goolf-1.4.10.eb index ef45494212..7b5f1aee64 100644 --- a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goolf-1.4.10.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/gperf'], - 'dirs': [] - } + 'files': ['bin/gperf'], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-4.0.6.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-4.0.6.eb index 574b337302..6b2cf27684 100644 --- a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-4.0.6.eb @@ -15,8 +15,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/gperf'], - 'dirs': [] - } + 'files': ['bin/gperf'], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-5.3.0.eb index c2990d1702..d55ea61bd0 100644 --- a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-5.3.0.eb @@ -16,8 +16,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/gperf'], - 'dirs': [] - } + 'files': ['bin/gperf'], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gpsmpi/gpsmpi-2014.12.eb b/easybuild/easyconfigs/g/gpsmpi/gpsmpi-2014.12.eb index a65b441539..57ee805544 100644 --- a/easybuild/easyconfigs/g/gpsmpi/gpsmpi-2014.12.eb +++ b/easybuild/easyconfigs/g/gpsmpi/gpsmpi-2014.12.eb @@ -21,8 +21,7 @@ comp = (compname, compver) dependencies = [ comp, - (mpilib, mpiver, '', comp ), + (mpilib, mpiver, '', comp), ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/g/gpsolf/gpsolf-2014.12.eb b/easybuild/easyconfigs/g/gpsolf/gpsolf-2014.12.eb index 5eacc9a99c..6a6f1377bc 100644 --- a/easybuild/easyconfigs/g/gpsolf/gpsolf-2014.12.eb +++ b/easybuild/easyconfigs/g/gpsolf/gpsolf-2014.12.eb @@ -33,4 +33,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb index 5cea12d320..ef2423ee53 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb @@ -14,8 +14,8 @@ source_urls = ['https://software.ecmwf.int/wiki/download/attachments/3473437/'] sources = [SOURCE_TAR_GZ] dependencies = [ - ('JasPer', '1.900.1'), - ] + ('JasPer', '1.900.1'), +] preconfigopts = 'FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb index 8e5630b19c..c0f9f1c6d8 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb @@ -13,8 +13,8 @@ source_urls = ['https://software.ecmwf.int/wiki/download/attachments/3473437/'] sources = [SOURCE_TAR_GZ] dependencies = [ - ('JasPer', '1.900.1'), - ] + ('JasPer', '1.900.1'), +] preconfigopts = 'FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb index 2e926b4cab..384aa93ebf 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb @@ -14,8 +14,8 @@ source_urls = ['https://software.ecmwf.int/wiki/download/attachments/3473437/'] sources = [SOURCE_TAR_GZ] dependencies = [ - ('JasPer', '1.900.1'), - ] + ('JasPer', '1.900.1'), +] preconfigopts = 'FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb index 831f1d1677..048ac9570d 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb @@ -15,8 +15,8 @@ source_urls = ['https://software.ecmwf.int/wiki/download/attachments/3473437/'] sources = [SOURCE_TAR_GZ] dependencies = [ - ('JasPer', '1.900.1'), - ] + ('JasPer', '1.900.1'), +] preconfigopts = 'FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' diff --git a/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb b/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb index 785c4e7264..cd4e4b08f5 100644 --- a/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb @@ -15,7 +15,7 @@ with_configure = True files_to_copy = ['lib', 'include'] -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libgtest.la', 'lib/libgtest_main.la'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb index 17fa80e4df..bfbad1d7a3 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb @@ -13,19 +13,19 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] dependencies = [ - ('libtool', '2.4.2'), - ('GMP', '5.0.5'), - ('libunistring', '0.9.3'), - ('pkg-config', '0.27.1'), - ('libffi', '3.0.11'), - ('libreadline', '6.2'), - ] + ('libtool', '2.4.2'), + ('GMP', '5.0.5'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.27.1'), + ('libffi', '3.0.11'), + ('libreadline', '6.2'), +] configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], - 'dirs': [] - } + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb index 80c9c68431..04db861e00 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb @@ -12,19 +12,19 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] dependencies = [ - ('libtool', '2.4.2'), - ('GMP', '5.0.5'), - ('libunistring', '0.9.3'), - ('pkg-config', '0.27.1'), - ('libffi', '3.0.11'), - ('libreadline', '6.2'), - ] + ('libtool', '2.4.2'), + ('GMP', '5.0.5'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.27.1'), + ('libffi', '3.0.11'), + ('libreadline', '6.2'), +] configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], - 'dirs': [] - } + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb index 67e9066e3c..0d3cfc351b 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb @@ -13,19 +13,19 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] dependencies = [ - ('libtool', '2.4.2'), - ('GMP', '5.0.5'), - ('libunistring', '0.9.3'), - ('pkg-config', '0.27.1'), - ('libffi', '3.0.11'), - ('libreadline', '6.2'), - ] + ('libtool', '2.4.2'), + ('GMP', '5.0.5'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.27.1'), + ('libffi', '3.0.11'), + ('libreadline', '6.2'), +] configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], - 'dirs': [] - } + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} moduleclass = 'devel' -- GitLab From 4003f08fad0bbdc1ea347feb21e4ee6a1931264d Mon Sep 17 00:00:00 2001 From: damianam Date: Thu, 28 Jan 2016 13:43:42 +0100 Subject: [PATCH 0270/2133] Update CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb --- .../c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 3638002800..f2ca68b5c1 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -25,7 +25,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} -source_urls = ['http://developer.download.nvidia.com/compute/cuda/7.5/Prod/local_installers/'] +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_linux.run'] checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] -- GitLab From 3018abe57cd88301d1450dc21ac2630e4cf643ac Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:04:06 +0100 Subject: [PATCH 0271/2133] Style fixes with autopep8: i Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb | 2 +- .../i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb | 1 - .../i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb | 1 - .../i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb | 4 ++-- .../i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb | 4 ++-- .../IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../IPython-3.1.0-intel-2015a-Python-2.7.9.eb | 2 +- .../IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb | 2 +- .../IPython-3.2.0-intel-2015a-Python-2.7.9.eb | 2 +- .../Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb | 6 +++--- .../i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb | 6 +++--- .../i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb | 6 +++--- .../i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb | 6 +++--- .../i/Inspector/Inspector-2013_update6.eb | 2 +- ...Instant-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 12 ++++++------ .../Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 12 ++++++------ .../Instant-1.0.0-ictce-4.0.6-Python-2.7.3.eb | 12 ++++++------ .../Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb | 12 ++++++------ .../i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb | 6 +++--- .../easyconfigs/i/Iperf/Iperf-2.0.5-goolf-1.4.10.eb | 6 +++--- .../easyconfigs/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb | 6 +++--- .../easyconfigs/i/Iperf/Iperf-2.0.5-ictce-5.3.0.eb | 6 +++--- easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb | 1 - .../easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb | 1 - .../i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb | 1 - .../i/iccifort/iccifort-2013_sp1.4.211.eb | 1 - .../easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb | 1 - .../i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb | 1 - .../i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb | 1 - easybuild/easyconfigs/i/iiqmpi/iiqmpi-3.3.0.eb | 6 +++--- easybuild/easyconfigs/i/iiqmpi/iiqmpi-4.4.13.eb | 6 +++--- .../i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb | 1 - .../i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb | 1 - .../imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb | 2 +- .../imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb | 4 ++-- .../easyconfigs/i/intel-para/intel-para-2014.12.eb | 1 - easybuild/easyconfigs/i/intel/intel-2016.00.eb | 2 +- easybuild/easyconfigs/i/intel/intel-2016.01.eb | 2 +- .../i/intltool/intltool-0.51.0-intel-2015b.eb | 2 +- easybuild/easyconfigs/i/iompi/iompi-2015.01.eb | 1 - easybuild/easyconfigs/i/iompi/iompi-2015.02.eb | 1 - easybuild/easyconfigs/i/iompi/iompi-2015.03.eb | 1 - easybuild/easyconfigs/i/iompi/iompi-6.6.4-no-OFED.eb | 1 - easybuild/easyconfigs/i/iompi/iompi-6.6.4.eb | 1 - easybuild/easyconfigs/i/ipsmpi/ipsmpi-2014.12.eb | 1 - easybuild/easyconfigs/i/iqacml/iqacml-3.7.3.eb | 6 +++--- easybuild/easyconfigs/i/iqacml/iqacml-4.4.13.eb | 8 ++++---- 47 files changed, 77 insertions(+), 95 deletions(-) diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb index 776e9a7846..70a1e78b61 100644 --- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -34,7 +34,7 @@ files_to_copy = ["bin", "script", "README", "ChangeLog", "NEWS"] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", - "idba_ud", "parallel_blat", "idba_tran_test"]], + "idba_ud", "parallel_blat", "idba_tran_test"]], 'dirs': [""], } diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb index 0c2d1cc059..03ab71fb09 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb @@ -29,4 +29,3 @@ modextrapaths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb index 0fb795f7eb..ba5278c540 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb @@ -29,4 +29,3 @@ modextrapaths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb index 2f880e4689..da34c32da1 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = "IOR" version = "2.10.3" -versionsuffix= "-mpiio" +versionsuffix = "-mpiio" homepage = 'http://sourceforge.net/projects/ior-sio/' description = """ The IOR software is used for benchmarking parallel file systems @@ -26,7 +26,7 @@ sources = [SOURCE_TGZ] buildopts = ' mpiio' files_to_copy = [(['src/C/IOR'], 'bin'), - "README", "RELEASE_LOG", "UNDOCUMENTED_OPTIONS", "USER_GUIDE", "scripts", "testing"] + "README", "RELEASE_LOG", "UNDOCUMENTED_OPTIONS", "USER_GUIDE", "scripts", "testing"] sanity_check_paths = { 'files': ["bin/IOR"], diff --git a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb index ac67b88a09..7502a94f71 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = "IOR" version = "2.10.3" -versionsuffix= "-mpiio" +versionsuffix = "-mpiio" homepage = 'http://sourceforge.net/projects/ior-sio/' description = """ The IOR software is used for benchmarking parallel file systems @@ -26,7 +26,7 @@ sources = [SOURCE_TGZ] buildopts = ' mpiio' files_to_copy = [(['src/C/IOR'], 'bin'), - "README", "RELEASE_LOG", "UNDOCUMENTED_OPTIONS", "USER_GUIDE", "scripts", "testing"] + "README", "RELEASE_LOG", "UNDOCUMENTED_OPTIONS", "USER_GUIDE", "scripts", "testing"] sanity_check_paths = { 'files': ["bin/IOR"], diff --git a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb index 92f605169b..8f516796f6 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -37,6 +37,6 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], } -sanity_check_commands = [('iptest','')] +sanity_check_commands = [('iptest', '')] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb index 4ddce0d142..97bb8abc44 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb @@ -40,6 +40,6 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], } -sanity_check_commands = [('iptest','')] +sanity_check_commands = [('iptest', '')] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb index ca831cfe27..f7ae347c5e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb @@ -40,6 +40,6 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], } -sanity_check_commands = [('iptest','')] +sanity_check_commands = [('iptest', '')] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb index 5b0893e10b..57149b7b99 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb @@ -40,6 +40,6 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], } -sanity_check_commands = [('iptest','')] +sanity_check_commands = [('iptest', '')] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb index cd6c0100f0..7c8fc6de1a 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb @@ -26,9 +26,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] sanity_check_paths = { - 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', + 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat']], - 'dirs': [] - } + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb index 051737c067..c22660d902 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb @@ -26,9 +26,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] sanity_check_paths = { - 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', + 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat']], - 'dirs': [] - } + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb index 6c6330c16b..38ffbd9b19 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb @@ -26,9 +26,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] sanity_check_paths = { - 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', + 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat']], - 'dirs': [] - } + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb index d47730c4ff..8e85417cc3 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb @@ -26,9 +26,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] sanity_check_paths = { - 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', + 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat']], - 'dirs': [] - } + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb index 21b9d17975..6959edee5c 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb @@ -4,7 +4,7 @@ version = '2013_update6' homepage = 'http://software.intel.com/en-us/intel-inspector-xe' description = "Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications" -toolchain = {'name':'dummy','version':'dummy'} +toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['inspector_xe_%s.tar.gz' % version] diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 277a6eef32..538671288f 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -20,13 +20,13 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = '-%s-%s' % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('SWIG', '2.0.4', versionsuffix), - ] + (python, pythonversion), + ('SWIG', '2.0.4', versionsuffix), +] sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/python%s/site-packages/instant' % pythonshortversion] - } + 'files': [], + 'dirs': ['bin', 'lib/python%s/site-packages/instant' % pythonshortversion] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 03e594c798..6966353326 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -19,13 +19,13 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = '-%s-%s' % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('SWIG', '2.0.4', versionsuffix), - ] + (python, pythonversion), + ('SWIG', '2.0.4', versionsuffix), +] sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/python%s/site-packages/instant' % pythonshortversion] - } + 'files': [], + 'dirs': ['bin', 'lib/python%s/site-packages/instant' % pythonshortversion] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-4.0.6-Python-2.7.3.eb index 564d83ba0f..9177b94846 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-4.0.6-Python-2.7.3.eb @@ -20,13 +20,13 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = '-%s-%s' % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('SWIG', '2.0.4', versionsuffix), - ] + (python, pythonversion), + ('SWIG', '2.0.4', versionsuffix), +] sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/python%s/site-packages/instant' % pythonshortversion] - } + 'files': [], + 'dirs': ['bin', 'lib/python%s/site-packages/instant' % pythonshortversion] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb index bc7d16b9ba..4e88df4047 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb @@ -21,13 +21,13 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = '-%s-%s' % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('SWIG', '2.0.4', versionsuffix), - ] + (python, pythonversion), + ('SWIG', '2.0.4', versionsuffix), +] sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/python%s/site-packages/instant' % pythonshortversion] - } + 'files': [], + 'dirs': ['bin', 'lib/python%s/site-packages/instant' % pythonshortversion] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb index 2bd2eaa620..974a5d000e 100644 --- a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb @@ -24,8 +24,8 @@ source_urls = [('http://sourceforge.net/projects/iperf/files', 'download')] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/iperf'], - 'dirs': [] - } + 'files': ['bin/iperf'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goolf-1.4.10.eb index c1d7b2439f..68b608ac4b 100644 --- a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goolf-1.4.10.eb @@ -23,8 +23,8 @@ source_urls = [('http://sourceforge.net/projects/iperf/files', 'download')] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['bin/iperf'], - 'dirs': [] - } + 'files': ['bin/iperf'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb index 27fbe32e7f..c6a180825f 100644 --- a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb @@ -24,8 +24,8 @@ source_urls = [('http://sourceforge.net/projects/iperf/files', 'download')] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/iperf'], - 'dirs': [] - } + 'files': ['bin/iperf'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-5.3.0.eb index a244a5f6bb..3bbd50af7c 100644 --- a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-5.3.0.eb @@ -25,8 +25,8 @@ source_urls = [('http://sourceforge.net/projects/iperf/files', 'download')] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/iperf'], - 'dirs': [] - } + 'files': ['bin/iperf'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb index f375c6b518..5850a5593b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb @@ -17,4 +17,3 @@ dontcreateinstalldir = 'True' # license file import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - diff --git a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb index edbddbc36d..6ae91f49df 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb @@ -21,4 +21,3 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") moduleclass = 'compiler' - diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb index aca2626f97..5d89d21731 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb @@ -21,4 +21,3 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") moduleclass = 'compiler' - diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.4.211.eb index 767174222a..8132cf523d 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.4.211.eb @@ -15,4 +15,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb index e3dcbcdd25..4e061aba7c 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb @@ -17,4 +17,3 @@ dontcreateinstalldir = 'True' # license file import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb index b4eb7cc8a8..73e504fad6 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -18,4 +18,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb index 7d57b6f4a5..5df1cad542 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -20,4 +20,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/iiqmpi/iiqmpi-3.3.0.eb b/easybuild/easyconfigs/i/iiqmpi/iiqmpi-3.3.0.eb index 3044633d52..fc4f68936d 100644 --- a/easybuild/easyconfigs/i/iiqmpi/iiqmpi-3.3.0.eb +++ b/easybuild/easyconfigs/i/iiqmpi/iiqmpi-3.3.0.eb @@ -17,9 +17,9 @@ dependencies = [ ] modextravars = { - 'MPICH_CC':'icc', - 'MPICH_F77':'ifort', - 'MPICH_F90':'ifort', + 'MPICH_CC': 'icc', + 'MPICH_F77': 'ifort', + 'MPICH_F90': 'ifort', } moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iiqmpi/iiqmpi-4.4.13.eb b/easybuild/easyconfigs/i/iiqmpi/iiqmpi-4.4.13.eb index 1091bb646e..df8e9f4731 100644 --- a/easybuild/easyconfigs/i/iiqmpi/iiqmpi-4.4.13.eb +++ b/easybuild/easyconfigs/i/iiqmpi/iiqmpi-4.4.13.eb @@ -17,9 +17,9 @@ dependencies = [ ] modextravars = { - 'MPICH_CC':'icc', - 'MPICH_F77':'ifort', - 'MPICH_F90':'ifort', + 'MPICH_CC': 'icc', + 'MPICH_F77': 'ifort', + 'MPICH_F90': 'ifort', } moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb index c7ad8e1fbd..11818df675 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb @@ -20,4 +20,3 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") moduleclass = 'numlib' - diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb index 58af733372..83e7ad590d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb @@ -19,4 +19,3 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic interfaces = True moduleclass = 'numlib' - diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb index 3b5d9dbf2b..f295b50925 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -16,7 +16,7 @@ checksums = ['47567e38801efe273b36b5250c759af7'] dontcreateinstalldir = 'True' -#license file +# license file import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb index ea1d887cb5..e40fb8448a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -16,7 +16,7 @@ checksums = ['b57ff502b5f97f2f783e4bbda7ce42b3'] dontcreateinstalldir = 'True' -#license file +# license file import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") @@ -34,5 +34,5 @@ postinstallcmds = [ ] modextravars = { - 'MKL_EXAMPLES' : '%(installdir)s/mkl/examples/', + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', } diff --git a/easybuild/easyconfigs/i/intel-para/intel-para-2014.12.eb b/easybuild/easyconfigs/i/intel-para/intel-para-2014.12.eb index 071bb1cdbb..d41e8ec250 100644 --- a/easybuild/easyconfigs/i/intel-para/intel-para-2014.12.eb +++ b/easybuild/easyconfigs/i/intel-para/intel-para-2014.12.eb @@ -25,4 +25,3 @@ dependencies = [ moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/intel/intel-2016.00.eb b/easybuild/easyconfigs/i/intel/intel-2016.00.eb index 0b62fdc0f4..241463337a 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.00.eb @@ -19,7 +19,7 @@ dependencies = [ ('icc', compver, gccsuff), ('ifort', compver, gccsuff), ('impi', '5.1.1.109', '', ('iccifort', '%s%s' % (compver, gccsuff))), - ('imkl', '11.3.0.109', '', ('iimpi', '%s%s' % (version,gccsuff))), + ('imkl', '11.3.0.109', '', ('iimpi', '%s%s' % (version, gccsuff))), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.01.eb b/easybuild/easyconfigs/i/intel/intel-2016.01.eb index 766d5b1fda..37f96fa014 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.01.eb @@ -19,7 +19,7 @@ dependencies = [ ('icc', compver, gccsuff), ('ifort', compver, gccsuff), ('impi', '5.1.2.150', '', ('iccifort', '%s%s' % (compver, gccsuff))), - ('imkl', '11.3.1.150', '', ('iimpi', '%s%s' % (version,gccsuff))), + ('imkl', '11.3.1.150', '', ('iimpi', '%s%s' % (version, gccsuff))), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2015b.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2015b.eb index 42ab6e143c..722616eb78 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2015b.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = """intltool is a set of tools to centralize translation of toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/i/iompi/iompi-2015.01.eb b/easybuild/easyconfigs/i/iompi/iompi-2015.01.eb index 6392c4027f..5bd039e031 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2015.01.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2015.01.eb @@ -17,4 +17,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb b/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb index 698ba1f804..726413e162 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb @@ -17,4 +17,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/iompi/iompi-2015.03.eb b/easybuild/easyconfigs/i/iompi/iompi-2015.03.eb index 539222425a..83b42beffd 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2015.03.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2015.03.eb @@ -17,4 +17,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/iompi/iompi-6.6.4-no-OFED.eb b/easybuild/easyconfigs/i/iompi/iompi-6.6.4-no-OFED.eb index 091224afc0..50058717bb 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-6.6.4-no-OFED.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-6.6.4-no-OFED.eb @@ -20,4 +20,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/iompi/iompi-6.6.4.eb b/easybuild/easyconfigs/i/iompi/iompi-6.6.4.eb index 8dccca825e..a2a368a96a 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-6.6.4.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-6.6.4.eb @@ -19,4 +19,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/ipsmpi/ipsmpi-2014.12.eb b/easybuild/easyconfigs/i/ipsmpi/ipsmpi-2014.12.eb index 4a33e11b3a..6aff711eb4 100644 --- a/easybuild/easyconfigs/i/ipsmpi/ipsmpi-2014.12.eb +++ b/easybuild/easyconfigs/i/ipsmpi/ipsmpi-2014.12.eb @@ -24,4 +24,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/iqacml/iqacml-3.7.3.eb b/easybuild/easyconfigs/i/iqacml/iqacml-3.7.3.eb index 09d75e1ad8..14df692f5c 100644 --- a/easybuild/easyconfigs/i/iqacml/iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/i/iqacml/iqacml-3.7.3.eb @@ -34,9 +34,9 @@ dependencies = [ ] modextravars = { - 'MPICH_CC':'icc', - 'MPICH_F77':'ifort', - 'MPICH_F90':'ifort', + 'MPICH_CC': 'icc', + 'MPICH_F77': 'ifort', + 'MPICH_F90': 'ifort', } moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iqacml/iqacml-4.4.13.eb b/easybuild/easyconfigs/i/iqacml/iqacml-4.4.13.eb index 3027178ee5..1c12d8bcc8 100644 --- a/easybuild/easyconfigs/i/iqacml/iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/i/iqacml/iqacml-4.4.13.eb @@ -6,7 +6,7 @@ version = '4.4.13' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, QLogic MPI and AMD Core Math Library (ACML).""" -toolchain = {'name':'dummy','version':'dummy'} +toolchain = {'name': 'dummy', 'version': 'dummy'} compv = '2011.13.367' @@ -19,7 +19,7 @@ tcname = 'iiqmpi' tcver = '4.4.13' tc = (tcname, tcver) -## deps for interface build +# deps for interface build dependencies = [ ('icc', compv), ('ifort', compv), @@ -31,8 +31,8 @@ dependencies = [ modextravars = { 'MPICH_CC': 'icc', - 'MPICH_F77':'ifort', - 'MPICH_F90':'ifort' + 'MPICH_F77': 'ifort', + 'MPICH_F90': 'ifort' } moduleclass = 'toolchain' -- GitLab From 382987c15e71679b606c4b6e1eadd58b3b162050 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:43:18 +0100 Subject: [PATCH 0272/2133] Style fixes with autopep8: l Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../l/LLVM/LLVM-3.6.2-intel-2015a-Python-2.7.9.eb | 4 ++-- .../easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb | 4 ++-- .../easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015b.eb | 4 ++-- .../easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb | 4 ++-- .../easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015b.eb | 4 ++-- .../easyconfigs/l/LLVM/LLVM-3.7.1-intel-2015b.eb | 4 ++-- .../l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb | 8 ++++---- easybuild/easyconfigs/l/LZO/LZO-2.06-goolf-1.4.10.eb | 8 ++++---- easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-4.0.6.eb | 8 ++++---- easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.1.1.eb | 8 ++++---- easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.3.0.eb | 8 ++++---- .../l/LibUUID/LibUUID-1.0.3-intel-2015a.eb | 4 ++-- .../l/LibUUID/LibUUID-1.0.3-intel-2015b.eb | 4 ++-- .../l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb | 2 +- .../l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb | 2 +- .../l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb | 2 +- .../easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb | 2 +- .../l/Libint/Libint-1.1.4-gmacml-1.7.0.eb | 2 +- .../l/Libint/Libint-1.1.4-goalf-1.1.0-no-OFED.eb | 2 +- .../l/Libint/Libint-1.1.4-goolf-1.4.10.eb | 2 +- .../l/Libint/Libint-1.1.4-ictce-3.2.2.u3.eb | 2 +- .../l/Libint/Libint-1.1.4-ictce-4.1.13.eb | 2 +- .../easyconfigs/l/Libint/Libint-1.1.4-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/Libint/Libint-1.1.4-ictce-5.5.0.eb | 2 +- .../easyconfigs/l/Libint/Libint-1.1.4-intel-2014b.eb | 2 +- .../easyconfigs/l/Libint/Libint-1.1.4-intel-2015a.eb | 2 +- .../easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.eb | 2 +- .../l/Libint/Libint-1.1.4-intel-para-2014.12.eb | 2 +- .../l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb | 12 ++++++------ .../easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb | 12 ++++++------ .../libGLU/libGLU-9.0.0-intel-2015a-Python-2.7.10.eb | 4 ++-- .../l/libGLU/libGLU-9.0.0-intel-2015b-Mesa-11.0.8.eb | 4 ++-- .../easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015b.eb | 4 ++-- .../l/libICE/libICE-1.0.8-goolf-1.4.10.eb | 4 ++-- .../l/libICE/libICE-1.0.8-goolf-1.5.14.eb | 4 ++-- .../l/libICE/libICE-1.0.8-ictce-4.1.13.eb | 4 ++-- .../easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb | 4 ++-- .../easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb | 4 ++-- .../easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb | 4 ++-- .../easyconfigs/l/libSM/libSM-1.2.1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/l/libSM/libSM-1.2.1-goolf-1.5.14.eb | 4 ++-- .../easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb | 4 ++-- .../easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb | 4 ++-- .../easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb | 4 ++-- .../easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb | 4 ++-- .../l/libX11/libX11-1.6.1-goolf-1.4.10.eb | 6 +++--- .../l/libX11/libX11-1.6.1-goolf-1.5.14.eb | 6 +++--- .../l/libX11/libX11-1.6.1-ictce-4.1.13.eb | 6 +++--- .../easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb | 6 +++--- .../easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb | 6 +++--- .../l/libX11/libX11-1.6.2-foss-2014b-Python-2.7.8.eb | 6 +++--- .../libX11/libX11-1.6.2-intel-2014b-Python-2.7.8.eb | 6 +++--- .../libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb | 6 +++--- .../libX11/libX11-1.6.3-goolf-1.5.14-Python-2.7.9.eb | 6 +++--- .../libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb | 6 +++--- .../libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb | 6 +++--- .../libX11/libX11-1.6.3-intel-2015b-Python-2.7.10.eb | 6 +++--- .../libX11/libX11-1.6.3-intel-2015b-Python-2.7.11.eb | 6 +++--- .../libXext/libXext-1.3.2-foss-2014b-Python-2.7.8.eb | 8 ++++---- .../l/libXext/libXext-1.3.2-goolf-1.4.10.eb | 8 ++++---- .../l/libXext/libXext-1.3.2-ictce-4.1.13.eb | 8 ++++---- .../l/libXext/libXext-1.3.2-ictce-5.3.0.eb | 8 ++++---- .../libXext-1.3.2-intel-2014b-Python-2.7.8.eb | 8 ++++---- .../l/libXext/libXext-1.3.2-intel-2014b.eb | 8 ++++---- .../l/libXext/libXext-1.3.3-goolf-1.5.14.eb | 6 +++--- .../libXext-1.3.3-intel-2015a-Python-2.7.10.eb | 6 +++--- .../l/libXext/libXext-1.3.3-intel-2015a.eb | 6 +++--- .../libXext-1.3.3-intel-2015b-Python-2.7.11.eb | 6 +++--- .../l/libXext/libXext-1.3.3-intel-2015b.eb | 6 +++--- .../l/libXfixes/libXfixes-5.0.1-goolf-1.4.10.eb | 4 ++-- .../l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb | 4 ++-- .../l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb | 4 ++-- .../l/libXfixes/libXfixes-5.0.1-intel-2015a.eb | 4 ++-- .../l/libXfixes/libXfixes-5.0.1-intel-2015b.eb | 4 ++-- .../easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb | 4 ++-- .../easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb | 4 ++-- .../l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb | 4 ++-- .../easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb | 4 ++-- .../l/libXinerama/libXinerama-1.1.3-foss-2014b.eb | 4 ++-- .../l/libXinerama/libXinerama-1.1.3-intel-2014b.eb | 4 ++-- .../libXinerama-1.1.3-intel-2015b-Python-2.7.11.eb | 2 +- .../l/libXinerama/libXinerama-1.1.3-intel-2015b.eb | 2 +- .../l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb | 4 ++-- .../l/libXmu/libXmu-1.1.2-goolf-1.5.14.eb | 4 ++-- .../easyconfigs/l/libXp/libXp-1.0.2-goolf-1.4.10.eb | 10 +++++----- .../easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb | 10 +++++----- .../easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb | 10 +++++----- .../easyconfigs/l/libXp/libXp-1.0.3-goolf-1.5.14.eb | 10 +++++----- .../easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb | 10 +++++----- .../easyconfigs/l/libXt/libXt-1.1.4-goolf-1.4.10.eb | 6 +++--- .../easyconfigs/l/libXt/libXt-1.1.4-goolf-1.5.14.eb | 6 +++--- .../easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb | 6 +++--- .../easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb | 6 +++--- .../easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb | 6 +++--- .../l/libXt/libXt-1.1.4-intel-2015a-Python-2.7.10.eb | 6 +++--- .../l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb | 6 +++--- .../l/libXt/libXt-1.1.5-intel-2015b-Python-2.7.11.eb | 6 +++--- .../easyconfigs/l/libXt/libXt-1.1.5-intel-2015b.eb | 6 +++--- .../libdap-3.14.0-intel-2015a-Python-2.7.10.eb | 4 ++-- .../libdap-3.14.0-intel-2015b-Python-2.7.10.eb | 4 ++-- .../l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb | 6 +++--- .../l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb | 6 +++--- .../l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb | 6 +++--- .../l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb | 6 +++--- .../l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb | 6 +++--- .../l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb | 6 +++--- .../l/libdrm/libdrm-2.4.59-intel-2015a.eb | 6 +++--- .../l/libdrm/libdrm-2.4.64-intel-2015b.eb | 6 +++--- .../l/libdrm/libdrm-2.4.66-intel-2015b.eb | 6 +++--- .../l/libpng/libpng-1.6.21-intel-2016a.eb | 2 +- .../libpthread-stubs-0.3-foss-2014b.eb | 6 +++--- .../libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb | 8 ++++---- .../libpthread-stubs-0.3-goolf-1.4.10.eb | 8 ++++---- .../libpthread-stubs-0.3-ictce-4.0.6.eb | 8 ++++---- .../libpthread-stubs-0.3-ictce-4.1.13.eb | 6 +++--- .../libpthread-stubs-0.3-ictce-5.3.0.eb | 8 ++++---- .../libpthread-stubs-0.3-ictce-5.5.0.eb | 6 +++--- .../libpthread-stubs-0.3-intel-2014b.eb | 6 +++--- .../libpthread-stubs-0.3-intel-2015a.eb | 6 +++--- .../libpthread-stubs-0.3-intel-2015b.eb | 6 +++--- .../l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb | 8 ++++---- .../libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb | 8 ++++---- .../libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb | 8 ++++---- .../libreadline-6.2-goalf-1.1.0-no-OFED.eb | 8 ++++---- .../libreadline-6.2-goalf-1.5.12-no-OFED.eb | 8 ++++---- .../libreadline-6.2-gompi-1.4.12-no-OFED.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-goolf-1.4.10.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-goolf-1.5.14.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-ictce-4.0.10.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-ictce-4.0.6.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-ictce-4.1.13.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-ictce-5.2.0.eb | 10 +++++----- .../l/libreadline/libreadline-6.2-ictce-5.3.0.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-ictce-5.5.0.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-intel-2015a.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-iomkl-4.6.13.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-iqacml-3.7.3.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-iqacml-4.4.13.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-GCC-4.8.2.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-GCC-4.9.2.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb | 2 +- .../l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-foss-2014b.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-foss-2015.05.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-foss-2015a.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-foss-2015b.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-foss-2016a.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-gimkl-2.11.5.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-gompi-1.5.16.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-goolf-1.4.10.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-goolf-1.5.14.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-goolf-1.7.20.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-ictce-6.2.5.eb | 2 +- .../l/libreadline/libreadline-6.3-ictce-6.3.5.eb | 2 +- .../l/libreadline/libreadline-6.3-ictce-7.1.2.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-ictce-7.3.5.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-intel-2014.06.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-intel-2014b.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-intel-2015a.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-intel-2015b.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-intel-2016a.eb | 8 ++++---- .../l/libtool/libtool-2.4.2-ictce-4.0.6.eb | 2 +- .../l/libtool/libtool-2.4.2-ictce-4.1.13.eb | 2 +- .../libunistring-0.9.3-GNU-4.9.3-2.25.eb | 8 ++++---- .../libunistring-0.9.3-goalf-1.1.0-no-OFED.eb | 8 ++++---- .../libunistring/libunistring-0.9.3-goolf-1.4.10.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-intel-2015a.eb | 8 ++++---- .../easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb | 1 - .../easyconfigs/l/libxc/libxc-2.0.1-ictce-4.1.13.eb | 1 - .../easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb | 1 - .../easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb | 1 - .../easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb | 1 - .../l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb | 10 +++++----- .../l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb | 10 +++++----- .../libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb | 10 +++++----- .../libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb | 10 +++++----- .../l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb | 10 +++++----- .../libxcb-1.11.1-intel-2015b-Python-2.7.10.eb | 10 +++++----- .../libxcb-1.11.1-intel-2015b-Python-2.7.11.eb | 10 +++++----- .../libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 10 +++++----- .../l/libxcb/libxcb-1.8-goolf-1.4.10-Python-2.7.3.eb | 10 +++++----- .../l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.3.eb | 10 +++++----- .../l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb | 10 +++++----- .../l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb | 10 +++++----- .../l/libxcb/libxcb-1.8-ictce-5.3.0-Python-2.7.3.eb | 10 +++++----- .../l/libxcb/libxcb-1.8-intel-2014b-Python-2.7.8.eb | 10 +++++----- .../libxkbcommon-0.5.0-intel-2015b-Python-2.7.11.eb | 2 +- .../l/libxkbcommon/libxkbcommon-0.5.0-intel-2015b.eb | 2 +- .../likwid-3.0.0-goalf-1.1.0-no-OFED-pinomp.eb | 4 ++-- .../l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED.eb | 2 +- .../l/likwid/likwid-3.0.0-goolf-1.4.10-pinomp.eb | 4 ++-- .../l/likwid/likwid-3.0.0-goolf-1.4.10.eb | 2 +- .../l/likwid/likwid-3.0.0-ictce-4.1.13-pinomp.eb | 2 +- .../l/likwid/likwid-3.0.0-ictce-4.1.13.eb | 2 +- .../l/likwid/likwid-3.0.0-ictce-5.3.0-pinomp.eb | 2 +- .../easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0.eb | 2 +- 209 files changed, 617 insertions(+), 622 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a-Python-2.7.9.eb index dcb8e49ef1..3c0e36d72c 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a-Python-2.7.9.eb @@ -29,8 +29,8 @@ builddependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' sanity_check_paths = { - 'files' : ['bin/llvm-ar'], - 'dirs' : ['include/llvm', 'include/llvm-c'], + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], } separate_build_dir = True diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb index 0e2be216c9..bb160486fd 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb @@ -26,8 +26,8 @@ builddependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' sanity_check_paths = { - 'files' : ['bin/llvm-ar'], - 'dirs' : ['include/llvm', 'include/llvm-c'], + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], } separate_build_dir = True diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015b.eb index ae23f4c83c..435d7783c6 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015b.eb @@ -26,8 +26,8 @@ builddependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' sanity_check_paths = { - 'files' : ['bin/llvm-ar'], - 'dirs' : ['include/llvm', 'include/llvm-c'], + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], } separate_build_dir = True diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb index 622b77ee48..88dcd90478 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb @@ -26,8 +26,8 @@ builddependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' sanity_check_paths = { - 'files' : ['bin/llvm-ar'], - 'dirs' : ['include/llvm', 'include/llvm-c'], + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], } separate_build_dir = True diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015b.eb index b7b0fd0d07..28f4906cec 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015b.eb @@ -26,8 +26,8 @@ builddependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' sanity_check_paths = { - 'files' : ['bin/llvm-ar'], - 'dirs' : ['include/llvm', 'include/llvm-c'], + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], } separate_build_dir = True diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2015b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2015b.eb index e0f3bf3a62..4bf8e3225f 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2015b.eb @@ -26,8 +26,8 @@ builddependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' sanity_check_paths = { - 'files' : ['bin/llvm-ar'], - 'dirs' : ['include/llvm', 'include/llvm-c'], + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], } separate_build_dir = True diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb index 01b0d95ad8..94a0908fdc 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb @@ -21,11 +21,11 @@ source_urls = [homepage + 'download/'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib', 'include'] - } + 'files': [], + 'dirs': ['lib', 'include'] +} -runtest= 'test' +runtest = 'test' parallel = 1 # this is a very conservative choice diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.06-goolf-1.4.10.eb b/easybuild/easyconfigs/l/LZO/LZO-2.06-goolf-1.4.10.eb index 4244d4fadb..82b1a9bd7b 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.06-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.06-goolf-1.4.10.eb @@ -21,11 +21,11 @@ source_urls = [homepage + 'download/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib', 'include'] - } + 'files': [], + 'dirs': ['lib', 'include'] +} -runtest= 'test' +runtest = 'test' parallel = 1 # this is a very conservative choice diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-4.0.6.eb b/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-4.0.6.eb index 115d1188ad..3dc6b8939e 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-4.0.6.eb @@ -21,11 +21,11 @@ source_urls = [homepage + 'download/'] toolchain = {'name': 'ictce', 'version': '4.0.6'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib', 'include'] - } + 'files': [], + 'dirs': ['lib', 'include'] +} -runtest= 'test' +runtest = 'test' parallel = 1 # this is a very conservative choice diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.1.1.eb b/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.1.1.eb index 266ce97e25..91bc730999 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.1.1.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.1.1.eb @@ -21,11 +21,11 @@ source_urls = [homepage + 'download/'] toolchain = {'name': 'ictce', 'version': '5.1.1'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib', 'include'] - } + 'files': [], + 'dirs': ['lib', 'include'] +} -runtest= 'test' +runtest = 'test' parallel = 1 # this is a very conservative choice diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.3.0.eb index d1e8d56383..5b7a6a1f5c 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.3.0.eb @@ -21,11 +21,11 @@ source_urls = [homepage + 'download/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib', 'include'] - } + 'files': [], + 'dirs': ['lib', 'include'] +} -runtest= 'test' +runtest = 'test' parallel = 1 # this is a very conservative choice diff --git a/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2015a.eb index 579d4bd995..4d767e1cf3 100644 --- a/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2015a.eb @@ -8,11 +8,11 @@ description = """Portable uuid C library""" toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = [SOURCEFORGE_SOURCE] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files' : ['include/uuid/uuid.h', 'lib/libuuid.a','lib/libuuid.%s' % SHLIB_EXT], + 'files': ['include/uuid/uuid.h', 'lib/libuuid.a', 'lib/libuuid.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2015b.eb b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2015b.eb index 052b80a1b3..d231b0ce29 100644 --- a/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2015b.eb @@ -8,11 +8,11 @@ description = """Portable uuid C library""" toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = [SOURCEFORGE_SOURCE] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files' : ['include/uuid/uuid.h', 'lib/libuuid.a','lib/libuuid.%s' % SHLIB_EXT], + 'files': ['include/uuid/uuid.h', 'lib/libuuid.a', 'lib/libuuid.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb index 7d4d9128c9..bb2161814b 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb index e7bca79f1d..0457658fa7 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb index 4f2df44352..1eb630e450 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb index ba9b735bea..8892a51e3b 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-gmacml-1.7.0.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-gmacml-1.7.0.eb index 2c0f30db6f..d9c94abb26 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-gmacml-1.7.0.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-gmacml-1.7.0.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-goalf-1.1.0-no-OFED.eb index 03c9b2dc7a..c04b9aefa2 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-goolf-1.4.10.eb index 730a15d185..2a492f12bc 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-goolf-1.4.10.eb @@ -17,7 +17,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-3.2.2.u3.eb index f3c3b23d4a..43b19b6334 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-3.2.2.u3.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb index 4e57ea2500..148e3670c0 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-5.3.0.eb index 785e595968..df06fc7ec9 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-5.3.0.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-5.5.0.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-5.5.0.eb index 401ec7cb9e..edcbb88f18 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-5.5.0.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2014b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2014b.eb index e84c9a7220..e0416eeeb5 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2014b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2014b.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015a.eb index 2cf26e1b10..eff3b17ce6 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015a.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.eb index 1e71a38b55..0728b4341f 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb index 131e4988f1..44424f9578 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb @@ -17,7 +17,7 @@ sanity_check_paths = { 'files': ["include/lib%(x)s/lib%(x)s.h" % {'x': x} for x in ["deriv", "int", "r12"]] + ["include/libint/hrr_header.h", "include/libint/vrr_header.h"] + ["lib/lib%s.a" % x for x in ["deriv", "int", "r12"]], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb index 36b7df3cbb..143cec9144 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb @@ -26,15 +26,15 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} # fi. http://ftp.yar.ru/pub/source/lftp/lftp-4.4.1.tar.bz2 sources = [SOURCE_TAR_BZ2] source_urls = [ - 'http://ftp.yar.ru/pub/source/lftp/', - 'http://ftp.yar.ru/pub/source/lftp/old/', - ] + 'http://ftp.yar.ru/pub/source/lftp/', + 'http://ftp.yar.ru/pub/source/lftp/old/', +] dependencies = [('gnutls', '3.1.8')] sanity_check_paths = { - 'files': ['bin/lftp'], - 'dirs': [] - } + 'files': ['bin/lftp'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb index 9d1f79e19b..e96735ec2c 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb @@ -25,15 +25,15 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} # fi. http://ftp.yar.ru/pub/source/lftp/lftp-4.4.1.tar.bz2 sources = [SOURCE_TAR_BZ2] source_urls = [ - 'http://ftp.yar.ru/pub/source/lftp/', - 'http://ftp.yar.ru/pub/source/lftp/old/', - ] + 'http://ftp.yar.ru/pub/source/lftp/', + 'http://ftp.yar.ru/pub/source/lftp/old/', +] dependencies = [('gnutls', '3.1.8')] sanity_check_paths = { - 'files': ['bin/lftp'], - 'dirs': [] - } + 'files': ['bin/lftp'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015a-Python-2.7.10.eb index 8b9006f86d..c4c01e4178 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015a-Python-2.7.10.eb @@ -18,8 +18,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['lib/libGLU.so.1'], - 'dirs' : [], + 'files': ['lib/libGLU.so.1'], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015b-Mesa-11.0.8.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015b-Mesa-11.0.8.eb index 2d27e3100e..1d535efa3e 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015b-Mesa-11.0.8.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015b-Mesa-11.0.8.eb @@ -20,8 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['lib/libGLU.so.1'], - 'dirs' : [], + 'files': ['lib/libGLU.so.1'], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015b.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015b.eb index c0145295eb..bc9de7e0c8 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2015b.eb @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['lib/libGLU.so.1'], - 'dirs' : [], + 'files': ['lib/libGLU.so.1'], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.4.10.eb index e1317b6a06..42c22fbb11 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.4.10.eb @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], - 'dirs' : [], + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.5.14.eb index fad83246f3..45efaa2f59 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.5.14.eb @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], - 'dirs' : [], + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb index a224ca2f47..cbf26ccb0e 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], - 'dirs' : [], + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb index 84dfd42c65..c6c611bb2b 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], - 'dirs' : [], + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb index 3280a4d8e4..bb3839e6a6 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb @@ -21,8 +21,8 @@ builddependencies = [ sanity_check_paths = { - 'files' : ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], - 'dirs' : [], + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb index c7f664c8c8..0fb685525a 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb @@ -20,8 +20,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], - 'dirs' : [], + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb index 87ccf251e1..d28d3a6e76 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb @@ -20,8 +20,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], - 'dirs' : [], + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.4.10.eb index aa6111e5a0..69237fa741 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.4.10.eb @@ -21,8 +21,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], - 'dirs' : [], + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.5.14.eb index c115e440d5..e7ecc39a17 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.5.14.eb @@ -21,8 +21,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], - 'dirs' : [], + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb index 14074eae88..de61279284 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb @@ -21,8 +21,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], - 'dirs' : [], + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb index ee47bc867f..b2524399f7 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb @@ -21,8 +21,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], - 'dirs' : [], + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb index 8182108112..a15bba69ef 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb @@ -21,8 +21,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], - 'dirs' : [], + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb index 7d8fcfe61a..2a2391d847 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb @@ -21,8 +21,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], - 'dirs' : [], + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb index 3cd80afcd1..641ea44476 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb @@ -21,8 +21,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], - 'dirs' : [], + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.4.10.eb index 520bd74e88..90e0e2d976 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.4.10.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb index aee383b326..b7f55fcda1 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb index 693be4e809..89a1e29d9b 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb index 0e6ea38eed..fddb03dd7f 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb index 893f0011c6..3522b7de99 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-foss-2014b-Python-2.7.8.eb index 2f11de3348..01231ac640 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-foss-2014b-Python-2.7.8.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2014b-Python-2.7.8.eb index 6dc47a39ef..0932594590 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2014b-Python-2.7.8.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb index ee582416a0..ef095b7705 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-goolf-1.5.14-Python-2.7.9.eb index 7e6d887343..9826dc599d 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-goolf-1.5.14-Python-2.7.9.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb index a4a7437300..f3cc16617c 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb index fa0d2300e6..f4b3c5923c 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.10.eb index 90a1e61002..57e06f392a 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.10.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.11.eb index ce11a9ade3..3280e3a1e6 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015b-Python-2.7.11.eb @@ -27,9 +27,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-foss-2014b-Python-2.7.8.eb index 2ed55c95cd..4ef33fe479 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-foss-2014b-Python-2.7.8.eb @@ -17,16 +17,16 @@ builddependencies = [ ('kbproto', '1.0.6'), ] dependencies = [ - ('xproto','7.0.26'), + ('xproto', '7.0.26'), ('libX11', '1.6.2', versionsuffix), ('xextproto', '7.3.0'), ] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.4.10.eb index 4a8d61c266..2584eff6b6 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.4.10.eb @@ -13,16 +13,16 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] dependencies = [ - ('xproto','7.0.23'), + ('xproto', '7.0.23'), ('libX11', '1.6.1'), ('xextproto', '7.2.1'), ] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb index 638857be64..b016a23bf8 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb @@ -13,16 +13,16 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] dependencies = [ - ('xproto','7.0.23'), + ('xproto', '7.0.23'), ('libX11', '1.6.1'), ('xextproto', '7.2.1'), ] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb index c45e32b915..e25402f03d 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb @@ -13,16 +13,16 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] dependencies = [ - ('xproto','7.0.23'), + ('xproto', '7.0.23'), ('libX11', '1.6.1'), ('xextproto', '7.2.1'), ] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b-Python-2.7.8.eb index 4dd886a4bf..70f0ca40ea 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b-Python-2.7.8.eb @@ -15,7 +15,7 @@ source_urls = [XORG_LIB_SOURCE] versionsuffix = '-Python-2.7.8' builddependencies = [ ('kbproto', '1.0.6'), - ('xproto','7.0.26'), + ('xproto', '7.0.26'), ('xextproto', '7.3.0'), ] dependencies = [ @@ -24,9 +24,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb index 8ff72de9ba..1eeae06c66 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb @@ -18,15 +18,15 @@ dependencies = [ ] builddependencies = [ - ('xproto','7.0.26'), + ('xproto', '7.0.26'), ('xextproto', '7.2.1'), ] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb index 63124eca9a..f5d31320dd 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb @@ -24,9 +24,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb index a959a12b0a..fea0b330b9 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb @@ -25,9 +25,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb index 7499144fec..c076690abe 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb @@ -24,9 +24,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb index d0916f41c9..23544e2ee3 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb @@ -25,9 +25,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb index 3b75bb1efa..93ffb79a95 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb @@ -24,9 +24,9 @@ dependencies = [ sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', - 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', - ] + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] ], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-goolf-1.4.10.eb index 501a07d2d9..aa1121d881 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-goolf-1.4.10.eb @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], - 'dirs' : [], + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb index b97a4a2793..67b2754c02 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], - 'dirs' : [], + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb index a90ec28a7d..e22050059e 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], - 'dirs' : [], + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb index 51127a8194..fd77718af8 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], - 'dirs' : [], + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015b.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015b.eb index 84e087e7bc..35d7f6f284 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015b.eb @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], - 'dirs' : [], + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb index 5f423967c0..8b0e336093 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb @@ -20,8 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], - 'dirs' : [], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb index 4b0cae6a95..dc21c6f8e9 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb @@ -20,8 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], - 'dirs' : [], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb index ebca121b10..0f71868663 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb @@ -20,8 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], - 'dirs' : [], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb index 0ed8458cff..6943d3e084 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -19,8 +19,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], - 'dirs' : [], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb index 1eaec43d4e..eaa232fe89 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb @@ -20,8 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.so', 'lib/libXi.a'], - 'dirs' : [], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.so', 'lib/libXi.a'], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb index 418bfdfe23..0ed8e42a20 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb @@ -19,8 +19,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], - 'dirs' : [], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2014b.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2014b.eb index aa81cc7f3c..0364d9613f 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2014b.eb @@ -18,8 +18,8 @@ builddependencies = [ ('xextproto', '7.3.0'), ] dependencies = [ - ('xproto','7.0.26'), - ('libX11', '1.6.2', pythonversion ), + ('xproto', '7.0.26'), + ('libX11', '1.6.2', pythonversion), ('libXext', '1.3.2', pythonversion), ] diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2014b.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2014b.eb index bb8afc5c0c..5df23592a5 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2014b.eb @@ -18,8 +18,8 @@ builddependencies = [ ('xextproto', '7.3.0'), ] dependencies = [ - ('xproto','7.0.26'), - ('libX11', '1.6.2', pythonversion ), + ('xproto', '7.0.26'), + ('libX11', '1.6.2', pythonversion), ('libXext', '1.3.2', pythonversion), ] diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2015b-Python-2.7.11.eb index df35769e55..0dc7137ea0 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2015b-Python-2.7.11.eb @@ -19,7 +19,7 @@ builddependencies = [ ] dependencies = [ - ('xproto','7.0.28'), + ('xproto', '7.0.28'), ('libX11', '1.6.3', versionsuffix), ('libXext', '1.3.3', versionsuffix), ] diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2015b.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2015b.eb index c836ab425a..0325a41bd3 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2015b.eb @@ -18,7 +18,7 @@ builddependencies = [ ] dependencies = [ - ('xproto','7.0.28'), + ('xproto', '7.0.28'), ('libX11', '1.6.3', '-Python-2.7.10'), ('libXext', '1.3.3'), ] diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb index 8db3290cf3..5db2a158ca 100644 --- a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb @@ -19,8 +19,8 @@ dependencies = [ ] sanity_check_paths = { 'files': ['lib/%s' % x for x in [ - '%(name)s.a', '%(name)s.so', - ] + '%(name)s.a', '%(name)s.so', + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.5.14.eb index 2c502db1e9..d781bd04fe 100644 --- a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.5.14.eb @@ -19,8 +19,8 @@ dependencies = [ ] sanity_check_paths = { 'files': ['lib/%s' % x for x in [ - '%(name)s.a', '%(name)s.so', - ] + '%(name)s.a', '%(name)s.so', + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.4.10.eb index 7e4d47cef9..cd4cbda0f2 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.4.10.eb @@ -13,14 +13,14 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ - ('xextproto', '7.2.1'), - ('printproto', '1.0.5'), + ('xextproto', '7.2.1'), + ('printproto', '1.0.5'), ] dependencies = [ - ('libX11', '1.6.1'), - ('libXext', '1.3.2'), - ('libXau', '1.0.8'), + ('libX11', '1.6.1'), + ('libXext', '1.3.2'), + ('libXau', '1.0.8'), ] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['libXp.a', 'libXp.%s' % SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb index f3cb59abe1..fcb4c60df7 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb @@ -13,14 +13,14 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ - ('xextproto', '7.2.1'), - ('printproto', '1.0.5'), + ('xextproto', '7.2.1'), + ('printproto', '1.0.5'), ] dependencies = [ - ('libX11', '1.6.1'), - ('libXext', '1.3.2'), - ('libXau', '1.0.8'), + ('libX11', '1.6.1'), + ('libXext', '1.3.2'), + ('libXau', '1.0.8'), ] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['libXp.a', 'libXp.%s' % SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb index 5a95f178ee..88ac2990ec 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb @@ -13,14 +13,14 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ - ('xextproto', '7.2.1'), - ('printproto', '1.0.5'), + ('xextproto', '7.2.1'), + ('printproto', '1.0.5'), ] dependencies = [ - ('libX11', '1.6.1'), - ('libXext', '1.3.2'), - ('libXau', '1.0.8'), + ('libX11', '1.6.1'), + ('libXext', '1.3.2'), + ('libXau', '1.0.8'), ] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['libXp.a', 'libXp.%s' % SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-goolf-1.5.14.eb index 04dbfd1701..e680164e0b 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-goolf-1.5.14.eb @@ -13,14 +13,14 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ - ('xextproto', '7.3.0'), - ('printproto', '1.0.5'), + ('xextproto', '7.3.0'), + ('printproto', '1.0.5'), ] dependencies = [ - ('libX11', '1.6.3', '-Python-2.7.9'), - ('libXext', '1.3.3'), - ('libXau', '1.0.8'), + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), ] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['libXp.a', 'libXp.%s' % SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb index c09d0e3c06..da13ac755a 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb @@ -13,14 +13,14 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ - ('xextproto', '7.3.0'), - ('printproto', '1.0.5'), + ('xextproto', '7.3.0'), + ('printproto', '1.0.5'), ] dependencies = [ - ('libX11', '1.6.3', '-Python-2.7.9'), - ('libXext', '1.3.3'), - ('libXau', '1.0.8'), + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.4.10.eb index 0a3d6df938..a620b54e13 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.4.10.eb @@ -22,15 +22,15 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in [ + 'files': ['include/X11/%s' % x for x in [ 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', - ] + ] ], - 'dirs' : [], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.5.14.eb index d22341b9fc..a04d966743 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.5.14.eb @@ -22,15 +22,15 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in [ + 'files': ['include/X11/%s' % x for x in [ 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', - ] + ] ], - 'dirs' : [], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb index 0419ecbed2..6224c7a3e2 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb @@ -22,15 +22,15 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in [ + 'files': ['include/X11/%s' % x for x in [ 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', - ] + ] ], - 'dirs' : [], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb index 978dd4006b..6fbde3ec7e 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb @@ -22,15 +22,15 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in [ + 'files': ['include/X11/%s' % x for x in [ 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', - ] + ] ], - 'dirs' : [], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb index f903c01872..6f79135801 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb @@ -25,15 +25,15 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in [ + 'files': ['include/X11/%s' % x for x in [ 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', - ] + ] ], - 'dirs' : [], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-Python-2.7.10.eb index 85062e12a3..ba1f626efb 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-Python-2.7.10.eb @@ -26,15 +26,15 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in [ + 'files': ['include/X11/%s' % x for x in [ 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', - ] + ] ], - 'dirs' : [], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb index 507c378340..60c2f35304 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb @@ -27,15 +27,15 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in [ + 'files': ['include/X11/%s' % x for x in [ 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', - ] + ] ], - 'dirs' : [], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2015b-Python-2.7.11.eb index a4877fe346..347a5460d3 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2015b-Python-2.7.11.eb @@ -26,15 +26,15 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in [ + 'files': ['include/X11/%s' % x for x in [ 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', - ] + ] ], - 'dirs' : [], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2015b.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2015b.eb index 9454e5904b..c0989734a0 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2015b.eb @@ -25,15 +25,15 @@ builddependencies = [ ] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in [ + 'files': ['include/X11/%s' % x for x in [ 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', - ] + ] ], - 'dirs' : [], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015a-Python-2.7.10.eb index 63172f59f4..05588e3a1b 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015a-Python-2.7.10.eb @@ -11,7 +11,7 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://www.opendap.org/pub/source/'] +source_urls = ['http://www.opendap.org/pub/source/'] sources = [SOURCE_TAR_GZ] patches = ['%(name)s-%(version)s_flex.patch'] @@ -28,7 +28,7 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015b-Python-2.7.10.eb index f70b2b33c4..7cb1004504 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.14.0-intel-2015b-Python-2.7.10.eb @@ -11,7 +11,7 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://www.opendap.org/pub/source/'] +source_urls = ['http://www.opendap.org/pub/source/'] sources = [SOURCE_TAR_GZ] patches = ['%(name)s-%(version)s_flex.patch'] @@ -28,7 +28,7 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb index dbc45bd35c..35962e9634 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb @@ -8,7 +8,7 @@ description = """Direct Rendering Manager runtime library.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://dri.freedesktop.org/libdrm/'] +source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, - 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb index 69b418577f..81433d6c74 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb @@ -8,7 +8,7 @@ description = """Direct Rendering Manager runtime library.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://dri.freedesktop.org/libdrm/'] +source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, - 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb index 390148b693..928624815a 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb @@ -8,7 +8,7 @@ description = """Direct Rendering Manager runtime library.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://dri.freedesktop.org/libdrm/'] +source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, - 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb index 0b86566ae8..726eea719e 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """Direct Rendering Manager runtime library.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://dri.freedesktop.org/libdrm/'] +source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, - 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb index 96c26fee1c..b3743448e4 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = """Direct Rendering Manager runtime library.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://dri.freedesktop.org/libdrm/'] +source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, - 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb index aaa4f55198..1d6950b4e9 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb @@ -8,7 +8,7 @@ description = """Direct Rendering Manager runtime library.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://dri.freedesktop.org/libdrm/'] +source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, - 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb index bf98667278..a9bc97da28 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb @@ -6,7 +6,7 @@ version = '2.4.59' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" -source_urls = ['http://dri.freedesktop.org/libdrm/'] +source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, - 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.64-intel-2015b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.64-intel-2015b.eb index 40c401fcce..699155c11d 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.64-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.64-intel-2015b.eb @@ -6,7 +6,7 @@ version = '2.4.64' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" -source_urls = ['http://dri.freedesktop.org/libdrm/'] +source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015b'} @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, - 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.66-intel-2015b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.66-intel-2015b.eb index 8d5e86157a..c3b9d88a24 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.66-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.66-intel-2015b.eb @@ -6,7 +6,7 @@ version = '2.4.66' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" -source_urls = ['http://dri.freedesktop.org/libdrm/'] +source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015b'} @@ -17,8 +17,8 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2016a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2016a.eb index 7ea89634eb..db360bc83f 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2016a.eb @@ -19,7 +19,7 @@ configopts = "--with-pic" majminver = ''.join(version.split('.')[:2]) sanity_check_paths = { 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', - 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' %(majminver, SHLIB_EXT)], + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], } diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2014b.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2014b.eb index 9e928c536d..a10468dde6 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2014b.eb @@ -7,14 +7,14 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'foss', 'version': '2014b'} sanity_check_paths = { - 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] , + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb index 9739f76ef1..511ed358b0 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb @@ -7,14 +7,14 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] - } + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [] +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goolf-1.4.10.eb index 1a74d61a74..211abf16ff 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goolf-1.4.10.eb @@ -7,13 +7,13 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] - } + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [] +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb index f71c39521b..1ab3a5ccf4 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb @@ -7,14 +7,14 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '4.0.6'} sanity_check_paths = { - 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] - } + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [] +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.1.13.eb index f73ab22a6e..8d7fb1e79f 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.1.13.eb @@ -7,14 +7,14 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '4.1.13'} sanity_check_paths = { - 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] , + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.3.0.eb index 8789568941..ea261c17d2 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.3.0.eb @@ -7,15 +7,15 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] - } + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [] +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.5.0.eb index 718b266c0a..ef62013559 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-5.5.0.eb @@ -7,14 +7,14 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.5.0'} sanity_check_paths = { - 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] , + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2014b.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2014b.eb index 46dee523f9..6b19a1bcd1 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2014b.eb @@ -7,14 +7,14 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} sanity_check_paths = { - 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] , + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015a.eb index 3665102104..fca6a08168 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015a.eb @@ -7,14 +7,14 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} sanity_check_paths = { - 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] , + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015b.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015b.eb index aec5e572ed..b147185e9d 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015b.eb @@ -7,14 +7,14 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015b'} sanity_check_paths = { - 'files' : ['lib/pkgconfig/pthread-stubs.pc'], - 'dirs': [] , + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb index f9b6b2a61b..4dd7cf1754 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9-20130406')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb index 3eb170a630..9d00ffb356 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9-20130406')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb index b1fad1251e..0643af2756 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9-20130406')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb index f943ccf7e0..588120ecab 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9-20130406')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb index d504b4bb9d..7da7fb3704 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb index 1c4ed75037..7c3f729114 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9-20130406')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb index 763615c3b8..1a77989db2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9-20130406')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb index 0a9aa5e42c..b6b43d3824 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb index 7f0acba39d..80b3a5a0d2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb index 9d6b94d269..854b550334 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb index a2a91a9783..2efb23ba2e 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb index 82d3bb3ea3..d88ab955d5 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb index 0ea31c3644..962152ab77 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb index d91a3d0cbd..b8808453c0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb index 85c94bcdf6..8f1f90ef44 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb index 7b606618cd..982a87c7a5 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb @@ -9,7 +9,7 @@ allow users to edit command lines as they are typed in. Both Emacs and vi editin The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" -toolchain = {'name': 'ictce', 'version' : '5.2.0'} +toolchain = {'name': 'ictce', 'version': '5.2.0'} toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb index 569becdb9b..eef6f459fc 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb index c0482afd80..74795ae7ed 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb index d963e36805..ab71b53ec7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb index 9554501c19..cd50046e7d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb index e5a19f2764..5642e6cf66 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb index 6c11c363a6..076e004cc9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb index 1069375589..e3b44ca6d3 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb index 33f071a9b3..614b7bd324 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb index 18966e6606..89fb87f2b4 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb index c91b6b9470..8b23cf9ec2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb @@ -20,10 +20,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb index 10721a7658..900f704348 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb index 3c101707a6..46e89b5a96 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb @@ -24,7 +24,7 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb index c63d31b97c..b7b9cde8c0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb index 8b18b445d2..c11aec2551 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 8985f04b52..7ee9565173 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb index 505614848e..648d05fb6e 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb index 12cfef1cc3..0b20f1e897 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb index 4d15c99139..b43dd2d7e6 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '6.0')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb index 7eea47c4c6..24911170bc 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb index 77b77c5ab3..bbba152986 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb index a703a43f65..b30c90c988 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb index 3b29814b1f..c30f50b9af 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb index 1b6851f0cd..f3b5e8f280 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb index bf05a3f8b5..9556601362 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb @@ -26,7 +26,7 @@ sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', - 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb index ae449f5493..a59ced555e 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb @@ -26,7 +26,7 @@ sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', - 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb index c0c7a99d1b..6db8fe535c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb index aba2f07841..f1faaddd9c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb index 0c39d000e3..b50756b18b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb index 009d1d8c22..b04629e2d3 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb index dcae291ca2..5a7988af7c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb index 631e51d648..b871f9f93f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb index 555538dfd5..0762f90f29 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '6.0')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb index cf4ec0fba3..2d8ce10f06 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.""" -toolchain = {'name': 'ictce', 'version' : '4.0.6'} +toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb index a9c0566710..3c57c305b2 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.""" -toolchain = {'name': 'ictce', 'version' : '4.1.13'} +toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GNU-4.9.3-2.25.eb index 9c592ae30c..82f0603122 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GNU-4.9.3-2.25.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb index 533de69912..59ff430657 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb index 31485301e1..35adecc8cc 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb @@ -14,10 +14,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb index 18d1b43266..038fce3de2 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb @@ -17,10 +17,10 @@ patches = ['libunistring_icc_builtin_nan-inf.patch'] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb index a07834afed..7f7fae3c87 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb @@ -17,10 +17,10 @@ patches = ['libunistring_icc_builtin_nan-inf.patch'] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb index 088b49a64a..41074c5f41 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb @@ -17,10 +17,10 @@ patches = ['libunistring_icc_builtin_nan-inf.patch'] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb index f0bcc7d4a6..bd766f2e39 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb @@ -32,4 +32,3 @@ sanity_check_paths = { parallel = 1 moduleclass = 'chem' - diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-4.1.13.eb index add9d8667d..2df71cc7a7 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-4.1.13.eb @@ -32,4 +32,3 @@ sanity_check_paths = { parallel = 1 moduleclass = 'chem' - diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb index f7564e13c2..f86e8ff9fb 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb @@ -32,4 +32,3 @@ sanity_check_paths = { parallel = 1 moduleclass = 'chem' - diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb index 02c561f849..4c45b545b5 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb @@ -30,4 +30,3 @@ sanity_check_paths = { parallel = 1 moduleclass = 'chem' - diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb index f008d8268a..e6561d3ed6 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb @@ -30,4 +30,3 @@ sanity_check_paths = { parallel = 1 moduleclass = 'chem' - diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb index 642e8c5309..104ccdae65 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -26,10 +26,10 @@ dependencies = [ #preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb index 930f6a164f..72ed48fe99 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -24,10 +24,10 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb index bd5e7ed56d..26de0f9322 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb @@ -9,7 +9,7 @@ description = """The X protocol C-language Binding (XCB) is a replacement for Xl toolchain = {'name': 'goolf', 'version': '1.5.14'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -21,10 +21,10 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb index 09a13b616d..4f2074c3fb 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -24,10 +24,10 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb index 68acb79d5b..d72a9273ac 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -24,10 +24,10 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb index 482b2014e9..6621cf1702 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -24,10 +24,10 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb index c9239b151b..cc7392bf9e 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -24,10 +24,10 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb index c58daba38a..2a52455403 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """The X protocol C-language Binding (XCB) is a replacement for Xl toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] patches = ['libxcb-no-pthread-stubs.patch'] @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.4.10-Python-2.7.3.eb index 3be1736940..a52d5bb05d 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.4.10-Python-2.7.3.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] patches = ['libxcb-no-pthread-stubs.patch'] @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.3.eb index a3fa51e67e..056448ccd2 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.3.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'goolf', 'version': '1.5.14'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] patches = ['libxcb-no-pthread-stubs.patch'] @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb index 6d757e7d79..1368050899 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """The X protocol C-language Binding (XCB) is a replacement for Xl toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] patches = ['libxcb-no-pthread-stubs.patch'] @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb index 09100be56b..68e4849e58 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """The X protocol C-language Binding (XCB) is a replacement for Xl toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] patches = ['libxcb-no-pthread-stubs.patch'] @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-5.3.0-Python-2.7.3.eb index 879b645f96..16f804c17d 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-5.3.0-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """The X protocol C-language Binding (XCB) is a replacement for Xl toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] patches = ['libxcb-no-pthread-stubs.patch'] @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2014b-Python-2.7.8.eb index eca2fdff48..8c055b9572 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2014b-Python-2.7.8.eb @@ -9,7 +9,7 @@ description = """The X protocol C-language Binding (XCB) is a replacement for Xl toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] patches = ['libxcb-no-pthread-stubs.patch'] @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.5.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.5.0-intel-2015b-Python-2.7.11.eb index 5308b095b3..c8fafe0222 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.5.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.5.0-intel-2015b-Python-2.7.11.eb @@ -12,7 +12,7 @@ description = """xkbcommon is a library to handle keyboard descriptions, toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xkbcommon.org/download/'] +source_urls = ['http://xkbcommon.org/download/'] sources = [SOURCELOWER_TAR_XZ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.5.0-intel-2015b.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.5.0-intel-2015b.eb index b315eb6d84..936890773f 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.5.0-intel-2015b.eb @@ -11,7 +11,7 @@ description = """xkbcommon is a library to handle keyboard descriptions, toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xkbcommon.org/download/'] +source_urls = ['http://xkbcommon.org/download/'] sources = [SOURCELOWER_TAR_XZ] dependencies = [ diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED-pinomp.eb b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED-pinomp.eb index e17929c01b..132721bab5 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED-pinomp.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED-pinomp.eb @@ -16,13 +16,13 @@ source_urls = [GOOGLECODE_SOURCE] patches = ['pinomp-pthread-overload.patch'] skipsteps = ['configure'] -buildopts='CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { 'files': ["bin/likwid-features", "bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", "bin/likwid-topology", - "lib/liblikwidpin.%s" % SHLIB_EXT , "lib/liblikwid.a"], + "lib/liblikwidpin.%s" % SHLIB_EXT, "lib/liblikwid.a"], 'dirs': ["man/man1"] } diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED.eb index 9d0cf1054d..669fa552aa 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [GOOGLECODE_SOURCE] skipsteps = ['configure'] -buildopts='CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goolf-1.4.10-pinomp.eb b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goolf-1.4.10-pinomp.eb index 3855b155c5..0c0b62a221 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goolf-1.4.10-pinomp.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goolf-1.4.10-pinomp.eb @@ -16,13 +16,13 @@ source_urls = [GOOGLECODE_SOURCE] patches = ['pinomp-pthread-overload.patch'] skipsteps = ['configure'] -buildopts='CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { 'files': ["bin/likwid-features", "bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", "bin/likwid-topology", - "lib/liblikwidpin.%s" % SHLIB_EXT , "lib/liblikwid.a"], + "lib/liblikwidpin.%s" % SHLIB_EXT, "lib/liblikwid.a"], 'dirs': ["man/man1"] } diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goolf-1.4.10.eb index 8d8e1a8a56..ec93432ba4 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goolf-1.4.10.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [GOOGLECODE_SOURCE] skipsteps = ['configure'] -buildopts='CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13-pinomp.eb b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13-pinomp.eb index 2933d46267..e4ad87b307 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13-pinomp.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13-pinomp.eb @@ -16,7 +16,7 @@ source_urls = [GOOGLECODE_SOURCE] patches = ['pinomp-pthread-overload.patch'] skipsteps = ['configure'] -buildopts='CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13.eb b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13.eb index 39f9e9f76b..5861b6ec0b 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [GOOGLECODE_SOURCE] skipsteps = ['configure'] -buildopts='CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0-pinomp.eb b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0-pinomp.eb index 07a812856a..8e3bb39ecc 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0-pinomp.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0-pinomp.eb @@ -16,7 +16,7 @@ source_urls = [GOOGLECODE_SOURCE] patches = ['pinomp-pthread-overload.patch'] skipsteps = ['configure'] -buildopts='CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0.eb index 5202c65045..38eedbb46e 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [GOOGLECODE_SOURCE] skipsteps = ['configure'] -buildopts='CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { -- GitLab From 3223d9827492bd9f69f4b8d5a7ee83aff5ea7d7a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:45:38 +0100 Subject: [PATCH 0273/2133] Style fixes with autopep8: c Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../c/CAP3/CAP3-20071221-intel-x86.eb | 2 +- .../c/CAP3/CAP3-20071221-intel-x86_64.eb | 2 +- .../c/CAP3/CAP3-20071221-opteron.eb | 2 +- .../c/CCfits/CCfits-2.4-goolf-1.4.10.eb | 2 +- .../c/CCfits/CCfits-2.4-ictce-4.1.13.eb | 2 +- .../c/CCfits/CCfits-2.4-ictce-5.3.0.eb | 2 +- .../CD-HIT-4.5.4-ictce-5.3.0-2011-03-07.eb | 2 +- .../CD-HIT-4.6.1-foss-2015b-2012-08-27.eb | 2 +- .../CD-HIT-4.6.1-goolf-1.4.10-2012-08-27.eb | 2 +- .../CD-HIT-4.6.1-ictce-5.5.0-2012-08-27.eb | 2 +- .../CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb | 2 +- .../CD-HIT-4.6.4-foss-2015b-2015-0603.eb | 2 +- .../c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb | 4 ++-- .../c/CFITSIO/CFITSIO-3.34-ictce-4.1.13.eb | 4 ++-- .../c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb | 4 ++-- .../CGAL/CGAL-4.0-ictce-4.0.6-Python-2.7.3.eb | 1 - .../CGAL/CGAL-4.0-ictce-5.3.0-Python-2.7.3.eb | 1 - ...6-intel-2015a-GLib-2.44.1-Python-2.7.10.eb | 2 +- .../CGAL-4.6-intel-2015a-Python-2.7.10.eb | 2 +- .../CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb | 2 +- .../CGAL-4.6.3-intel-2015b-Python-2.7.10.eb | 2 +- .../CONTRAfold-2.02-goolf-1.4.10.eb | 2 +- .../CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb | 20 +++++++++---------- ...P2K-20111205-goalf-1.1.0-no-OFED-libsmm.eb | 18 ++++++++--------- .../CP2K-20111205-goalf-1.1.0-no-OFED-psmp.eb | 14 ++++++------- .../CP2K/CP2K-20111205-goalf-1.1.0-no-OFED.eb | 12 +++++------ .../CP2K/CP2K-20111205-goolf-1.4.10-libsmm.eb | 20 +++++++++---------- .../c/CP2K/CP2K-20111205-goolf-1.4.10-psmp.eb | 14 ++++++------- .../c/CP2K/CP2K-20111205-goolf-1.4.10.eb | 14 ++++++------- .../c/CP2K/CP2K-20111205-ictce-3.2.2.u3.eb | 12 +++++------ easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb | 2 +- .../c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb | 2 +- .../c/CVS/CVS-1.11.23-GCC-4.8.2.eb | 2 +- .../c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb | 4 ++-- .../c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb | 4 ++-- .../ClustalW2-2.1-goalf-1.1.0-no-OFED.eb | 6 +++--- .../c/ClustalW2/ClustalW2-2.1-goolf-1.4.10.eb | 6 +++--- .../c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb | 6 +++--- .../c/ClustalW2/ClustalW2-2.1-ictce-5.3.0.eb | 6 +++--- ...-binary-Linux-x86_64-rhel-6-python-gtk2.eb | 3 +-- .../Corkscrew-2.0-goalf-1.1.0-no-OFED.eb | 6 +++--- .../c/Corkscrew/Corkscrew-2.0-goolf-1.4.10.eb | 6 +++--- .../c/Corkscrew/Corkscrew-2.0-ictce-4.0.6.eb | 6 +++--- .../c/Corkscrew/Corkscrew-2.0-ictce-5.3.0.eb | 6 +++--- .../c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb | 4 ++-- .../easyconfigs/c/Cuby/Cuby-4-intel-2014b.eb | 4 ++-- .../Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- .../c/cURL/cURL-7.37.1-foss-2014b.eb | 2 +- .../c/cURL/cURL-7.37.1-foss-2015a.eb | 2 +- .../c/cURL/cURL-7.37.1-intel-2014b.eb | 2 +- .../c/cURL/cURL-7.37.1-intel-2015a.eb | 2 +- .../ccache-3.1.9-goalf-1.1.0-no-OFED.eb | 6 +++--- .../c/ccache/ccache-3.1.9-goolf-1.4.10.eb | 6 +++--- .../c/ccache/ccache-3.1.9-ictce-4.0.6.eb | 7 +++---- .../c/ccache/ccache-3.1.9-ictce-5.3.0.eb | 7 +++---- .../c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb | 6 +++--- .../c/cflow/cflow-1.4-goolf-1.4.10.eb | 6 +++--- .../c/cflow/cflow-1.4-ictce-4.0.6.eb | 7 +++---- .../c/cflow/cflow-1.4-ictce-5.3.0.eb | 7 +++---- .../c/cgdb/cgdb-0.6.5-goalf-1.1.0-no-OFED.eb | 12 +++++------ .../c/cgdb/cgdb-0.6.5-goolf-1.4.10.eb | 12 +++++------ .../c/cgdb/cgdb-0.6.5-ictce-4.0.6.eb | 12 +++++------ .../c/cgdb/cgdb-0.6.5-ictce-5.3.0.eb | 12 +++++------ .../c/ctffind/ctffind-4.0.8-intel-2014b.eb | 2 +- .../cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb | 2 +- .../cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb | 3 +-- .../cutadapt-1.5-foss-2014b-Python-2.7.8.eb | 3 +-- .../cutadapt-1.5-intel-2014b-Python-2.7.8.eb | 2 +- .../cutadapt-1.6-foss-2014b-Python-2.7.8.eb | 3 +-- .../cutadapt-1.7-foss-2014b-Python-2.7.8.eb | 3 +-- .../cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb | 3 +-- ...cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 2 +- 73 files changed, 185 insertions(+), 197 deletions(-) diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb index 0c1d5284b7..98b5be9cc7 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb @@ -19,7 +19,7 @@ sources = ['cap3.linux.tar'] checksums = [('md5', '55f57f61e588d4de06c0506cf2696c29')] sanity_check_paths = { - 'files': ['cap3','formcon'], + 'files': ['cap3', 'formcon'], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb index 0962339a29..a459a2b2ae 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb @@ -19,7 +19,7 @@ sources = ['cap3.linux.x86_64.tar'] checksums = [('md5', '0fbb95c3fcbfb2b1afcebc5f7e2b4343')] sanity_check_paths = { - 'files': ['cap3','formcon'], + 'files': ['cap3', 'formcon'], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb index 3e19f30c49..574d59a93d 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb @@ -19,7 +19,7 @@ sources = ['cap3.linux.opteron64.tar'] checksums = [('md5', '2d924766f6e8b5cf03bd2db81016d821')] sanity_check_paths = { - 'files': ['cap3','formcon'], + 'files': ['cap3', 'formcon'], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CCfits/CCfits-2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CCfits/CCfits-2.4-goolf-1.4.10.eb index d575fbe895..587da5f4ec 100644 --- a/easybuild/easyconfigs/c/CCfits/CCfits-2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CCfits/CCfits-2.4-goolf-1.4.10.eb @@ -13,7 +13,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://heasarc.gsfc.nasa.gov/fitsio/CCfits/'] sources = [SOURCE_TAR_GZ] -dependencies = [('CFITSIO','3.34')] +dependencies = [('CFITSIO', '3.34')] sanity_check_paths = { 'files': ['bin/cookbook', 'lib/libCCfits.%s' % SHLIB_EXT, 'lib/pkgconfig/CCfits.pc'], diff --git a/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-4.1.13.eb b/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-4.1.13.eb index 3375f207b2..1c12c8c026 100644 --- a/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-4.1.13.eb @@ -13,7 +13,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://heasarc.gsfc.nasa.gov/fitsio/CCfits/'] sources = [SOURCE_TAR_GZ] -dependencies = [('CFITSIO','3.34')] +dependencies = [('CFITSIO', '3.34')] sanity_check_paths = { 'files': ['bin/cookbook', 'lib/libCCfits.%s' % SHLIB_EXT, 'lib/pkgconfig/CCfits.pc'], diff --git a/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-5.3.0.eb index a344cd2ac0..15a5ec31e9 100644 --- a/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-5.3.0.eb @@ -13,7 +13,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://heasarc.gsfc.nasa.gov/fitsio/CCfits/'] sources = [SOURCE_TAR_GZ] -dependencies = [('CFITSIO','3.34')] +dependencies = [('CFITSIO', '3.34')] sanity_check_paths = { 'files': ['bin/cookbook', 'lib/libCCfits.%s' % SHLIB_EXT, 'lib/pkgconfig/CCfits.pc'], diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.5.4-ictce-5.3.0-2011-03-07.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.5.4-ictce-5.3.0-2011-03-07.eb index 5c78fcfbe5..e4650118de 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.5.4-ictce-5.3.0-2011-03-07.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.5.4-ictce-5.3.0-2011-03-07.eb @@ -11,7 +11,7 @@ easyblock = "MakeCp" name = 'CD-HIT' version = '4.5.4' -versionsuffix='-2011-03-07' +versionsuffix = '-2011-03-07' homepage = 'http://www.bioinformatics.org/cd-hit/' description = """CD-HIT stands for Cluster Database at High Identity with Tolerance. The program diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-foss-2015b-2012-08-27.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-foss-2015b-2012-08-27.eb index d4682f582d..2fdb2ffa3d 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-foss-2015b-2012-08-27.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-foss-2015b-2012-08-27.eb @@ -26,7 +26,7 @@ buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd-hit-div", "cd-hit-454"] # this is the real EasyBuild line to copy all the executables and perl scripts to "bin" -files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt" ] +files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt"] sanity_check_paths = { 'files': ["bin/%s" % x for x in list_of_executables], diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-goolf-1.4.10-2012-08-27.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-goolf-1.4.10-2012-08-27.eb index f2058ca8b6..c3e01a8650 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-goolf-1.4.10-2012-08-27.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-goolf-1.4.10-2012-08-27.eb @@ -26,7 +26,7 @@ buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd-hit-div", "cd-hit-454"] # this is the real EasyBuild line to copy all the executables and perl scripts to "bin" -files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt" ] +files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt"] sanity_check_paths = { 'files': ["bin/%s" % x for x in list_of_executables], diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-ictce-5.5.0-2012-08-27.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-ictce-5.5.0-2012-08-27.eb index 83b5369b71..5563d4c561 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-ictce-5.5.0-2012-08-27.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-ictce-5.5.0-2012-08-27.eb @@ -26,7 +26,7 @@ buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd-hit-div", "cd-hit-454"] # this is the real EasyBuild line to copy all the executables and perl scripts to "bin" -files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt" ] +files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt"] sanity_check_paths = { 'files': ["bin/%s" % x for x in list_of_executables], diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb index b3d2485ff0..268e532192 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb @@ -35,7 +35,7 @@ files_to_copy = [ "doc", "license.txt", "psi-cd-hit/README.psi-cd-hit", - ] +] sanity_check_paths = { 'files': ["bin/%s" % x for x in list_of_executables], diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-foss-2015b-2015-0603.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-foss-2015b-2015-0603.eb index e2e712b7d5..832db33507 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-foss-2015b-2015-0603.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-foss-2015b-2015-0603.eb @@ -26,7 +26,7 @@ buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd-hit-div", "cd-hit-454"] # this is the real EasyBuild line to copy all the executables and perl scripts to "bin" -files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt" ] +files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt"] sanity_check_paths = { 'files': ["bin/%s" % x for x in list_of_executables], diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb index 3373480b9b..9a156bffea 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb @@ -15,8 +15,8 @@ source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { - 'files':["lib/libcfitsio.a"], - 'dirs':["include"], + 'files': ["lib/libcfitsio.a"], + 'dirs': ["include"], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-4.1.13.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-4.1.13.eb index 7086648457..0fc72a1115 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-4.1.13.eb @@ -15,8 +15,8 @@ source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { - 'files':["lib/libcfitsio.a"], - 'dirs':["include"], + 'files': ["lib/libcfitsio.a"], + 'dirs': ["include"], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb index bbd4471f37..bf8fb571c8 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb @@ -15,8 +15,8 @@ source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { - 'files':["lib/libcfitsio.a"], - 'dirs':["include"], + 'files': ["lib/libcfitsio.a"], + 'dirs': ["include"], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-4.0.6-Python-2.7.3.eb index 83a1ddddd0..09a71c9763 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-4.0.6-Python-2.7.3.eb @@ -24,4 +24,3 @@ dependencies = [ ] moduleclass = 'numlib' - diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-5.3.0-Python-2.7.3.eb index 1e713bc44a..c407409f32 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-5.3.0-Python-2.7.3.eb @@ -25,4 +25,3 @@ dependencies = [ ] moduleclass = 'numlib' - diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-GLib-2.44.1-Python-2.7.10.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-GLib-2.44.1-Python-2.7.10.eb index 9dca8053a4..566b71d5c5 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-GLib-2.44.1-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-GLib-2.44.1-Python-2.7.10.eb @@ -17,7 +17,7 @@ pysuff = '-Python-2.7.10' versionsuffix = '%s%s' % ('-GLib-2.44.1', pysuff) dependencies = [ - #GMP does not compile correctly with ICC on Haswell architecture using pre 2015b toolchain + # GMP does not compile correctly with ICC on Haswell architecture using pre 2015b toolchain ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), ('Boost', '1.58.0', pysuff), ('MPFR', '3.1.2', '-GMP-6.0.0a'), diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb index f6286f011c..ff84775666 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb @@ -17,7 +17,7 @@ pythonversion = '2.7.10' versionsuffix = "-Python-%s" % pythonversion dependencies = [ -#GMP does not compile correctly with ICC on Haswell architecture + # GMP does not compile correctly with ICC on Haswell architecture ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), ('Boost', '1.58.0', versionsuffix), ('MPFR', '3.1.2', '-GMP-6.0.0a'), diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb index b27b5edd11..59646f1f0f 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb @@ -17,7 +17,7 @@ pythonversion = '2.7.9' versionsuffix = "-Python-%s" % pythonversion dependencies = [ -#GMP does not compile correctly with ICC on Haswell architecture + # GMP does not compile correctly with ICC on Haswell architecture ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), ('Boost', '1.58.0', versionsuffix), ('MPFR', '3.1.2', '-GMP-6.0.0a'), diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6.3-intel-2015b-Python-2.7.10.eb index f4f6ee73bf..40ba6d07e7 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6.3-intel-2015b-Python-2.7.10.eb @@ -24,7 +24,7 @@ dependencies = [ ] builddependencies = [ -#CGAL 4.6.3 does not build with CMake 3.3.2! + # CGAL 4.6.3 does not build with CMake 3.3.2! ('CMake', '3.2.3'), ] diff --git a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb index 34d8a45119..77c3defd88 100644 --- a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb @@ -14,7 +14,7 @@ description = ''' CONditional TRAining for RNA Secondary Structure Prediction ' toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] -sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_'))] +sources = ['%s_v%s.tar.gz' % (name.lower(), version.replace('.', '_'))] patches = ['contrafold-gcc47.patch'] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb index fb47d44650..ae5eb6f8dc 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb @@ -13,25 +13,25 @@ toolchain = {'name': 'gmacml', 'version': '1.7.0'} sources = [SOURCE_TAR_GZ] patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch', - ] + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch', +] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), +] dependencies = [ - ('Libint', '1.1.4'), - ('libsmm', version), - ] + ('Libint', '1.1.4'), + ('libsmm', version), +] # don't use parallel make, results in compilation failure # because Fortran module files aren't created before they are needed parallel = 1 # regression test reports failures (1/2196 tests fail with segfault) -ignore_regtest_fails=True +ignore_regtest_fails = True moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED-libsmm.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED-libsmm.eb index b2c0a55708..3ecba232f1 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED-libsmm.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED-libsmm.eb @@ -13,19 +13,19 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCE_TAR_GZ] patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch' - ] + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' +] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') +] dependencies = [ - ('Libint', '1.1.4'), - ('libsmm', '20111205') - ] + ('Libint', '1.1.4'), + ('libsmm', '20111205') +] # don't use parallel make, results in compilation failure # because Fortran module files aren't created before they are needed diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED-psmp.eb index 09bbad25c0..ede4ebe0fc 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED-psmp.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED-psmp.eb @@ -13,15 +13,15 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCE_TAR_GZ] patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch', - 'fix_psmp_build.patch' - ] + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch', + 'fix_psmp_build.patch' +] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') +] dependencies = [('Libint', '1.1.4')] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED.eb index 06ae6f9444..e3679af61b 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goalf-1.1.0-no-OFED.eb @@ -12,14 +12,14 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCE_TAR_GZ] patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch' - ] + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' +] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') +] dependencies = [('Libint', '1.1.4')] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-libsmm.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-libsmm.eb index 7366879bfd..70f7866473 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-libsmm.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-libsmm.eb @@ -13,25 +13,25 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch' - ] + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' +] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') +] dependencies = [ - ('Libint', '1.1.4'), - ('libsmm', '20111205') - ] + ('Libint', '1.1.4'), + ('libsmm', '20111205') +] # don't use parallel make, results in compilation failure # because Fortran module files aren't created before they are needed parallel = 1 # about 100 tests fail -ignore_regtest_fails=True +ignore_regtest_fails = True moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-psmp.eb index a2f304ace2..df760b1c15 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-psmp.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-psmp.eb @@ -13,15 +13,15 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch', - 'fix_psmp_build.patch' - ] + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch', + 'fix_psmp_build.patch' +] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') +] dependencies = [('Libint', '1.1.4')] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10.eb index 3d113cc1d8..10f8d7440a 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10.eb @@ -12,14 +12,14 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch' - ] + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' +] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') +] dependencies = [('Libint', '1.1.4')] @@ -28,6 +28,6 @@ dependencies = [('Libint', '1.1.4')] parallel = 1 # about 100 tests fail -ignore_regtest_fails=True +ignore_regtest_fails = True moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-3.2.2.u3.eb index 1862b31e51..6e21a831bc 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-3.2.2.u3.eb @@ -12,14 +12,14 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} sources = [SOURCE_TAR_GZ] patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch' - ] + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' +] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') +] dependencies = [('Libint', '1.1.4')] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb index 4c8b4e861d..299410b70c 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb @@ -31,7 +31,7 @@ if OS_NAME in ['fedora', 'redhat']: elif OS_NAME in ["RHEL", "SL", "centos"]: system = 'rhel%s.x' % OS_VERSION.split('.')[0] elif OS_NAME in ['debian'] and OS_VERSION.startswith('6.'): - system = 'ubuntu10.04' + system = 'ubuntu10.04' elif OS_NAME in ['debian', 'ubuntu']: if OS_VERSION in ['11.10', '10.04']: system = 'ubuntu%s' % OS_VERSION diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb index b7d1981966..9b2a072f8b 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb @@ -31,7 +31,7 @@ if OS_NAME in ['fedora', 'redhat']: elif OS_NAME in ["RHEL", "SL", "centos"]: system = 'rhel%s.x' % OS_VERSION.split('.')[0] elif OS_NAME in ['debian'] and OS_VERSION.startswith('6.'): - system = 'ubuntu10.04' + system = 'ubuntu10.04' elif OS_NAME in ['debian', 'ubuntu']: if OS_VERSION in ['11.10', '10.04']: system = 'ubuntu%s' % OS_VERSION diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb index 19a3bd716f..b8b9c80a8d 100644 --- a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb @@ -19,7 +19,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = ['CVS-1.11.23-zlib-1.patch', 'CVS-1.11.23-getline.patch'] -dependencies = [('zlib','1.2.8')] +dependencies = [('zlib', '1.2.8')] sanity_check_paths = { 'files': ['bin/cvs', 'bin/cvsbug', 'bin/rcs2log'], diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb index 4e4589531c..eb2d005b6f 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb @@ -32,13 +32,13 @@ installopts += 'cp -a README doc/ %(installdir)s' sanity_check_paths = { 'files': ["bin/%s" % x for x in ["chipcenter", "chipcor", "chipextract", "chippart", "chippeak", - "chipscore", "compactsga", "counts_filter", "countsga", "featreplace"]], + "chipscore", "compactsga", "counts_filter", "countsga", "featreplace"]], 'dirs': [] } # add tools dir to PATH modextrapaths = { - 'PATH': "tools", + 'PATH': "tools", } # fix shebang line in all provided perl scripts in tools folder diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb index cf00dd3653..dcbe783b38 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb @@ -32,13 +32,13 @@ installopts += 'cp -a README doc/ %(installdir)s' sanity_check_paths = { 'files': ["bin/%s" % x for x in ["chipcenter", "chipcor", "chipextract", "chippart", "chippeak", - "chipscore", "compactsga", "counts_filter", "countsga", "featreplace"]], + "chipscore", "compactsga", "counts_filter", "countsga", "featreplace"]], 'dirs': [] } # add tools dir to PATH modextrapaths = { - 'PATH': "tools", + 'PATH': "tools", } # fix shebang line in all provided perl scripts in tools folder diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goalf-1.1.0-no-OFED.eb index 141abe9b6a..0649ad44a0 100644 --- a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goalf-1.1.0-no-OFED.eb @@ -25,8 +25,8 @@ sources = ['%s-%s.tar.gz' % (name[:-1].lower(), version)] source_urls = ['ftp://ftp.ebi.ac.uk/pub/software/%s/%s' % (name.lower(), version)] sanity_check_paths = { - 'files': ['bin/clustalw2'], - 'dirs': [] - } + 'files': ['bin/clustalw2'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goolf-1.4.10.eb index 0c4dba86a6..de52a79a13 100644 --- a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goolf-1.4.10.eb @@ -25,8 +25,8 @@ sources = ['%s-%s.tar.gz' % (name[:-1].lower(), version)] source_urls = ['ftp://ftp.ebi.ac.uk/pub/software/%s/%s' % (name.lower(), version)] sanity_check_paths = { - 'files': ['bin/clustalw2'], - 'dirs': [] - } + 'files': ['bin/clustalw2'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb index 93dc9500bd..cad6e2ddab 100644 --- a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb @@ -25,8 +25,8 @@ sources = ['%s-%s.tar.gz' % (name[:-1].lower(), version)] source_urls = ['ftp://ftp.ebi.ac.uk/pub/software/%s/%s' % (name.lower(), version)] sanity_check_paths = { - 'files': ['bin/clustalw2'], - 'dirs': [] - } + 'files': ['bin/clustalw2'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-5.3.0.eb index 381ad621a9..068dfd89ce 100644 --- a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-5.3.0.eb @@ -26,8 +26,8 @@ sources = ['%s-%s.tar.gz' % (name[:-1].lower(), version)] source_urls = ['ftp://ftp.ebi.ac.uk/pub/software/%s/%s' % (name.lower(), version)] sanity_check_paths = { - 'files': ['bin/clustalw2'], - 'dirs': [] - } + 'files': ['bin/clustalw2'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb b/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb index 54e36207e0..1386d5329d 100644 --- a/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb +++ b/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb @@ -19,9 +19,8 @@ source_urls = ['http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/rel sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] sanity_check_paths = { - 'files': ["bin/coot" ], + 'files': ["bin/coot"], 'dirs': ["bin"] } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goalf-1.1.0-no-OFED.eb index 6a4d78599d..a41c761aaf 100644 --- a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goalf-1.1.0-no-OFED.eb @@ -21,8 +21,8 @@ source_urls = ['http://www.agroman.net/corkscrew/'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/corkscrew'], - 'dirs': [] - } + 'files': ['bin/corkscrew'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goolf-1.4.10.eb index 7810f1ee53..8e4f18d89d 100644 --- a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goolf-1.4.10.eb @@ -21,8 +21,8 @@ source_urls = ['http://www.agroman.net/corkscrew/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['bin/corkscrew'], - 'dirs': [] - } + 'files': ['bin/corkscrew'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-4.0.6.eb b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-4.0.6.eb index 3d22de6dc8..ebeb826b66 100644 --- a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-4.0.6.eb @@ -21,8 +21,8 @@ source_urls = ['http://www.agroman.net/corkscrew/'] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/corkscrew'], - 'dirs': [] - } + 'files': ['bin/corkscrew'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-5.3.0.eb index 5f4aa901ed..0afa91c77f 100644 --- a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-5.3.0.eb @@ -22,8 +22,8 @@ source_urls = ['http://www.agroman.net/corkscrew/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/corkscrew'], - 'dirs': [] - } + 'files': ['bin/corkscrew'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb index 94eaf15f8d..856776f4e7 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb @@ -38,8 +38,8 @@ configopts = "--with-qmake=$EBROOTQT/bin/qmake" sanity_check_paths = { 'files': ["bin/cube3%s" % x for x in ["", "-qt", "_clean", "_cmp", "_cut", "_diff", "_mean", "_merge", "_part", "_remap", "_score", "_stat", "_topoassist"]] + - ["bin/cube-config", "bin/tau2cube3", "include/cube3/Cube.h", "include/cube3/cube_error.h", - "include/stats/P2Statistic.h", "lib/libcube3.a", "lib/libcubew3.a", "lib/libstats.a"], + ["bin/cube-config", "bin/tau2cube3", "include/cube3/Cube.h", "include/cube3/cube_error.h", + "include/stats/P2Statistic.h", "lib/libcube3.a", "lib/libcubew3.a", "lib/libstats.a"], 'dirs': ["include/cubew3"], } diff --git a/easybuild/easyconfigs/c/Cuby/Cuby-4-intel-2014b.eb b/easybuild/easyconfigs/c/Cuby/Cuby-4-intel-2014b.eb index fee6df968e..f49b28d34f 100644 --- a/easybuild/easyconfigs/c/Cuby/Cuby-4-intel-2014b.eb +++ b/easybuild/easyconfigs/c/Cuby/Cuby-4-intel-2014b.eb @@ -14,13 +14,13 @@ description = """Cuby is a computational chemistry framework written in ruby. toolchain = {'name': 'intel', 'version': '2014b'} -#Source can be obtained via http://cuby.molecular.cz/?page=Downloads +# Source can be obtained via http://cuby.molecular.cz/?page=Downloads sources = ['cuby4.tgz'] dependencies = [('Ruby', '2.1.5')] sanity_check_paths = { - 'files': ['cuby4%s' % x for x in ['', '.rb' ]], + 'files': ['cuby4%s' % x for x in ['', '.rb']], 'dirs': ['classes'], } diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index 5b829d6a73..1a87b1c99c 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -21,8 +21,8 @@ cythonlibdir = 'lib/python' + pyshortver + '/site-packages/Cython-%(version)s-py dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], - 'dirs': ['%s/%%(name)s' % cythonlibdir], + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': ['%s/%%(name)s' % cythonlibdir], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb index 980fd8a13c..8b024b363b 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] -#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +# dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb index fcbb0636e8..6036dce5c2 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] -#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +# dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb index dfe1f4cd86..196d06a19d 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] -#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +# dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2015a.eb index 5e1e3ebad8..119999d59e 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2015a.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] -#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +# dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goalf-1.1.0-no-OFED.eb index 48fcc47836..bbabdb92a5 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goalf-1.1.0-no-OFED.eb @@ -21,8 +21,8 @@ source_urls = ['http://samba.org/ftp/ccache/'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/ccache'], - 'dirs': [] - } + 'files': ['bin/ccache'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goolf-1.4.10.eb index b642a5d551..3bf08594da 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goolf-1.4.10.eb @@ -21,8 +21,8 @@ source_urls = ['http://samba.org/ftp/ccache/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['bin/ccache'], - 'dirs': [] - } + 'files': ['bin/ccache'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-4.0.6.eb b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-4.0.6.eb index 4137d5afc8..3011b90d17 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-4.0.6.eb @@ -21,9 +21,8 @@ source_urls = ['http://samba.org/ftp/ccache/'] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/ccache'], - 'dirs': [] - } + 'files': ['bin/ccache'], + 'dirs': [] +} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-5.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-5.3.0.eb index b15c9ceaf9..84c3e7baf8 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-5.3.0.eb @@ -22,9 +22,8 @@ source_urls = ['http://samba.org/ftp/ccache/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/ccache'], - 'dirs': [] - } + 'files': ['bin/ccache'], + 'dirs': [] +} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb index 315f43e190..98800f3677 100644 --- a/easybuild/easyconfigs/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb @@ -22,8 +22,8 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/cflow'], - 'dirs': [] - } + 'files': ['bin/cflow'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb index 501b5edd24..bb9da36f80 100644 --- a/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb @@ -22,8 +22,8 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['bin/cflow'], - 'dirs': [] - } + 'files': ['bin/cflow'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-4.0.6.eb b/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-4.0.6.eb index 7c2775cbce..a3e495b0c6 100644 --- a/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-4.0.6.eb @@ -22,9 +22,8 @@ source_urls = [GNU_SOURCE] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/cflow'], - 'dirs': [] - } + 'files': ['bin/cflow'], + 'dirs': [] +} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb index 848eb6e899..107d08647f 100644 --- a/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb @@ -23,9 +23,8 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/cflow'], - 'dirs': [] - } + 'files': ['bin/cflow'], + 'dirs': [] +} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goalf-1.1.0-no-OFED.eb index 5a1aea2fb7..2112acc096 100644 --- a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goalf-1.1.0-no-OFED.eb @@ -21,13 +21,13 @@ source_urls = ['http://sourceforge.net/projects/cgdb/files', 'download'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} dependencies = [ - ('ncurses', '5.9'), - ('libreadline', '6.2') - ] + ('ncurses', '5.9'), + ('libreadline', '6.2') +] sanity_check_paths = { - 'files': ['bin/cgdb'], - 'dirs': [] - } + 'files': ['bin/cgdb'], + 'dirs': [] +} moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goolf-1.4.10.eb b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goolf-1.4.10.eb index 5efc1c2d3c..9684225cb7 100644 --- a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goolf-1.4.10.eb @@ -21,13 +21,13 @@ source_urls = ['http://sourceforge.net/projects/cgdb/files', 'download'] toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ - ('ncurses', '5.9'), - ('libreadline', '6.2') - ] + ('ncurses', '5.9'), + ('libreadline', '6.2') +] sanity_check_paths = { - 'files': ['bin/cgdb'], - 'dirs': [] - } + 'files': ['bin/cgdb'], + 'dirs': [] +} moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-4.0.6.eb b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-4.0.6.eb index b3656ba859..3cff32f247 100644 --- a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-4.0.6.eb @@ -21,13 +21,13 @@ source_urls = ['http://sourceforge.net/projects/cgdb/files', 'download'] toolchain = {'version': '4.0.6', 'name': 'ictce'} dependencies = [ - ('ncurses', '5.9'), - ('libreadline', '6.2') - ] + ('ncurses', '5.9'), + ('libreadline', '6.2') +] sanity_check_paths = { - 'files': ['bin/cgdb'], - 'dirs': [] - } + 'files': ['bin/cgdb'], + 'dirs': [] +} moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-5.3.0.eb b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-5.3.0.eb index c3ce823fd9..eb6eb8ffbf 100644 --- a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-5.3.0.eb @@ -22,13 +22,13 @@ source_urls = ['http://sourceforge.net/projects/cgdb/files', 'download'] toolchain = {'name': 'ictce', 'version': '5.3.0'} dependencies = [ - ('ncurses', '5.9'), - ('libreadline', '6.2') - ] + ('ncurses', '5.9'), + ('libreadline', '6.2') +] sanity_check_paths = { - 'files': ['bin/cgdb'], - 'dirs': [] - } + 'files': ['bin/cgdb'], + 'dirs': [] +} moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.8-intel-2014b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.8-intel-2014b.eb index 70b9a6c76d..6af0d95360 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.8-intel-2014b.eb @@ -1,4 +1,4 @@ -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'ctffind' version = '4.0.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb index 59cb6d8b45..6104aff87d 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -31,7 +31,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/calign.%s' % SHLIB_EXT,], + 'files': ['bin/cutadapt', 'lib/python2.7/site-packages/cutadapt/calign.%s' % SHLIB_EXT, ], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb index f90288e47d..47e9fde842 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb @@ -31,7 +31,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/calign.%s' % SHLIB_EXT,], + 'files': ['bin/cutadapt', 'lib/python2.7/site-packages/cutadapt/calign.%s' % SHLIB_EXT, ], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb index a308b21130..bb39813021 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb @@ -29,9 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt',], + 'files': ['bin/cutadapt', ], 'dirs': [], } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb index 3303167a21..b50da0fe87 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb @@ -29,9 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt',], + 'files': ['bin/cutadapt', ], 'dirs': [], } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb index dbc8a13634..259ebe78db 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], + 'files': ['bin/cutadapt', 'lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb index 83a8d8a50d..a12667f4b2 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb @@ -29,9 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt',], + 'files': ['bin/cutadapt', ], 'dirs': [], } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb index f879b0939f..6968ed00cd 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb @@ -29,9 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt',], + 'files': ['bin/cutadapt', ], 'dirs': [], } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb index 60048badc4..9fe18ae0c4 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb @@ -29,9 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt',], + 'files': ['bin/cutadapt', ], 'dirs': [], } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb index a69f7bc2f8..880a7ad08e 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -29,7 +29,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], + 'files': ['bin/cutadapt', 'lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } -- GitLab From ea08830553c0f7e83ac34c7c77b8eaa1d904340a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:48:41 +0100 Subject: [PATCH 0274/2133] Style fixes with autopep8: m Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb | 2 +- ....1.0.20150731-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/m/MATLAB/MATLAB-2012b.eb | 2 +- .../m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb | 6 ++-- .../m/MCL/MCL-12.135-goolf-1.4.10.eb | 6 ++-- .../m/MCL/MCL-12.135-ictce-4.0.6.eb | 6 ++-- .../m/MCL/MCL-12.135-ictce-4.1.13.eb | 6 ++-- .../m/MCL/MCL-12.135-ictce-5.3.0.eb | 6 ++-- easybuild/easyconfigs/m/MCR/MCR-R2014a.eb | 5 ++-- easybuild/easyconfigs/m/MCR/MCR-R2015a.eb | 5 ++-- .../METIS-5.1.0-gimkl-2.11.5-32bitIDX.eb | 2 +- .../METIS/METIS-5.1.0-intel-2015a-32bitIDX.eb | 2 +- .../METIS/METIS-5.1.0-intel-2015b-32bitIDX.eb | 2 +- .../m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb | 2 +- .../m/MPC/MPC-1.0.2-intel-2015a.eb | 2 +- .../MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb | 8 +++--- .../MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb | 8 +++--- .../m/MUSCLE/MUSCLE-3.8.31-goolf-1.4.10.eb | 2 +- .../m/MUSCLE/MUSCLE-3.8.31-ictce-5.5.0.eb | 2 +- .../m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb | 2 +- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb | 6 ++-- .../MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb | 4 +-- .../m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb | 4 +-- ...ercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb | 6 ++-- .../Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- .../Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 2 +- ...7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 28 +++++++++---------- .../Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 28 +++++++++---------- .../Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb | 28 +++++++++---------- .../Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb | 14 +++++----- .../Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 28 +++++++++---------- .../m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb | 4 +-- .../m/MethPipe/MethPipe-3.0.1-intel-2014b.eb | 4 +-- .../m/Molden/Molden-5.0-ictce-4.1.13.eb | 4 +-- .../m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb | 2 +- .../m/MultiNest/MultiNest-3.10-intel-2015b.eb | 4 +-- .../MySQL-5.6.20-intel-2014b-clientonly.eb | 4 +-- .../MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb | 2 +- .../m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb | 6 ++-- .../easyconfigs/m/mc/mc-4.6.1-goolf-1.4.10.eb | 6 ++-- .../easyconfigs/m/mc/mc-4.6.1-ictce-4.0.6.eb | 6 ++-- .../easyconfigs/m/mc/mc-4.6.1-ictce-5.3.0.eb | 6 ++-- .../m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb | 6 ++-- .../m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb | 6 ++-- .../m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb | 10 +++---- .../m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb | 10 +++---- .../mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb | 6 ++-- .../m/mpiBLAST/mpiBLAST-1.6.0-goolf-1.4.10.eb | 6 ++-- .../m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb | 6 ++-- .../m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.2.0.eb | 6 ++-- .../m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.3.0.eb | 7 ++--- 54 files changed, 173 insertions(+), 172 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb index 9ced23daf9..e90e4b4187 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" -toolchain = {'name': 'goalf', 'version' : '1.1.0-no-OFED'} +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb index 5ab68f3355..74d5a36f68 100644 --- a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb @@ -32,7 +32,7 @@ dependencies = [ ('numpy', '1.7.1', versionsuffix), ] -options = {'modulename': name } +options = {'modulename': name} # specify that this asyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb index 79d3f53e5a..2f00cc2dbd 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -19,6 +19,6 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_ZIP] -dependencies = [('zlib','1.2.7')] +dependencies = [('zlib', '1.2.7')] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb index 8deb553751..ba3d36b9c7 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] -dependencies =[('Java', '1.7.0_10')] +dependencies = [('Java', '1.7.0_10')] import os license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'license.example.com') diff --git a/easybuild/easyconfigs/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb index 54d1c4d20b..e322ccb0af 100644 --- a/easybuild/easyconfigs/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb @@ -29,8 +29,8 @@ sources = ['mcl-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['http://micans.org/mcl/src/'] sanity_check_paths = { - 'files': ["bin/mcl"], - 'dirs': ["share"] - } + 'files': ["bin/mcl"], + 'dirs': ["share"] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-12.135-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MCL/MCL-12.135-goolf-1.4.10.eb index 0b7a65ab00..b1a95f4031 100644 --- a/easybuild/easyconfigs/m/MCL/MCL-12.135-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MCL/MCL-12.135-goolf-1.4.10.eb @@ -28,8 +28,8 @@ sources = ['mcl-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['http://micans.org/mcl/src/'] sanity_check_paths = { - 'files': ["bin/mcl"], - 'dirs': ["share"] - } + 'files': ["bin/mcl"], + 'dirs': ["share"] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.0.6.eb b/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.0.6.eb index b2dec05ab5..232ec42670 100644 --- a/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.0.6.eb @@ -29,8 +29,8 @@ sources = ['mcl-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['http://micans.org/mcl/src/'] sanity_check_paths = { - 'files': ["bin/mcl"], - 'dirs': ["share"] - } + 'files': ["bin/mcl"], + 'dirs': ["share"] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.1.13.eb b/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.1.13.eb index 26b2a9bb86..3edc17b8e9 100644 --- a/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-4.1.13.eb @@ -29,8 +29,8 @@ sources = ['mcl-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['http://micans.org/mcl/src/'] sanity_check_paths = { - 'files': ["bin/mcl"], - 'dirs': ["share"] - } + 'files': ["bin/mcl"], + 'dirs': ["share"] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-5.3.0.eb index b84227a558..0619f29465 100644 --- a/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-5.3.0.eb @@ -30,8 +30,8 @@ sources = ['mcl-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['http://micans.org/mcl/src/'] sanity_check_paths = { - 'files': ["bin/mcl"], - 'dirs': ["share"] - } + 'files': ["bin/mcl"], + 'dirs': ["share"] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb index 7efec1287d..939aae0af8 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb @@ -8,9 +8,10 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/'] +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/'] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] -dependencies =[('Java', '1.8.0_31')] +dependencies = [('Java', '1.8.0_31')] moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb index e0b5326bd6..29d916a9f4 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb @@ -8,9 +8,10 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/'] +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/'] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] -dependencies =[('Java', '1.8.0_31')] +dependencies = [('Java', '1.8.0_31')] moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-gimkl-2.11.5-32bitIDX.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-gimkl-2.11.5-32bitIDX.eb index 0d5b02189a..7ab7bcbfae 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-gimkl-2.11.5-32bitIDX.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-gimkl-2.11.5-32bitIDX.eb @@ -1,6 +1,6 @@ name = 'METIS' version = '5.1.0' -#default 32-bit IDTYPEWIDTH, no patch used +# default 32-bit IDTYPEWIDTH, no patch used versionsuffix = '-32bitIDX' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a-32bitIDX.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a-32bitIDX.eb index d937f515a8..b404314c3e 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a-32bitIDX.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a-32bitIDX.eb @@ -1,6 +1,6 @@ name = 'METIS' version = '5.1.0' -#default 32-bit IDTYPEWIDTH, no patch used +# default 32-bit IDTYPEWIDTH, no patch used versionsuffix = '-32bitIDX' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015b-32bitIDX.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015b-32bitIDX.eb index c9b8dd3d53..9810c2e1f2 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015b-32bitIDX.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015b-32bitIDX.eb @@ -1,6 +1,6 @@ name = 'METIS' version = '5.1.0' -#default 32-bit IDTYPEWIDTH, no patch used +# default 32-bit IDTYPEWIDTH, no patch used versionsuffix = '-32bitIDX' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' diff --git a/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb b/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb index e59bc43670..9077537b1d 100644 --- a/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb +++ b/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb @@ -19,7 +19,7 @@ source_urls = ['https://github.com/eturro/mmseq/archive/'] sources = ['%(version)s.tar.gz'] sanity_check_paths = { - 'files': ["bin/mmseq-linux", "bin/bam2hits-linux", "bin/extract_transcripts-linux" ], + 'files': ["bin/mmseq-linux", "bin/bam2hits-linux", "bin/extract_transcripts-linux"], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.0.2-intel-2015a.eb b/easybuild/easyconfigs/m/MPC/MPC-1.0.2-intel-2015a.eb index 6763501bb4..191f33c725 100644 --- a/easybuild/easyconfigs/m/MPC/MPC-1.0.2-intel-2015a.eb +++ b/easybuild/easyconfigs/m/MPC/MPC-1.0.2-intel-2015a.eb @@ -25,6 +25,6 @@ runtest = 'check' sanity_check_paths = { 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], 'dirs': [] - } +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb index c0d8ea5a48..d500bd8bd3 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb @@ -14,11 +14,11 @@ sources = [SOURCELOWER_TAR_BZ2] patches = ['MPFR_ictce_remove-deprecated-mp.patch'] -gmp='GMP' -gmpver='6.0.0a' -versionsuffix='-%s-%s' % (gmp,gmpver) +gmp = 'GMP' +gmpver = '6.0.0a' +versionsuffix = '-%s-%s' % (gmp, gmpver) -#GMP does not compile correctly with ICC on Haswell architecture +# GMP does not compile correctly with ICC on Haswell architecture dependencies = [(gmp, gmpver, '', ('GCC', '4.9.2'))] runtest = 'check' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb index 4afd6ab5dc..ed339c9c95 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb @@ -14,11 +14,11 @@ sources = [SOURCELOWER_TAR_BZ2] patches = ['MPFR_ictce_remove-deprecated-mp.patch'] -gmp='GMP' -gmpver='6.0.0a' -versionsuffix='-%s-%s' % (gmp,gmpver) +gmp = 'GMP' +gmpver = '6.0.0a' +versionsuffix = '-%s-%s' % (gmp, gmpver) -#GMP does not compile correctly with ICC on Haswell architecture +# GMP does not compile correctly with ICC on Haswell architecture dependencies = [(gmp, gmpver, '', ('GCC', '4.9.2'))] runtest = 'check' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-goolf-1.4.10.eb index 0ce77f4dfa..f41c1f7758 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'MUSCLE' version = '3.8.31' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-ictce-5.5.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-ictce-5.5.0.eb index ebd4dcac83..2998cc688a 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-ictce-5.5.0.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'MUSCLE' version = '3.8.31' diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb index 94a699dcb4..cd0624726e 100644 --- a/easybuild/easyconfigs/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb @@ -29,7 +29,7 @@ dependencies = [('GTI', '1.2.0')] builddependencies = [('CMake', '2.8.10.2')] -configopts = ' -DCMAKE_BUILD_TYPE=Release -DGTI_INSTALL_PREFIX=${EBROOTGTI}' +configopts = ' -DCMAKE_BUILD_TYPE=Release -DGTI_INSTALL_PREFIX=${EBROOTGTI}' sanity_check_paths = { 'files': ["bin/mustrun", "include/mustConfig.h"], diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb index 53cdff914e..22a7f9f02e 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb @@ -13,12 +13,12 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] builddependencies = [('Bison', '2.5')] -rdma_type = "gen2" # 'gen2' or 'udapl' +rdma_type = "gen2" # 'gen2' or 'udapl' -## enable building of MPE routines +# enable building of MPE routines withmpe = True -## parallel build tends to fail +# parallel build tends to fail parallel = 1 moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb index 6e95bf258a..8d84225619 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb @@ -6,14 +6,14 @@ version = '10.0.21' homepage = 'https://mariadb.org/' description = """MariaDB An enhanced, drop-in replacement for MySQL.""" -toolchain = {'name': 'GNU' , 'version': '4.9.3-2.25'} +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://downloads.mariadb.org/f/mariadb-10.0.21/source/'] dependencies = [ ('zlib', '1.2.8'), - ('ncurses' , '5.9'), + ('ncurses', '5.9'), ('libedit', '20150325'), ('libxml2', '2.9.2'), ] diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb index ec2fa1dac8..9e7b790697 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb @@ -6,7 +6,7 @@ version = '5.5.29' homepage = 'https://mariadb.org/' description = """MariaDB An enhanced, drop-in replacement for MySQL.""" -toolchain = {'name': 'ictce' , 'version': '4.1.13'} +toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCELOWER_TAR_GZ] @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['define_unreachable_builtin.patch'] dependencies = [ - ('ncurses' , '5.9'), + ('ncurses', '5.9'), ('libreadline', '6.2'), ] diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb index 791d375531..f2baa1d123 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb @@ -22,8 +22,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['bin/hg'], - 'dirs': ['lib/python%s/site-packages/mercurial' % pythonshortversion] - } + 'files': ['bin/hg'], + 'dirs': ['lib/python%s/site-packages/mercurial' % pythonshortversion] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 9fed17ec40..2c72b2e6f5 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -49,7 +49,7 @@ dependencies = [ ('eudev', '3.0'), ] -#Use the os provided libudev or the EB provided eudev +# Use the os provided libudev or the EB provided eudev #osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index ddd54508d0..1a69d47441 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -46,7 +46,7 @@ dependencies = [ ('eudev', '3.0'), ] -#Use the os provided libudev or the EB provided eudev +# Use the os provided libudev or the EB provided eudev #osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 3e51cbc3cf..9d960059a5 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -45,7 +45,7 @@ dependencies = [ ('eudev', '3.1.2'), ] -#Use the os provided libudev or the EB provided eudev +# Use the os provided libudev or the EB provided eudev #osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index 5bc1c00683..73b355c719 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -45,7 +45,7 @@ dependencies = [ ('eudev', '3.1.5'), ] -#Use the os provided libudev or the EB provided eudev +# Use the os provided libudev or the EB provided eudev #osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 071c95fba2..0cd27019ac 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -21,22 +21,22 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % ('Python', pythonver) dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('makedepend', '1.0.4'), - ('Python', pythonver), - ('libxml2', '2.8.0', versionsuffix), - ('glproto', '1.4.16'), - ('libdrm', '2.4.27') - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('makedepend', '1.0.4'), + ('Python', pythonver), + ('libxml2', '2.8.0', versionsuffix), + ('glproto', '1.4.16'), + ('libdrm', '2.4.27') +] osdependencies = [ - 'libX11-devel', # Xlibs.h - 'xorg-x11-proto-devel', # X.h, glproto, xproto - 'libXdamage-devel', - 'libXext-devel', - 'libXfixes-devel', - ] + 'libX11-devel', # Xlibs.h + 'xorg-x11-proto-devel', # X.h, glproto, xproto + 'libXdamage-devel', + 'libXext-devel', + 'libXfixes-devel', +] configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index 3fa0d3f751..a724cb0c52 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -20,22 +20,22 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % ('Python', pythonver) dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('makedepend', '1.0.4'), - ('Python', pythonver), - ('libxml2', '2.8.0', versionsuffix), - ('glproto', '1.4.16'), - ('libdrm', '2.4.27') - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('makedepend', '1.0.4'), + ('Python', pythonver), + ('libxml2', '2.8.0', versionsuffix), + ('glproto', '1.4.16'), + ('libdrm', '2.4.27') +] osdependencies = [ - 'libX11-devel', # Xlibs.h - 'xorg-x11-proto-devel', # X.h, glproto, xproto - 'libXdamage-devel', - 'libXext-devel', - 'libXfixes-devel', - ] + 'libX11-devel', # Xlibs.h + 'xorg-x11-proto-devel', # X.h, glproto, xproto + 'libXdamage-devel', + 'libXext-devel', + 'libXfixes-devel', +] configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb index 864dc0bea3..70a2816d6b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb @@ -21,22 +21,22 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % ('Python', pythonver) dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('makedepend', '1.0.4'), - ('Python', pythonver), - ('libxml2', '2.8.0', versionsuffix), - ('glproto', '1.4.16'), - ('libdrm', '2.4.27') - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('makedepend', '1.0.4'), + ('Python', pythonver), + ('libxml2', '2.8.0', versionsuffix), + ('glproto', '1.4.16'), + ('libdrm', '2.4.27') +] osdependencies = [ - 'libX11-devel', # Xlibs.h - 'xorg-x11-proto-devel', # X.h, glproto, xproto - 'libXdamage-devel', - 'libXext-devel', - 'libXfixes-devel', - ] + 'libX11-devel', # Xlibs.h + 'xorg-x11-proto-devel', # X.h, glproto, xproto + 'libXdamage-devel', + 'libXext-devel', + 'libXfixes-devel', +] configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb index 4ae1b34911..0371483898 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb @@ -21,13 +21,13 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % ('Python', pythonver) dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('makedepend', '1.0.4'), - ('Python', pythonver), - ('libxml2', '2.8.0', versionsuffix), - ('glproto', '1.4.16'), - ('libdrm', '2.4.27') + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('makedepend', '1.0.4'), + ('Python', pythonver), + ('libxml2', '2.8.0', versionsuffix), + ('glproto', '1.4.16'), + ('libdrm', '2.4.27') ] osdependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 8f7b8fd9e1..7e87cc2bd4 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -22,22 +22,22 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % ('Python', pythonver) dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('makedepend', '1.0.4'), - ('Python', pythonver), - ('libxml2', '2.8.0', versionsuffix), - ('glproto', '1.4.16'), - ('libdrm', '2.4.27') - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('makedepend', '1.0.4'), + ('Python', pythonver), + ('libxml2', '2.8.0', versionsuffix), + ('glproto', '1.4.16'), + ('libdrm', '2.4.27') +] osdependencies = [ - 'libX11-devel', # Xlibs.h - 'xorg-x11-proto-devel', # X.h, glproto, xproto - 'libXdamage-devel', - 'libXext-devel', - 'libXfixes-devel', - ] + 'libX11-devel', # Xlibs.h + 'xorg-x11-proto-devel', # X.h, glproto, xproto + 'libXdamage-devel', + 'libXext-devel', + 'libXfixes-devel', +] configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" diff --git a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb index 5ee01321f8..3af2bae350 100644 --- a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb @@ -32,8 +32,8 @@ files_to_copy = ["bin", "docs"] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["allelicmeth", "amrfinder", "amrtester", "bsrate", "dmr", - "duplicate-remover", "hmr", "hmr_plant", "lc_approx","levels", - "merge-bsrate", "merge-methcounts", "methcounts","methdiff", + "duplicate-remover", "hmr", "hmr_plant", "lc_approx", "levels", + "merge-bsrate", "merge-methcounts", "methcounts", "methdiff", "methstates", "pmd", "rmapbs", "rmapbs-pe", "roimethstat", "to-mr"]], 'dirs': ['docs'], } diff --git a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb index 546db6338a..3f4fca5919 100644 --- a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb +++ b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb @@ -32,8 +32,8 @@ files_to_copy = ["bin", "docs"] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["allelicmeth", "amrfinder", "amrtester", "bsrate", "dmr", - "duplicate-remover", "hmr", "hmr_plant", "lc_approx","levels", - "merge-bsrate", "merge-methcounts", "methcounts","methdiff", + "duplicate-remover", "hmr", "hmr_plant", "lc_approx", "levels", + "merge-bsrate", "merge-methcounts", "methcounts", "methdiff", "methstates", "pmd", "rmapbs", "rmapbs-pe", "roimethstat", "to-mr"]], 'dirs': ['docs'], } diff --git a/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb index 33a900aecd..23f121832f 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb @@ -15,9 +15,9 @@ source_urls = ['ftp://ftp.cmbi.ru.nl/pub/molgraph/molden'] buildopts = 'CC="$CC" FC="$F90" molden' -files_to_copy = [(['molden'],'bin'), 'CopyRight', 'README', 'REGISTER'] +files_to_copy = [(['molden'], 'bin'), 'CopyRight', 'README', 'REGISTER'] -sanity_check_paths={ +sanity_check_paths = { 'files': ['bin/molden', 'README', 'REGISTER'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb index aa2cc82aa9..5da93a4bfe 100644 --- a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'MotEvo' version = '1.02' diff --git a/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2015b.eb b/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2015b.eb index 1640a34512..37117a4be0 100644 --- a/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2015b.eb +++ b/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2015b.eb @@ -18,8 +18,8 @@ builddependencies = [('CMake', '3.4.0')] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ackley', 'eggboxC', 'eggboxC++', 'gaussian', 'gauss_shell', 'himmelblau', 'obj_detect', 'rosenbrock']] + - ['lib/lib%s' % x for x in ['multinest.a', 'multinest_mpi.a', 'multinest_mpi.%s' % SHLIB_EXT, 'multinest.%s' % SHLIB_EXT]] + - ['include/multinest.h'], + ['lib/lib%s' % x for x in ['multinest.a', 'multinest_mpi.a', 'multinest_mpi.%s' % SHLIB_EXT, 'multinest.%s' % SHLIB_EXT]] + + ['include/multinest.h'], 'dirs': ['modules'], } diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb index b14d94df84..50dda691db 100644 --- a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb @@ -8,7 +8,7 @@ homepage = 'http://www.mysql.com/' description = """MySQL is (as of March 2014) the world's second most widely used open-source relational database management system (RDBMS).""" -#http://dev.mysql.com/get/Downloads/MySQL-5.6/mysql-5.6.20.tar.gz +# http://dev.mysql.com/get/Downloads/MySQL-5.6/mysql-5.6.20.tar.gz source_urls = ['http://dev.mysql.com/get/Downloads/MySQL-%(version_major_minor)s/'] sources = [SOURCELOWER_TAR_GZ] @@ -20,7 +20,7 @@ dependencies = [ ('libevent', '2.0.21'), ('libreadline', '6.3'), ('zlib', '1.2.8'), -# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb index bae1276ac2..6b59f1b4bf 100644 --- a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), ('libedit', '20150325'), ('zlib', '1.2.8'), -# ('OpenSSL', '1.0.1p'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb index ecfb57dda3..a05d906924 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb @@ -24,8 +24,8 @@ source_urls = ['http://www.ibiblio.org/pub/Linux/utils/file/managers/mc/'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/mc'], - 'dirs': [] - } + 'files': ['bin/mc'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mc/mc-4.6.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mc/mc-4.6.1-goolf-1.4.10.eb index 438ec80d0e..87c8b17b1f 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.6.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.6.1-goolf-1.4.10.eb @@ -23,8 +23,8 @@ source_urls = ['http://www.ibiblio.org/pub/Linux/utils/file/managers/mc/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['bin/mc'], - 'dirs': [] - } + 'files': ['bin/mc'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-4.0.6.eb index ec94a5a333..9830f37904 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-4.0.6.eb @@ -24,8 +24,8 @@ source_urls = ['http://www.ibiblio.org/pub/Linux/utils/file/managers/mc/'] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/mc'], - 'dirs': [] - } + 'files': ['bin/mc'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-5.3.0.eb index f390a24559..7047839f2d 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-5.3.0.eb @@ -25,8 +25,8 @@ source_urls = ['http://www.ibiblio.org/pub/Linux/utils/file/managers/mc/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/mc'], - 'dirs': [] - } + 'files': ['bin/mc'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb index f389f06807..13a13c28d8 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb @@ -25,9 +25,9 @@ parallel = 1 buildopts = ' CC="$CC"' files_to_copy = [ - (['mdtest'], 'bin'), - "README", - "COPYRIGHT", + (['mdtest'], 'bin'), + "README", + "COPYRIGHT", ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb index 9444c160fd..fdcf4609af 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb @@ -25,9 +25,9 @@ parallel = 1 buildopts = ' CC="$CC"' files_to_copy = [ - (['mdtest'], 'bin'), - "README", - "COPYRIGHT", + (['mdtest'], 'bin'), + "README", + "COPYRIGHT", ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb index a7dcc82e62..6a4c7c8893 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb @@ -25,11 +25,11 @@ parallel = 1 buildopts = ' CC="$CC"' files_to_copy = [ - (['mdtest'], 'bin'), - (['mdtest.1'], 'man/man1'), - "README", - "RELEASE_LOG", - "scripts" + (['mdtest'], 'bin'), + (['mdtest.1'], 'man/man1'), + "README", + "RELEASE_LOG", + "scripts" ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb index 2085a445de..31e12db3cc 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb @@ -25,11 +25,11 @@ parallel = 1 buildopts = ' CC="$CC"' files_to_copy = [ - (['mdtest'], 'bin'), - (['mdtest.1'], 'man/man1'), - "README", - "RELEASE_LOG", - "scripts" + (['mdtest'], 'bin'), + (['mdtest.1'], 'man/man1'), + "README", + "RELEASE_LOG", + "scripts" ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb index dd7cd82090..b4ca6871ed 100644 --- a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb @@ -34,9 +34,9 @@ patches = ['mpiBLAST_disable-ncbi-X11-apps.patch'] buildopts = 'ncbi all' sanity_check_paths = { - 'files': ["bin/mpiblast"], - 'dirs': [] - } + 'files': ["bin/mpiblast"], + 'dirs': [] +} parallel = 1 diff --git a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goolf-1.4.10.eb index 7996ccccb1..273a8c9d5f 100644 --- a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goolf-1.4.10.eb @@ -33,9 +33,9 @@ patches = ['mpiBLAST_disable-ncbi-X11-apps.patch'] buildopts = 'ncbi all' sanity_check_paths = { - 'files': ["bin/mpiblast"], - 'dirs': [] - } + 'files': ["bin/mpiblast"], + 'dirs': [] +} parallel = 1 diff --git a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb index ed6214c594..f14049a15f 100644 --- a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb @@ -34,9 +34,9 @@ patches = ['mpiBLAST_disable-ncbi-X11-apps.patch'] buildopts = 'ncbi all' sanity_check_paths = { - 'files': ["bin/mpiblast"], - 'dirs': [] - } + 'files': ["bin/mpiblast"], + 'dirs': [] +} parallel = 1 diff --git a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.2.0.eb b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.2.0.eb index 61e20d4024..1bb43bc486 100644 --- a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.2.0.eb @@ -34,9 +34,9 @@ patches = ['mpiBLAST_disable-ncbi-X11-apps.patch'] buildopts = 'ncbi all' sanity_check_paths = { - 'files': ["bin/mpiblast"], - 'dirs': [] - } + 'files': ["bin/mpiblast"], + 'dirs': [] +} parallel = 1 diff --git a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.3.0.eb b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.3.0.eb index 7a012e8c9b..58c91d09bc 100644 --- a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.3.0.eb @@ -23,7 +23,6 @@ description = """mpiBLAST is a freely available, open-source, parallel implement mpiBLAST is also portable across many different platforms and operating systems.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'usempi': True} @@ -36,9 +35,9 @@ patches = ['mpiBLAST_disable-ncbi-X11-apps.patch'] buildopts = 'ncbi all' sanity_check_paths = { - 'files': ["bin/mpiblast"], - 'dirs': [] - } + 'files': ["bin/mpiblast"], + 'dirs': [] +} parallel = 1 -- GitLab From 62c3145818af1fe8990393b588edf7b01e305900 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:49:23 +0100 Subject: [PATCH 0275/2133] Style fixes with autopep8: n Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb | 6 +++--- .../NCBI-Toolkit/NCBI-Toolkit-9.0.0-goolf-1.4.10.eb | 6 +++--- .../n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-ictce-4.0.6.eb | 12 ++++++------ easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb | 2 +- .../n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb | 2 +- .../n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb | 2 +- easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb | 2 +- .../easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb | 2 +- ....revision2-intel-2014b-2013-10-17-Python-2.7.8.eb | 2 +- ...ision26243-intel-2014b-2014-09-10-Python-2.7.8.eb | 2 +- ...sion26243-intel-2015b-2014-09-10-Python-2.7.10.eb | 2 +- .../n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 6 +++--- .../ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 6 +++--- .../ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 6 +++--- .../n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb | 6 +++--- .../n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb | 6 +++--- .../n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 6 +++--- .../n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 6 +++--- .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 6 +++--- .../n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 6 +++--- .../n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 6 +++--- .../n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 6 +++--- .../n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 6 +++--- .../n/ncurses/ncurses-5.9-gompi-1.5.16.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goolf-1.7.20.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 6 +++--- .../n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 6 +++--- .../n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 6 +++--- .../n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-5.4.0.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 6 +++--- .../n/ncurses/ncurses-5.9-intel-2014.06.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 6 +++--- .../n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 6 +++--- .../n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 6 +++--- .../n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb | 6 +++--- .../n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb | 6 +++--- .../n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb | 6 +++--- .../n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb | 2 +- .../easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb | 2 +- .../n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb | 2 +- .../n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb | 4 ++-- .../easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb | 1 - .../easyconfigs/n/netloc/netloc-0.5-GCC-4.8.3.eb | 2 +- .../n/netloc/netloc-0.5-gcccuda-2.6.10.eb | 2 +- .../n/nettle/nettle-2.6-goalf-1.1.0-no-OFED.eb | 3 ++- .../easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb | 3 ++- .../n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb | 3 ++- .../n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb | 2 +- .../easyconfigs/n/ns/ns-2.35-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/n/ns/ns-2.35-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/n/ns/ns-2.35-ictce-5.3.0.eb | 2 +- .../numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb | 2 +- .../numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb | 12 ++++++------ .../numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 12 ++++++------ 84 files changed, 216 insertions(+), 214 deletions(-) diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb index c5936a51c7..c4688cb405 100644 --- a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb @@ -34,8 +34,8 @@ dependencies = [('Boost', '1.51.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' sanity_check_paths = { - 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], - 'dirs': [] - } + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goolf-1.4.10.eb index b889e93516..b11e19a831 100644 --- a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goolf-1.4.10.eb @@ -33,8 +33,8 @@ dependencies = [('Boost', '1.51.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' sanity_check_paths = { - 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], - 'dirs': [] - } + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-ictce-4.0.6.eb b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-ictce-4.0.6.eb index af1e8856cf..7d8e37d42d 100644 --- a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-ictce-4.0.6.eb @@ -29,17 +29,17 @@ sources = ['ncbi_cxx--%s.tar.gz' % src_ver] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/%s' % src_ver] patches = [ - 'NCBI-Toolkit_make-install-fix.patch', - 'NCBI-Toolkit-9.0.0_ictce-fixes.patch' - ] + 'NCBI-Toolkit_make-install-fix.patch', + 'NCBI-Toolkit-9.0.0_ictce-fixes.patch' +] dependencies = [('Boost', '1.51.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' sanity_check_paths = { - 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], - 'dirs': [] - } + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb index 91425320d2..98cce01c87 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb @@ -22,7 +22,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/nc%s' % x for x in ['ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename']] + - ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb index b849d1d7cc..b0e417a669 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb @@ -38,7 +38,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/nc%s' % x for x in ('ap', 'ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + - ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb index 3f22d89443..cb8f9487e8 100644 --- a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb @@ -6,7 +6,7 @@ homepage = 'http://www.nemo-ocean.eu/' description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for oceanographic research, operational oceanography seasonal forecast and climate studies.""" -toolchain = {'name': 'ictce','version': '6.1.5'} +toolchain = {'name': 'ictce', 'version': '6.1.5'} toolchainopts = {'opt': False, 'optarch': False} # authenticated SVN access required diff --git a/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb b/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb index 6fc9490675..4804968338 100644 --- a/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb +++ b/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb @@ -12,7 +12,7 @@ description = """NEdit is a multi-purpose text editor for the X Window System, toolchain = {'version': 'dummy', 'name': 'dummy'} subdir = '_'.join(version.split('-')[0].split('.')) -source_urls = ['http://ftp.vim.org/editors/NEdit/v%s/executables' % subdir ] +source_urls = ['http://ftp.vim.org/editors/NEdit/v%s/executables' % subdir] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] modextrapaths = { diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb index 292a68dda4..6a655087df 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb @@ -9,7 +9,7 @@ description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fa dimensions, of arbitrary input size, and of complex data.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = { 'dynamic': True } +toolchainopts = {'dynamic': True} source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.3.revision2-intel-2014b-2013-10-17-Python-2.7.8.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.3.revision2-intel-2014b-2013-10-17-Python-2.7.8.eb index 0e843ffa38..acc8037f03 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.3.revision2-intel-2014b-2013-10-17-Python-2.7.8.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.3.revision2-intel-2014b-2013-10-17-Python-2.7.8.eb @@ -12,7 +12,7 @@ description = """NWChem aims to provide its users with computational chemistry t toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'i8': True} -source_urls = [ 'http://www.nwchem-sw.org/download.php?f='] +source_urls = ['http://www.nwchem-sw.org/download.php?f='] verdate = '2013-10-17' sources = ['Nwchem-%s-src.%s.tar.gz' % (version, verdate)] diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb index 2eefc9a7f3..ec0a191ad4 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb @@ -12,7 +12,7 @@ description = """NWChem aims to provide its users with computational chemistry t toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'i8': True} -source_urls = [ 'http://www.nwchem-sw.org/download.php?f='] +source_urls = ['http://www.nwchem-sw.org/download.php?f='] verdate = '2014-09-10' sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.10.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.10.eb index 918b9ffd9a..cfb063858e 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.10.eb @@ -12,7 +12,7 @@ description = """NWChem aims to provide its users with computational chemistry t toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'i8': True} -source_urls = [ 'http://www.nwchem-sw.org/download.php?f='] +source_urls = ['http://www.nwchem-sw.org/download.php?f='] verdate = '2014-09-10' sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb index 4ef7a218bc..cf94b3ef4d 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb @@ -20,7 +20,7 @@ r = 'R' rver = '3.0.2' rversuf = '-bare' -versionsuffix = '-%s-%s%s' % (r, rver,rversuf) +versionsuffix = '-%s-%s%s' % (r, rver, rversuf) dependencies = [ (r, rver, rversuf), diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 634fda5b4d..701d4f5b32 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 4f21474dcf..5039753d61 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index a71c6aab72..19a447fb27 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index f2a6bbb76a..fba7788bef 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 5ef3e822ad..0af76e5309 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 96cc600747..f539996103 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index a1409a10e6..266e0372ef 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb index 6b7bb1c347..6aaa93881b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb index 01680ab5b7..376ac3284c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb index 6f00fdbd51..b4e88ed329 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index 37a2fff35a..597f627fd5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index 96e1f45472..18b80dd5b4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 5dd295c39e..5e59d7a015 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 3071876ad2..0e4f38f6b4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index c5e4c7e93d..e71416ed21 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb index a769a56170..7d22fac6d5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 5125329966..f71a1ebf66 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb index 82fd4d66d0..7496dc385d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index 7278bb4ccf..6fba11778b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index 37d7e04809..f3025721f3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index cff4af273d..a3e060e522 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index b529181479..e5277365c6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index aaa5b2bd78..dcacd6eb8f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index f8ee92d094..4438ab7164 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -30,9 +30,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 9936cdbc6c..5bf835f0f9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index b5428d27b0..b8cefe2085 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 21128a21c5..bd62e235e7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb index e272a823d6..c1ef51469e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index fa8d19afbb..a193ec004c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index cdf8cdb5ce..95a00cbe48 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb index 9a1708ba34..676d1b38e4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 36b5053e62..fd2250632c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 292cec33e2..1862eb1eb3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 0b4bbba9ad..5dc04b26ca 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index b5099d8795..4ebf61d594 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 94e44f7817..8e3894ae7f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index b1c1a88d75..1871a9bd84 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index fed58a89dd..67488363dc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index bf996a362f..278feeefd1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.4.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.4.0.eb index 3c9a948aef..63a4e678bd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.4.0.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index 671b5796ac..acf30f2ceb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index 61118f9005..d70ebf22fe 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index 278cc8d64a..19ed9c2c9e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -29,9 +29,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 38c7d07988..eba66cce94 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb index d67fc45cbf..252f009474 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 9fa751952c..176634e08b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 24097805bc..3d58c86438 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 115d1bd981..f18c6b0cd2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index e4351873f4..56c27e1dd1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 529b47259f..2360219b0e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index dd70b0800a..16f90cd0e9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb index eab9da36db..2ec6dcb703 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb index 4012f0e69b..4f00fe676a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb @@ -25,9 +25,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb index 6029357e96..83fce4b28a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb @@ -25,9 +25,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb index 852b0df6bb..e9bc3f20c2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb @@ -25,9 +25,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb index 1cf87a93d6..47fa2b79af 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb @@ -7,7 +7,7 @@ description = """NetCDF (network Common Data Form) is a set of software librarie scientific data.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'pic':True} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [ diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb index 2e121dba81..36ab674b3d 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb @@ -7,7 +7,7 @@ description = """NetCDF (network Common Data Form) is a set of software librarie scientific data.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'pic':True} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [ diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb index a518b2a451..46676df71b 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb @@ -7,7 +7,7 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" -toolchain = {'name':'ictce','version':'4.1.13'} +toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb index 9caf198302..e5e9ad231d 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb @@ -6,8 +6,8 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" -toolchain = {'name':'ictce','version':'4.1.13'} -toolchainopts = {'pic':True} +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [ diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb index f0b637b12c..1b6d9c1fa7 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb @@ -35,4 +35,3 @@ configopts = [ ] moduleclass = 'data' - diff --git a/easybuild/easyconfigs/n/netloc/netloc-0.5-GCC-4.8.3.eb b/easybuild/easyconfigs/n/netloc/netloc-0.5-GCC-4.8.3.eb index 26ee8e7734..f7783bd576 100644 --- a/easybuild/easyconfigs/n/netloc/netloc-0.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/netloc/netloc-0.5-GCC-4.8.3.eb @@ -20,6 +20,6 @@ dependencies = [ ] configopts = '--with-hwloc=$EBROOTHWLOC ' # hwloc support -configopts += '--with-jansson=$EBROOTJANSSON ' # jansson support +configopts += '--with-jansson=$EBROOTJANSSON ' # jansson support moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb b/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb index 71e8c66169..e1ffe4c74f 100644 --- a/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb @@ -17,7 +17,7 @@ dependencies = [ ] configopts = '--with-hwloc=$EBROOTHWLOC ' # hwloc support -configopts += '--with-jansson=$EBROOTJANSSON ' # jansson support +configopts += '--with-jansson=$EBROOTJANSSON ' # jansson support # fi. http://www.open-mpi.org/software/netloc/v0.5/downloads/netloc-0.5.tar.gz source_urls = [homepage + '/v%(version_major_minor)s/downloads'] diff --git a/easybuild/easyconfigs/n/nettle/nettle-2.6-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/nettle/nettle-2.6-goalf-1.1.0-no-OFED.eb index 7b56d0898a..19f109d73f 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-2.6-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-2.6-goalf-1.1.0-no-OFED.eb @@ -15,7 +15,8 @@ dependencies = [('GMP', '5.0.5')] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb index d09168b7c8..afeba6c842 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb @@ -15,7 +15,8 @@ dependencies = [('GMP', '5.0.5')] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb index d17a6ef2c2..264418e53b 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb @@ -20,7 +20,8 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb b/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb index 51c10e822d..0a34435fbe 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb @@ -16,7 +16,7 @@ sources = ['node-v%(version)s.tar.gz'] source_urls = ['http://nodejs.org/dist/v%(version)s/'] -dependencies = [('Python','2.7.5')] +dependencies = [('Python', '2.7.5')] sanity_check_paths = { 'files': ["bin/node", "bin/npm", ], diff --git a/easybuild/easyconfigs/n/ns/ns-2.35-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ns/ns-2.35-goalf-1.1.0-no-OFED.eb index 174f9bf7e2..29818dfb05 100644 --- a/easybuild/easyconfigs/n/ns/ns-2.35-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ns/ns-2.35-goalf-1.1.0-no-OFED.eb @@ -20,7 +20,7 @@ dependencies = [ ('Tcl', tcl_ver), ('Tk', tcl_ver), ('otcl', '1.14'), - ('tclcl' , '1.20'), + ('tclcl', '1.20'), ] configopts = "--with-otcl=$EBROOTOTCL --with-tcl=$EBROOTTCL --with-tcl-ver=$EBVERSIONTCL " diff --git a/easybuild/easyconfigs/n/ns/ns-2.35-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ns/ns-2.35-goolf-1.4.10.eb index 057d7763d5..860b1cd2b3 100644 --- a/easybuild/easyconfigs/n/ns/ns-2.35-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ns/ns-2.35-goolf-1.4.10.eb @@ -22,7 +22,7 @@ dependencies = [ ('Tcl', tcl_ver), ('Tk', tcl_ver), ('otcl', '1.14'), - ('tclcl' , '1.20'), + ('tclcl', '1.20'), ] configopts = "--with-otcl=$EBROOTOTCL --with-tcl=$EBROOTTCL --with-tcl-ver=$EBVERSIONTCL " diff --git a/easybuild/easyconfigs/n/ns/ns-2.35-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ns/ns-2.35-ictce-5.3.0.eb index ded8fdd51c..ddad23bdff 100644 --- a/easybuild/easyconfigs/n/ns/ns-2.35-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ns/ns-2.35-ictce-5.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('Tcl', tcl_ver), ('Tk', tcl_ver), ('otcl', '1.14'), - ('tclcl' , '1.20'), + ('tclcl', '1.20'), ] configopts = "--with-otcl=$EBROOTOTCL --with-tcl=$EBROOTTCL --with-tcl-ver=$EBVERSIONTCL " diff --git a/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb index adad31edb7..402bb7ef96 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb @@ -14,7 +14,7 @@ exts_defaultclass = 'PythonPackage' exts_filter = ('python -c "import %(ext_name)s"', '') pyver = '2.7.11' -versionsuffix= '-Python-%s' % pyver +versionsuffix = '-Python-%s' % pyver dependencies = [ ('Python', pyver), ('LLVM', '3.6.2'), diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb index 4606d670d0..b59dd7b4f3 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb @@ -21,14 +21,14 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('HDF5', '1.8.10', '-gpfs') - ] + (python, pythonver), + ('HDF5', '1.8.10', '-gpfs') +] eggname = '%s-%s-py%s-linux-x86_64.egg' % (name, version, pythonshortver) sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/%s/%s' % (pythonshortver, eggname, name)] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/%s/%s' % (pythonshortver, eggname, name)] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 23dc125463..0f25285835 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -21,14 +21,14 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('HDF5', '1.8.10', '-gpfs') - ] + (python, pythonver), + ('HDF5', '1.8.10', '-gpfs') +] eggname = '%s-%s-py%s-linux-x86_64.egg' % (name, version, pythonshortver) sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/%s/%s' % (pythonshortver, eggname, name)] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/%s/%s' % (pythonshortver, eggname, name)] +} moduleclass = 'math' -- GitLab From f61858583f54deac39719e9a2f7c77ce217030d5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:51:37 +0100 Subject: [PATCH 0276/2133] Style fixes with autopep8: o Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../o/ORCA/ORCA-2_9_1-linux_x86-64.eb | 16 +++++++------- .../ORCA-3_0_0-linux_x86-64_openmpi_165.eb | 16 +++++++------- .../ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb | 16 +++++++------- .../ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb | 16 +++++++------- .../ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb | 16 +++++++------- .../o/Oases/Oases-0.2.08-goolf-1.4.10.eb | 4 ++-- .../o/Oases/Oases-0.2.08-ictce-5.3.0.eb | 4 ++-- .../o/Oases/Oases-0.2.08-intel-2015a.eb | 2 +- ...-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 22 +++++++++---------- .../Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb | 22 +++++++++---------- .../Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb | 16 +++++++------- .../Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb | 16 +++++++------- .../OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb | 1 - .../OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb | 1 - .../o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb | 6 ++--- .../o/OpenCV/OpenCV-2.4.9-intel-2014b.eb | 6 ++--- ...enFOAM-Extend-3.0-goolf-1.4.10-20140227.eb | 2 +- .../OpenFOAM-Extend-3.1-gimkl-2.11.5.eb | 2 +- .../OpenFOAM-Extend-3.1-goolf-1.4.10.eb | 2 +- .../OpenFOAM-Extend-3.2-gimkl-2.11.5.eb | 2 +- .../o/OpenFOAM/OpenFOAM-2.0.1-goolf-1.4.10.eb | 4 ++-- .../o/OpenFOAM/OpenFOAM-2.0.1-ictce-6.1.5.eb | 4 ++-- .../OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb | 4 ++-- .../o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb | 4 ++-- .../o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb | 4 ++-- .../o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb | 4 ++-- .../o/OpenMD/OpenMD-2.2-ictce-7.1.2.eb | 2 +- .../o/OpenMD/OpenMD-2.2-intel-2014b.eb | 2 +- .../OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 2 +- .../OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 2 +- .../OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 4 ++-- .../OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 2 +- ...I-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb | 1 - 36 files changed, 115 insertions(+), 118 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index 76be1035a7..ae7ad64f4d 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -17,15 +17,15 @@ sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version dependencies = [('OpenMPI', '1.4.5', '-no-OFED', ('GCC', '4.6.3'))] sanity_check_paths = { - 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] - for y in ["", "_mpi"]] + \ - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ - ['orca', 'otool_cosmo'], + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca', 'otool_cosmo'], 'dirs': [], } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb index 3b66a977f7..1944afede8 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb @@ -18,15 +18,15 @@ sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] sanity_check_paths = { - 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] - for y in ["", "_mpi"]] + \ - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ - ['orca', 'otool_cosmo'], + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca', 'otool_cosmo'], 'dirs': [], } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb index c63048d89b..7c21787b12 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb @@ -20,15 +20,15 @@ sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] sanity_check_paths = { - 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] - for y in ["", "_mpi"]] + \ - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ - ['orca', 'otool_cosmo'], + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca', 'otool_cosmo'], 'dirs': [], } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb index 5a28bbce0d..4c7272b6aa 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb @@ -20,15 +20,15 @@ sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version dependencies = [('OpenMPI', openmpiversion, '-GCC-4.8.3')] sanity_check_paths = { - 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] - for y in ["", "_mpi"]] + \ - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ - ['orca', 'otool_cosmo'], + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca', 'otool_cosmo'], 'dirs': [], } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb index b63bd53de9..30c44ae3d4 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb @@ -20,15 +20,15 @@ sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] sanity_check_paths = { - 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] - for y in ["", "_mpi"]] + \ - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ - ['orca', 'otool_cosmo'], + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca', 'otool_cosmo'], 'dirs': [], } diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-goolf-1.4.10.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-goolf-1.4.10.eb index bc720f2ad4..d34174340c 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-goolf-1.4.10.eb @@ -33,9 +33,9 @@ source_urls = [ # listed make targets exclude 'doc' on purpose buildopts = ['VELVET_DIR=../velvet_%s cleanobj velvet oases' % velvetver] -files_to_copy = [(["oases"],'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.txt"] +files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.txt"] -sanity_check_paths={ +sanity_check_paths = { 'files': ["bin/oases", "LICENSE.txt", "README.txt"], 'dirs': ["data", "scripts", "src", "doc"] } diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-ictce-5.3.0.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-ictce-5.3.0.eb index 6954627e46..c408bf08bd 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-ictce-5.3.0.eb @@ -33,9 +33,9 @@ source_urls = [ # listed make targets exclude 'doc' on purpose buildopts = ['VELVET_DIR=../velvet_%s cleanobj velvet oases' % velvetver] -files_to_copy = [(["oases"],'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.txt"] +files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.txt"] -sanity_check_paths={ +sanity_check_paths = { 'files': ["bin/oases", "LICENSE.txt", "README.txt"], 'dirs': ["data", "scripts", "src", "doc"] } diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb index 9c657fda4a..ed69d393e3 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb @@ -36,7 +36,7 @@ parallel = 1 files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.txt"] -sanity_check_paths={ +sanity_check_paths = { 'files': ["bin/oases", "LICENSE.txt", "README.txt"], 'dirs': ["data", "scripts", "src", "doc"] } diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 15b1424e0d..575449dbbf 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -20,20 +20,20 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ("MDP", "3.3", versionsuffix), - ] + (python, pythonversion), + ("MDP", "3.3", versionsuffix), +] options = {'modulename': name} sanity_check_paths = { - 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in - [ - 'datasets', 'evaluation', 'examples', 'gradient', - 'nodes', 'parallel', 'tests', 'utils', - ] - ] - } + 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], + 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in + [ + 'datasets', 'evaluation', 'examples', 'gradient', + 'nodes', 'parallel', 'tests', 'utils', + ] + ] +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb index 95e21e11e7..2492882fca 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb @@ -21,20 +21,20 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ("MDP", "3.3", versionsuffix), - ] + (python, pythonversion), + ("MDP", "3.3", versionsuffix), +] options = {'modulename': name} sanity_check_paths = { - 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in - [ - 'datasets', 'evaluation', 'examples', 'gradient', - 'nodes', 'parallel', 'tests', 'utils', - ] - ] - } + 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], + 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in + [ + 'datasets', 'evaluation', 'examples', 'gradient', + 'nodes', 'parallel', 'tests', 'utils', + ] + ] +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb index e5cd3a5503..5d36b14860 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb @@ -20,17 +20,17 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ("MDP", "3.3", versionsuffix), - ] + (python, pythonversion), + ("MDP", "3.3", versionsuffix), +] options = {'modulename': name} sanity_check_paths = { - 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in - ['datasets', 'evaluation', 'examples', 'gradient', 'nodes', 'parallel', 'tests', 'utils'] - ] - } + 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], + 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in + ['datasets', 'evaluation', 'examples', 'gradient', 'nodes', 'parallel', 'tests', 'utils'] + ] +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb index a04089fb7d..8c7ce0f3fb 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb @@ -21,17 +21,17 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ("MDP", "3.3", versionsuffix), - ] + (python, pythonversion), + ("MDP", "3.3", versionsuffix), +] options = {'modulename': name} sanity_check_paths = { - 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in - ['datasets', 'evaluation', 'examples', 'gradient', 'nodes', 'parallel', 'tests', 'utils'] - ] - } + 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], + 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in + ['datasets', 'evaluation', 'examples', 'gradient', 'nodes', 'parallel', 'tests', 'utils'] + ] +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb index 97ff1d323e..3a54e8b3b2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb @@ -49,4 +49,3 @@ sanity_check_paths = { } moduleclass = 'numlib' - diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb index c678bbcc6e..870b4ca0ec 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb @@ -49,4 +49,3 @@ sanity_check_paths = { } moduleclass = 'numlib' - diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb index cda5e655b4..2faaba79a1 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - (java, javaver ,'', True), - ('ant', '1.9.3', '-%s-%s' % (java,javaver), True), + (java, javaver, '', True), + ('ant', '1.9.3', '-%s-%s' % (java, javaver), True), ('GLib', '2.40.0') ] @@ -64,7 +64,7 @@ configopts += '-DWITH_CUDA=OFF ' sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + - [ 'bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade'] ], + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb index 2db6adbc74..a10ea6a153 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - (java, javaver ,'', True), - ('ant', '1.9.3', '-%s-%s' % (java,javaver), True), + (java, javaver, '', True), + ('ant', '1.9.3', '-%s-%s' % (java, javaver), True), ('GLib', '2.40.0') ] @@ -64,7 +64,7 @@ configopts += '-DWITH_CUDA=OFF ' sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + - [ 'bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade'] ], + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb index a8de03c3a1..2a3beb3683 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb @@ -38,7 +38,7 @@ builddependencies = [ ('CMake', '2.8.12'), ] -prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) +prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) # too many builds in parallel actually slows down the build maxparallel = 4 diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb index 1fe977591c..06755b2786 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb @@ -40,7 +40,7 @@ builddependencies = [ ] -prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) +prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) # too many builds in parallel actually slows down the build maxparallel = 4 diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb index d845c52d8f..bebef71955 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb @@ -38,7 +38,7 @@ builddependencies = [ ('CMake', '2.8.12'), ] -prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) +prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) # too many builds in parallel actually slows down the build maxparallel = 4 diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb index e1a49bf5a0..4ddd37d882 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb @@ -40,7 +40,7 @@ builddependencies = [ ('CMake', '3.3.2'), ] -prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) +prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) # too many builds in parallel actually slows down the build maxparallel = 4 diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-goolf-1.4.10.eb index 9a63e57ca5..999d176f1a 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-goolf-1.4.10.eb @@ -16,8 +16,8 @@ sources = [ ] patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] + ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir + ] builddependencies = [('flex', '2.5.35')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-ictce-6.1.5.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-ictce-6.1.5.eb index 1020e0de70..65d62e3845 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-ictce-6.1.5.eb @@ -16,8 +16,8 @@ sources = [ ] patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] + ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir + ] builddependencies = [('flex', '2.5.38')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb index 47f96c354b..1ac57ee5f3 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb @@ -16,8 +16,8 @@ sources = [ ] patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] + ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir + ] builddependencies = [('flex', '2.5.35')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb index f8941ca15c..6d09f89ac2 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb @@ -16,8 +16,8 @@ sources = [ ] patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] + ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir + ] builddependencies = [('flex', '2.5.35')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb index 9a382ba0a0..9ab942e9ec 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb @@ -16,8 +16,8 @@ sources = [ ] patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] + ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir + ] builddependencies = [('flex', '2.5.35')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb index 3f4d83aade..0f4a8e96f8 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb @@ -16,8 +16,8 @@ sources = [ ] patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] + ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir + ] builddependencies = [('flex', '2.5.35')] diff --git a/easybuild/easyconfigs/o/OpenMD/OpenMD-2.2-ictce-7.1.2.eb b/easybuild/easyconfigs/o/OpenMD/OpenMD-2.2-ictce-7.1.2.eb index 2a9e21b8aa..9d61c22c09 100644 --- a/easybuild/easyconfigs/o/OpenMD/OpenMD-2.2-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/o/OpenMD/OpenMD-2.2-ictce-7.1.2.eb @@ -15,7 +15,7 @@ toolchainopts = {'usempi': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://openmd.org/releases'] -builddependencies = [('CMake' , '2.8.12')] +builddependencies = [('CMake', '2.8.12')] dependencies = [ ('Python', '2.7.8'), diff --git a/easybuild/easyconfigs/o/OpenMD/OpenMD-2.2-intel-2014b.eb b/easybuild/easyconfigs/o/OpenMD/OpenMD-2.2-intel-2014b.eb index 0ae135dd9d..1e5a20c6c0 100644 --- a/easybuild/easyconfigs/o/OpenMD/OpenMD-2.2-intel-2014b.eb +++ b/easybuild/easyconfigs/o/OpenMD/OpenMD-2.2-intel-2014b.eb @@ -15,7 +15,7 @@ toolchainopts = {'usempi': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://openmd.org/releases'] -builddependencies = [('CMake' , '2.8.12')] +builddependencies = [('CMake', '2.8.12')] dependencies = [ ('Python', '2.7.8'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index b176332293..417cf55b81 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'OpenMPI-1.6.5-vt_cupti_events.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', ] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index da09b2dec4..9701c637ed 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'OpenMPI-1.6.5-vt_cupti_events.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', ] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 192e287657..231057cda1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'OpenMPI-1.6.5-vt_cupti_events.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', ] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 6714cfb974..9c4d7ed9f6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'OpenMPI-1.6.5-vt_cupti_events.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', ] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index dcc884ec54..8b4682c1db 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'OpenMPI-1.6.5-vt_cupti_events.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', ] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index ef8df74e30..90ce3018de 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'OpenMPI-1.6.5-vt_cupti_events.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', ] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' @@ -23,7 +23,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] # needed for --with-openib -osdependencies = [('libibverbs-dev','libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index e9f2f244ec..46c5a002ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -18,7 +18,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] # needed for --with-openib -osdependencies = [('libibverbs-dev','libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index c6c6f0c9ab..341e512ab3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -29,4 +29,3 @@ sanity_check_paths = { } moduleclass = 'mpi' - -- GitLab From 9490716e9a66a984507aa6ec8ca11004eafebf75 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:52:33 +0100 Subject: [PATCH 0277/2133] Style fixes with autopep8: p Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- ...-3.3-p2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 18 +++++++++--------- .../PETSc-3.3-p2-ictce-4.0.6-Python-2.7.3.eb | 18 +++++++++--------- .../PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb | 18 +++++++++--------- .../p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb | 2 +- .../p/PLINK/PLINK-1.07-ictce-5.3.0.eb | 2 +- .../p/PLINK/PLINK-1.07-ictce-6.2.5.eb | 2 +- .../p/PRACE/PRACE-20130605-goolf-1.4.10.eb | 2 +- .../p/PRACE/PRACE-20130605-ictce-5.3.0.eb | 2 +- .../p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb | 2 +- ...0814-intel-2015a-mt-maxam7-Python-2.7.10.eb | 2 +- .../p/Pango/Pango-1.36.7-intel-2014b.eb | 16 ++++++++-------- .../p/Pango/Pango-1.37.2-intel-2015a.eb | 16 ++++++++-------- .../p/Pango/Pango-1.38.1-intel-2015b.eb | 16 ++++++++-------- .../p/ParFlow/ParFlow-605-goolf-1.4.10.eb | 4 ++-- .../ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb | 2 +- .../p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb | 2 +- .../p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb | 2 +- .../p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb | 2 +- .../p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb | 2 +- .../ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb | 2 +- .../p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb | 2 +- .../p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb | 2 +- .../p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb | 2 +- .../p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb | 2 +- .../p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb | 2 +- .../p/ParaView/ParaView-4.1.0-goolf-1.5.14.eb | 2 +- .../p/ParaView/ParaView-4.1.0-intel-2014b.eb | 2 +- ...View-4.3.1-intel-2015a-Python-2.7.10-mpi.eb | 14 +++++++------- ...ParaView-4.3.1-intel-2015a-Python-2.7.10.eb | 14 +++++++------- .../ParaView/ParaView-4.4.0-intel-2015b-mpi.eb | 16 ++++++++-------- .../p/ParaView/ParaView-4.4.0-intel-2015b.eb | 16 ++++++++-------- .../p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb | 8 ++++---- .../p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb | 8 ++++---- .../p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb | 10 +++++----- .../p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb | 10 +++++----- .../p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb | 2 +- .../p/Perl/Perl-5.18.2-ictce-5.5.0.eb | 2 +- .../p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 12 ++++++------ .../PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb | 2 +- .../PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 +- .../PyYAML-3.10-goolf-1.4.10-Python-2.7.3.eb | 1 - .../PyYAML-3.10-ictce-5.3.0-Python-2.7.3.eb | 1 - .../Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb | 6 +++--- .../Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 2 +- .../Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 2 +- .../p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 2 +- .../p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 2 +- .../p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 2 +- .../p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 2 +- .../p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 2 +- .../Python-2.7.10-GCC-4.9.3-2.25-bare.eb | 4 ++-- .../Python-2.7.10-GNU-4.9.3-2.25-bare.eb | 4 ++-- .../p/Python/Python-2.7.10-foss-2015a.eb | 6 +++--- .../p/Python/Python-2.7.10-foss-2015b.eb | 6 +++--- .../p/Python/Python-2.7.10-gimkl-2.11.5.eb | 6 +++--- .../p/Python/Python-2.7.10-goolf-1.4.10.eb | 6 +++--- .../p/Python/Python-2.7.10-goolf-1.7.20.eb | 6 +++--- .../p/Python/Python-2.7.10-intel-2015a.eb | 6 +++--- .../p/Python/Python-2.7.10-intel-2015b.eb | 6 +++--- .../p/Python/Python-2.7.11-foss-2016a.eb | 6 +++--- .../p/Python/Python-2.7.11-intel-2015b.eb | 6 +++--- .../p/Python/Python-2.7.11-intel-2016a.eb | 6 +++--- .../p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 2 +- .../p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 2 +- .../p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 2 +- .../p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 2 +- .../p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 2 +- .../p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 2 +- .../p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 2 +- .../Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 2 +- .../p/Python/Python-2.7.3-goolf-1.4.10.eb | 2 +- .../p/Python/Python-2.7.3-goolf-1.5.14.eb | 2 +- .../p/Python/Python-2.7.3-ictce-4.0.6.eb | 2 +- .../p/Python/Python-2.7.3-ictce-4.1.13.eb | 2 +- .../p/Python/Python-2.7.3-ictce-5.2.0.eb | 2 +- .../p/Python/Python-2.7.3-ictce-5.3.0.eb | 2 +- .../p/Python/Python-2.7.3-intel-2015a.eb | 2 +- .../p/Python/Python-2.7.3-iomkl-4.6.13.eb | 2 +- .../p/Python/Python-2.7.3-iqacml-3.7.3.eb | 2 +- .../Python-2.7.5-goalf-1.5.12-no-OFED.eb | 2 +- .../p/Python/Python-2.7.5-goolf-1.4.10.eb | 2 +- .../p/Python/Python-2.7.5-ictce-4.1.13.eb | 2 +- .../p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- .../p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- .../p/Python/Python-2.7.5-iqacml-3.7.3.eb | 2 +- .../p/Python/Python-2.7.6-goolf-1.4.10.eb | 2 +- .../p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 +- .../p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- .../p/Python/Python-2.7.8-foss-2014b.eb | 2 +- .../p/Python/Python-2.7.8-goolf-1.5.14.eb | 2 +- .../p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- .../p/Python/Python-2.7.8-intel-2014.06.eb | 2 +- .../p/Python/Python-2.7.8-intel-2014b.eb | 2 +- .../p/Python/Python-2.7.8-intel-2015a.eb | 6 +++--- .../Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb | 4 ++-- .../p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 6 +++--- .../Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb | 4 ++-- .../p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 6 +++--- .../Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb | 4 ++-- .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 6 +++--- .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 4 ++-- .../p/Python/Python-2.7.9-foss-2015.05.eb | 4 ++-- .../p/Python/Python-2.7.9-foss-2015a-bare.eb | 4 ++-- .../p/Python/Python-2.7.9-foss-2015a.eb | 4 ++-- .../p/Python/Python-2.7.9-gompi-1.5.16-bare.eb | 4 ++-- .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 4 ++-- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 2 +- .../p/Python/Python-2.7.9-intel-2015a-bare.eb | 4 ++-- .../p/Python/Python-2.7.9-intel-2015a.eb | 6 +++--- .../Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 2 +- .../p/Python/Python-3.2.3-goolf-1.4.10.eb | 2 +- .../p/Python/Python-3.2.3-ictce-4.0.6.eb | 2 +- .../p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- .../p/Python/Python-3.3.2-goolf-1.4.10.eb | 2 +- .../p/Python/Python-3.3.2-ictce-4.1.13.eb | 2 +- .../p/Python/Python-3.3.2-ictce-5.3.0.eb | 2 +- .../p/Python/Python-3.4.1-intel-2014b.eb | 2 +- .../p/Python/Python-3.4.1-intel-2015a.eb | 2 +- .../p/Python/Python-3.4.3-intel-2015a.eb | 8 ++++---- .../p/Python/Python-3.5.0-intel-2015b.eb | 8 ++++---- .../p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb | 4 ++-- .../p/packmol/packmol-13.243-ictce-4.1.13.eb | 4 ++-- ...4py-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 12 ++++++------ .../petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb | 12 ++++++------ .../petsc4py-3.3-ictce-4.0.6-Python-2.7.3.eb | 12 ++++++------ .../petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb | 12 ++++++------ .../phonopy-1.6.4-goolf-1.4.10-Python-2.7.3.eb | 1 - .../phonopy-1.6.4-ictce-5.3.0-Python-2.7.3.eb | 1 - .../pkg-config-0.27.1-goalf-1.1.0-no-OFED.eb | 2 +- .../pkg-config-0.27.1-ictce-4.0.6.eb | 2 +- .../easyconfigs/p/popt/popt-1.14-GCC-4.8.2.eb | 4 ++-- .../p/popt/popt-1.14-iccifort-2015.1.133.eb | 4 ++-- .../easyconfigs/p/popt/popt-1.16-GCC-4.9.2.eb | 7 +++---- .../printproto-1.0.5-goolf-1.4.10.eb | 2 +- .../p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb | 5 ++--- .../pscom-5.0.44-1-iccifort-2015.1.133.eb | 5 ++--- .../p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 5 +---- .../psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb | 3 +-- .../p/psmpi2/psmpi2-5.0.29-GCC-4.8.2-mt.eb | 1 - .../p/psmpi2/psmpi2-5.0.29-GCC-4.8.2.eb | 1 - ...pyTables-2.4.0-ictce-4.1.13-Python-2.7.3.eb | 16 ++++++++-------- 141 files changed, 311 insertions(+), 324 deletions(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 18d3b422b6..c4c168cc77 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -13,15 +13,15 @@ source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('Boost', '1.49.0', versionsuffix), - ('FIAT', '1.0.0', versionsuffix), - ('METIS', '5.0.2'), - ('ParMETIS', '4.0.2'), - ('ScientificPython', '2.8', versionsuffix), - ('SCOTCH', '5.1.12b_esmumps'), - ('SuiteSparse', '3.7.0', '-withparmetis'), # for CHOLMOD, UMFPACK - ('Hypre', '2.8.0b'), - ] + ('Boost', '1.49.0', versionsuffix), + ('FIAT', '1.0.0', versionsuffix), + ('METIS', '5.0.2'), + ('ParMETIS', '4.0.2'), + ('ScientificPython', '2.8', versionsuffix), + ('SCOTCH', '5.1.12b_esmumps'), + ('SuiteSparse', '3.7.0', '-withparmetis'), # for CHOLMOD, UMFPACK + ('Hypre', '2.8.0b'), +] patches = ['PETSc_ranlib-fix.patch'] diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-4.0.6-Python-2.7.3.eb index 268ce3ce62..d89cdda637 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-4.0.6-Python-2.7.3.eb @@ -13,15 +13,15 @@ source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('Boost', '1.49.0', versionsuffix), - ('FIAT', '1.0.0', versionsuffix), - ('METIS', '5.0.2'), - ('ParMETIS', '4.0.2'), - ('ScientificPython', '2.8', versionsuffix), - ('SCOTCH', '5.1.12b_esmumps'), - ('SuiteSparse', '3.7.0', '-withparmetis'), # for CHOLMOD, UMFPACK - ('Hypre', '2.8.0b'), - ] + ('Boost', '1.49.0', versionsuffix), + ('FIAT', '1.0.0', versionsuffix), + ('METIS', '5.0.2'), + ('ParMETIS', '4.0.2'), + ('ScientificPython', '2.8', versionsuffix), + ('SCOTCH', '5.1.12b_esmumps'), + ('SuiteSparse', '3.7.0', '-withparmetis'), # for CHOLMOD, UMFPACK + ('Hypre', '2.8.0b'), +] patches = ['PETSc_ranlib-fix.patch'] diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb index eae0fe6ff4..193d113315 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb @@ -14,15 +14,15 @@ source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('Boost', '1.49.0', versionsuffix), - ('FIAT', '1.0.0', versionsuffix), - ('METIS', '5.0.2'), - ('ParMETIS', '4.0.2'), - ('ScientificPython', '2.8', versionsuffix), - ('SCOTCH', '5.1.12b_esmumps'), - ('SuiteSparse', '3.7.0', '-withparmetis'), # for CHOLMOD, UMFPACK - ('Hypre', '2.8.0b'), - ] + ('Boost', '1.49.0', versionsuffix), + ('FIAT', '1.0.0', versionsuffix), + ('METIS', '5.0.2'), + ('ParMETIS', '4.0.2'), + ('ScientificPython', '2.8', versionsuffix), + ('SCOTCH', '5.1.12b_esmumps'), + ('SuiteSparse', '3.7.0', '-withparmetis'), # for CHOLMOD, UMFPACK + ('Hypre', '2.8.0b'), +] patches = ['PETSc_ranlib-fix.patch'] diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb index 608da74a7b..71cade10ff 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb @@ -6,7 +6,7 @@ # License:: MIT/GPL # ## -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'PLINK' version = '1.07' diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb index f40f41e978..136c6e53e0 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb @@ -6,7 +6,7 @@ # License:: MIT/GPL # ## -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'PLINK' version = '1.07' diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb index 785161afd7..0a3b48db5b 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'PLINK' version = '1.07' diff --git a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb index 849c3d613e..1cdadae78c 100644 --- a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb @@ -29,7 +29,7 @@ dependencies = [ ('tcsh', '6.18.01'), ('Tcl', '8.5.12'), ('Tk', '8.5.12'), - ('netCDF', '4.1.3'), # this one will also bring in HDF5 + ('netCDF', '4.1.3'), # this one will also bring in HDF5 ('Perl', '5.16.3'), ] diff --git a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb index 63cc6c8164..6807550e34 100644 --- a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('tcsh', '6.18.01'), ('Tcl', '8.5.12'), ('Tk', '8.5.12'), - ('netCDF', '4.1.3'), # this one will also bring in HDF5 + ('netCDF', '4.1.3'), # this one will also bring in HDF5 ('Perl', '5.16.3'), ] diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb index 2550e2c136..5fa710dd00 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb @@ -28,7 +28,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.1.3'), - ('Perl', '5.20.1', '-bare'), # for the test suite + ('Perl', '5.20.1', '-bare'), # for the test suite ] # Execute only the 'quick' tests and run 4 in parallel diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb index 46a224ce66..77a45e9e57 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb @@ -31,7 +31,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.2.3'), - ('Perl', '5.20.1', '-bare'), # for the test suite + ('Perl', '5.20.1', '-bare'), # for the test suite ] # Execute only the 'quick' tests and run 4 in parallel diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb index cf37090dbc..1dae0767df 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb @@ -16,17 +16,17 @@ source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] dependencies = [ - ('cairo', '1.12.18'), - ('fontconfig', '2.11.1'), - ('freetype', '2.5.3'), - ('GLib', '2.40.0'), - ('HarfBuzz', '0.9.35'), - ('GObject-Introspection', '1.42.0'), - ('libXft', '2.3.2'), + ('cairo', '1.12.18'), + ('fontconfig', '2.11.1'), + ('freetype', '2.5.3'), + ('GLib', '2.40.0'), + ('HarfBuzz', '0.9.35'), + ('GObject-Introspection', '1.42.0'), + ('libXft', '2.3.2'), ] builddependencies = [ - ('M4', '1.4.17'), + ('M4', '1.4.17'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb index 6e8887ec4e..2a9ce4d26e 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb @@ -16,17 +16,17 @@ source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] dependencies = [ - ('cairo', '1.14.2'), - ('fontconfig', '2.11.94'), - ('freetype', '2.6'), - ('GLib', '2.44.1'), - ('HarfBuzz', '1.0.1'), - ('GObject-Introspection', '1.44.0'), - ('libXft', '2.3.2', '-libX11-1.6.3-Python-2.7.10'), + ('cairo', '1.14.2'), + ('fontconfig', '2.11.94'), + ('freetype', '2.6'), + ('GLib', '2.44.1'), + ('HarfBuzz', '1.0.1'), + ('GObject-Introspection', '1.44.0'), + ('libXft', '2.3.2', '-libX11-1.6.3-Python-2.7.10'), ] builddependencies = [ - ('M4', '1.4.17'), + ('M4', '1.4.17'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.38.1-intel-2015b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.38.1-intel-2015b.eb index bcb85326ff..cf2b642da8 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.38.1-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.38.1-intel-2015b.eb @@ -16,17 +16,17 @@ source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] dependencies = [ - ('cairo', '1.14.4'), - ('fontconfig', '2.11.94', '-libpng-1.6.19'), - ('freetype', '2.6.1', '-libpng-1.6.19'), - ('GLib', '2.47.1'), - ('HarfBuzz', '1.1.0'), - ('GObject-Introspection', '1.47.1'), - ('libXft', '2.3.2', '-libX11-1.6.3-Python-2.7.10'), + ('cairo', '1.14.4'), + ('fontconfig', '2.11.94', '-libpng-1.6.19'), + ('freetype', '2.6.1', '-libpng-1.6.19'), + ('GLib', '2.47.1'), + ('HarfBuzz', '1.1.0'), + ('GObject-Introspection', '1.47.1'), + ('libXft', '2.3.2', '-libX11-1.6.3-Python-2.7.10'), ] builddependencies = [ - ('Autotools', '20150215', '', ('GNU', '4.9.3-2.25')), + ('Autotools', '20150215', '', ('GNU', '4.9.3-2.25')), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/ParFlow/ParFlow-605-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParFlow/ParFlow-605-goolf-1.4.10.eb index 692186178b..52f17ce9e8 100644 --- a/easybuild/easyconfigs/p/ParFlow/ParFlow-605-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParFlow/ParFlow-605-goolf-1.4.10.eb @@ -24,8 +24,8 @@ preconfigopts = [ 'cd pftools &&', ] # copies of preconfigopts are required, not references, hence the [:] -prebuildopts = preconfigopts[:] -preinstallopts = preconfigopts[:] +prebuildopts = preconfigopts[:] +preinstallopts = preconfigopts[:] configopts = [ ' --with-amps=mpi1 --enable-timing --with-clm --with-silo=$EBROOTSILO --with-hypre=$EBROOTHYPRE', diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb index ace5dbc0de..42da94d19e 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] sources = ['ParMetis-%s.tar.gz' % version] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb index 1f858cb94c..9da0a95728 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] sources = ['ParMetis-%s.tar.gz' % version] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb index 8cf9a16e39..4357d1d8af 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] sources = ['ParMetis-%s.tar.gz' % version] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb index a0f67cdf0d..2cb2e02d6a 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] sources = ['ParMetis-%s.tar.gz' % version] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb index a0d6b8d1ed..9adb21d10a 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gmpolf', 'version': '1.4.8'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb index 7f8da3fb1c..7ab94b866f 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb index ad06991953..f751a31515 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb index ef702ef013..a91e416ba0 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb index a20f70af08..904b9fb5ff 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb index bf58fb84fb..c06c552596 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb @@ -13,7 +13,7 @@ download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] sources = ["ParaView-v%(version)s-source.tgz"] -dependencies = [('Qt','4.8.5')] +dependencies = [('Qt', '4.8.5')] builddependencies = [('CMake', '2.8.10.2')] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb index bfd42624ef..63df0fd35a 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb @@ -13,7 +13,7 @@ download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] sources = ["ParaView-v%(version)s-source.tar.gz"] -dependencies = [('Qt','4.8.5')] +dependencies = [('Qt', '4.8.5')] builddependencies = [('CMake', '2.8.10.2')] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-goolf-1.5.14.eb index 0e83d17a57..54eca56e62 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-goolf-1.5.14.eb @@ -13,7 +13,7 @@ download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] sources = ["ParaView-v%(version)s-source.tar.gz"] -dependencies = [('Qt','4.8.5')] +dependencies = [('Qt', '4.8.5')] builddependencies = [('CMake', '2.8.10.2')] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-intel-2014b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-intel-2014b.eb index 04255cc7c7..61e00cb01a 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-intel-2014b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-intel-2014b.eb @@ -13,7 +13,7 @@ download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] sources = ["ParaView-v%(version)s-source.tar.gz"] -dependencies = [('Qt','4.8.6')] +dependencies = [('Qt', '4.8.6')] builddependencies = [('CMake', '3.0.0')] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb index 609a7355cc..c8116fe14f 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb @@ -38,15 +38,15 @@ maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' -#Without internet connection turn off testing (uncomment the following line) +# Without internet connection turn off testing (uncomment the following line) #configopts += '-DBUILD_TESTING=OFF ' -#Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md -#and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly -#Without internet connection, comment the following two lines (configopts and prebuildopts) +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' -#The ParaView server can be cranky, test downloads are quite often failing, especially in the case -#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the -#first serial attempt would fail. +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. prebuildopts = 'make VTKData ;' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb index e5a49a6762..2e184fd801 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb @@ -37,15 +37,15 @@ maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' -#Without internet connection turn off testing (uncomment the following line) +# Without internet connection turn off testing (uncomment the following line) #configopts += '-DBUILD_TESTING=OFF ' -#Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md -#and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly -#Without internet connection, comment the following two lines (configopts and prebuildopts) +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' -#The ParaView server can be cranky, test downloads are quite often failing, especially in the case -#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the -#first serial attempt would fail. +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. prebuildopts = 'make VTKData ;' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb index d675f99ad1..2e7bc45270 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb @@ -18,7 +18,7 @@ patches = ['%(name)s-%(version)s_missingheader.patch'] python = 'Python' pyver = '2.7.10' -pysuff = '-%s-%s' % (python,pyver) +pysuff = '-%s-%s' % (python, pyver) dependencies = [ ('Mesa', '11.0.2', pysuff), ('libGLU', '9.0.0'), @@ -38,15 +38,15 @@ maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' -#Without internet connection turn off testing (uncomment the following line) +# Without internet connection turn off testing (uncomment the following line) #configopts += '-DBUILD_TESTING=OFF ' -#Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md -#and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly -#Without internet connection, comment the following two lines (configopts and prebuildopts) +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' -#The ParaView server can be cranky, test downloads are quite often failing, especially in the case -#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the -#first serial attempt would fail. +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. prebuildopts = 'make VTKData ;' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb index 63b92b07e5..0057213bea 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb @@ -17,7 +17,7 @@ patches = ['%(name)s-%(version)s_missingheader.patch'] python = 'Python' pyver = '2.7.10' -pysuff = '-%s-%s' % (python,pyver) +pysuff = '-%s-%s' % (python, pyver) dependencies = [ ('Mesa', '11.0.2', pysuff), ('libGLU', '9.0.0'), @@ -37,15 +37,15 @@ maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' -#Without internet connection turn off testing (uncomment the following line) +# Without internet connection turn off testing (uncomment the following line) #configopts += '-DBUILD_TESTING=OFF ' -#Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md -#and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly -#Without internet connection, comment the following two lines (configopts and prebuildopts) +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' -#The ParaView server can be cranky, test downloads are quite often failing, especially in the case -#of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the -#first serial attempt would fail. +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. prebuildopts = 'make VTKData ;' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb index 359a345c5b..61f6c03bfb 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb @@ -13,10 +13,10 @@ source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] patches = [ - 'intelmpi.patch', - # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version - 'old-libstdc++-hash_fun-map-set.patch', - ] + 'intelmpi.patch', + # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version + 'old-libstdc++-hash_fun-map-set.patch', +] # Pasha's makefile is not suited for parallel execution parallel = 1 diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb index cf6204baea..4043dd5630 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb @@ -14,10 +14,10 @@ source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] patches = [ - 'intelmpi.patch', - # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version - 'old-libstdc++-hash_fun-map-set.patch', - ] + 'intelmpi.patch', + # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version + 'old-libstdc++-hash_fun-map-set.patch', +] # Pasha's makefile is not suited for parallel execution parallel = 1 diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb index 65d0ec04e7..1d85521e58 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb @@ -13,12 +13,12 @@ source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] patches = [ - 'intelmpi.patch', - # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version of libstdc++ - # since 1.0.5 pasha tries to use 'backward/' instead of 'ext/' but this might fail on some systems. - 'old-libstdc++-hash_fun-map-set_pasha-1.0.5.patch', + 'intelmpi.patch', + # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version of libstdc++ + # since 1.0.5 pasha tries to use 'backward/' instead of 'ext/' but this might fail on some systems. + 'old-libstdc++-hash_fun-map-set_pasha-1.0.5.patch', - ] +] # Pasha's makefile is not suited for parallel execution parallel = 1 diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb index 67dc78ccc9..a72485e97d 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb @@ -14,12 +14,12 @@ source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] patches = [ - 'intelmpi.patch', - # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version of libstdc++ - # since 1.0.5 pasha tries to use 'backward/' instead of 'ext/' but this might fail on some systems. - 'old-libstdc++-hash_fun-map-set_pasha-1.0.5.patch', + 'intelmpi.patch', + # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version of libstdc++ + # since 1.0.5 pasha tries to use 'backward/' instead of 'ext/' but this might fail on some systems. + 'old-libstdc++-hash_fun-map-set_pasha-1.0.5.patch', - ] +] # Pasha's makefile is not suited for parallel execution parallel = 1 diff --git a/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb index 0a7acf4ed3..beddc1be80 100644 --- a/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb @@ -24,7 +24,7 @@ checksums = [('md5', '32b4d71b2ec9455c7db69516b1bd4910')] buildopts = ' CC="$CXX"' -files_to_copy = ["bin", "README" ] +files_to_copy = ["bin", "README"] sanity_check_paths = { 'files': ["bin/PeakSeq"], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.18.2-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.18.2-ictce-5.5.0.eb index 03576a1d0c..5e44fd7e98 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.18.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.18.2-ictce-5.5.0.eb @@ -210,7 +210,7 @@ exts_list = [ 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Moose', '2.1204', { - 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Params::Validate', '1.08', { 'source_tmpl': 'Params-Validate-1.08.tar.gz', diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index 864b80e95c..bca12c0034 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -31,12 +31,12 @@ cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSA files_to_copy = [ (['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), - "demo", - "gmt", - "gmt-web", - "test", - "README.md", - "RELEASE" + "demo", + "gmt", + "gmt-web", + "test", + "README.md", + "RELEASE" ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb index 3b3f47bdf1..909fa6783b 100644 --- a/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb @@ -23,7 +23,7 @@ sources = ['%(namelower)s-for-gti-%(version)s.tar.gz'] builddependencies = [('CMake', '2.8.10.2')] -configopts = ' -DCMAKE_BUILD_TYPE=Release -DBFD_FOUND=False -DPNMPI_HAVE_BFD=False' +configopts = ' -DCMAKE_BUILD_TYPE=Release -DBFD_FOUND=False -DPNMPI_HAVE_BFD=False' parallel = 1 diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index f0f5501b84..815c947eac 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -27,7 +27,7 @@ dependencies = [ (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), -# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.10-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.10-goolf-1.4.10-Python-2.7.3.eb index d2c2d3137f..9692920546 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.10-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.10-goolf-1.4.10-Python-2.7.3.eb @@ -30,4 +30,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.10-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.10-ictce-5.3.0-Python-2.7.3.eb index d3c883a5e6..0116c1297c 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.10-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.10-ictce-5.3.0-Python-2.7.3.eb @@ -30,4 +30,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb index 3d8ae78e2c..fd5dce2efb 100644 --- a/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb @@ -19,9 +19,9 @@ pyver = '2.7.3' versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pyver), - ('numpy','1.6.2', versionsuffix), - ('scipy', '0.11.0', versionsuffix), + (python, pyver), + ('numpy', '1.6.2', versionsuffix), + ('scipy', '0.11.0', versionsuffix), ] pyshortver = '.'.join(pyver.split('.')[:2]) diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index 43ff3feba7..6a564b9945 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index f825fd87bd..031662cad8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index 18d0d4a8df..e815cc69b5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index 23ddabe854..d698199a12 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index f747214b5c..dd9d71c15a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index 0228eae5be..809068de30 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index fc44c37e78..c781bfe8b7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb index 40981226c2..c19c897045 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb @@ -19,8 +19,8 @@ dependencies = [ ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb index 6ecda76511..094f5e83b0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb @@ -19,8 +19,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 8e4cfabe9d..91a293153e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -23,8 +23,8 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto -# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -44,7 +44,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index 45878617c6..0f080708a5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -23,8 +23,8 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # required for pycrypto -# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -44,7 +44,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb index 4ae2c2b5e6..d4350dca92 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb @@ -22,8 +22,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), -# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -43,7 +43,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb index 66bb207792..eef0597d02 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -23,8 +23,8 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.0.0a', '', ('GCC', '4.7.2')), # required for pycrypto -# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -44,7 +44,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb index e5f6c7aacc..09bb245d3a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -23,8 +23,8 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.0.0a', '', ('GCC', '4.8.4')), # required for pycrypto -# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -44,7 +44,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index f5c2309ea8..6af31b5b60 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -23,8 +23,8 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto -# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -44,7 +44,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb index a5115dc2be..147a7cab13 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -22,8 +22,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), -# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -43,7 +43,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 4bce06c8fe..1ea0118d0c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -23,8 +23,8 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -44,7 +44,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index c697adc7c7..b890f8cb1b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -23,8 +23,8 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -44,7 +44,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index b615ded539..0f80537c01 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -23,8 +23,8 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -44,7 +44,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index b447f3f5c5..458773a19c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index 3b9b9b0071..8847eb716a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index e9411a98a0..8721ba5f0a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index 9d81cee86b..feaf2e76ec 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index b7dfb64df9..6bbc4316af 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 5eb4c88938..b671309381 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index 878951cc6e..383cedbc17 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index 957d719fbd..ffaa43d1ef 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 49da1ce96f..b20ffd67fb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index ff029a2234..e087117a23 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 2ef8f9fc88..04f049367b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index b5075a6a9a..f3c7ccd43d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index e1bc68f6d1..65a7050c90 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 1f6678ca73..caf683b0c8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index bcc80770f8..a68ef18929 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index 262801c6c1..b36520e7e8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index 7713f86879..3806ea6dd7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -22,7 +22,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('CBLAS', '20110120'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index 0acac864f5..e8290ac41a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index b8e12d524c..ed2a7a5730 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index 9fda7777e6..45b1ca6a64 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index 6f7edf431e..33dce6f6ca 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 3c2a47e51e..0a01b973a0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index c8797b36e9..f5d6db6b40 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -23,7 +23,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('CBLAS', '20110120'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index de11eaf356..bccfcbf0c2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index b8f2f71c12..146417325f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index be1053a62d..a51d51c986 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index caf05b2cc7..16590efbbd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 5c19bcd953..c8491023d8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index f1ec579fbe..bcf88e98c9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -25,7 +25,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index b620899273..dfe5979c7c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 1ae3ec0c5f..54121e1a6f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index 60923e701c..4df02bbcfe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -22,8 +22,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] # order is important! @@ -41,7 +41,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb index 5c84059a20..445c53bfa6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb @@ -17,8 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb index 2e085966c7..4645a18ca8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -19,8 +19,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] @@ -42,7 +42,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb index 1e9572eb83..d17421caa5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb @@ -17,8 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb index 0c1b139dda..9c11f0e5c3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -19,8 +19,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] @@ -42,7 +42,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb index 3fafaaa920..e25539f74d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb @@ -17,8 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb index 186e5f94df..cab707ec57 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -19,8 +19,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] @@ -42,7 +42,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index 7f438347a5..3b6c965221 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -19,8 +19,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index abb705a349..75386ccc4a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -21,8 +21,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index dc26dc666b..a04b4992d3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -19,8 +19,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index bb297e5eb8..4d8258d281 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -21,8 +21,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index ad2c37f79a..e8eb88c738 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -18,8 +18,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 27281d943c..7739e8b255 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -21,8 +21,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index c011298dc9..41e6d0cc85 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -22,7 +22,7 @@ dependencies = [ ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), #('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index d6a4eb1b3c..f327891d4e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -19,8 +19,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 2c04d1e9a7..42e834b9da 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -21,8 +21,8 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -42,7 +42,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index 151d6f90e7..9282981b3f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index c2247793ab..98e26ec9ef 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index 77a4ae2161..b110143efd 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 24ea958ab0..4bc546cccb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index f23e383d17..0dc65b97ca 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb index 28d140c742..24ae167fb4 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index a66a2c142a..97e6c04ce7 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index f553cd209e..66630e9980 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index cdfe46f05e..d93f95e46a 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index dd4b3e999b..67e92c7ae0 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -19,8 +19,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev')] @@ -40,7 +40,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { @@ -97,7 +97,7 @@ exts_list = [ }), ('paramiko', '1.15.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), + }), ('pyparsing', '2.0.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index f6409a5d49..7a1cf602ae 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -19,8 +19,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev')] @@ -40,7 +40,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', # % numpyversion, ], }), ('scipy', scipyversion, { @@ -97,7 +97,7 @@ exts_list = [ }), ('paramiko', '1.15.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), + }), ('pyparsing', '2.0.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb index 8678c70192..f8e2358b4a 100644 --- a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -23,10 +23,10 @@ source_urls = [('http://sourceforge.net/projects/pbwa/files/latest', 'download') dependencies = [('BWA', '0.7.4')] -files_to_copy = [(['pBWA','qualfa2fq.pl','solid2fastq.pl' ], 'bin')] +files_to_copy = [(['pBWA', 'qualfa2fq.pl', 'solid2fastq.pl'], 'bin')] sanity_check_paths = { - 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], + 'files': ['bin/pBWA', 'bin/qualfa2fq.pl', 'bin/solid2fastq.pl'], 'dirs': ['.'], } diff --git a/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb b/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb index a6e1069f31..29c565eb8d 100644 --- a/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb @@ -13,9 +13,9 @@ source_urls = ['https://packmol.googlecode.com/files'] buildopts = 'FORTRAN="$F90"' -files_to_copy = [(['packmol'],'bin'), 'COPYING', 'AUTHORS', 'LICENSE'] +files_to_copy = [(['packmol'], 'bin'), 'COPYING', 'AUTHORS', 'LICENSE'] -sanity_check_paths={ +sanity_check_paths = { 'files': ['bin/packmol', 'COPYING', 'AUTHORS', 'LICENSE'], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 8d1c2ba947..3f1cdad255 100644 --- a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -16,16 +16,16 @@ python_version = "2.7.3" versionsuffix = '-%s-%s' % (python, python_version) dependencies = [ - (python, python_version), - ('PETSc', '3.3-p2', versionsuffix) - ] + (python, python_version), + ('PETSc', '3.3-p2', versionsuffix) +] py_short_ver = ".".join(python_version.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': [], - 'dirs': [pylibdir] - } + 'files': [], + 'dirs': [pylibdir] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb index bdc63798ec..0387cd385f 100644 --- a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb @@ -16,16 +16,16 @@ python_version = "2.7.3" versionsuffix = '-%s-%s' % (python, python_version) dependencies = [ - (python, python_version), - ('PETSc', '3.3-p2', versionsuffix) - ] + (python, python_version), + ('PETSc', '3.3-p2', versionsuffix) +] py_short_ver = ".".join(python_version.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': [], - 'dirs': [pylibdir] - } + 'files': [], + 'dirs': [pylibdir] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-4.0.6-Python-2.7.3.eb index 663ceba6be..72bb7cec06 100644 --- a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-4.0.6-Python-2.7.3.eb @@ -16,16 +16,16 @@ python_version = "2.7.3" versionsuffix = '-%s-%s' % (python, python_version) dependencies = [ - (python, python_version), - ('PETSc', '3.3-p2', versionsuffix) - ] + (python, python_version), + ('PETSc', '3.3-p2', versionsuffix) +] py_short_ver = ".".join(python_version.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': [], - 'dirs': [pylibdir] - } + 'files': [], + 'dirs': [pylibdir] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb index 6af9bfee59..50d6cb2145 100644 --- a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb @@ -17,16 +17,16 @@ python_version = "2.7.3" versionsuffix = '-%s-%s' % (python, python_version) dependencies = [ - (python, python_version), - ('PETSc', '3.3-p2', versionsuffix) - ] + (python, python_version), + ('PETSc', '3.3-p2', versionsuffix) +] py_short_ver = ".".join(python_version.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': [], - 'dirs': [pylibdir] - } + 'files': [], + 'dirs': [pylibdir] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-goolf-1.4.10-Python-2.7.3.eb index 2e67c2d367..72709131d2 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-goolf-1.4.10-Python-2.7.3.eb @@ -32,4 +32,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-ictce-5.3.0-Python-2.7.3.eb index c9d54a15dd..4f215834cc 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-ictce-5.3.0-Python-2.7.3.eb @@ -32,4 +32,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-goalf-1.1.0-no-OFED.eb index ec3f8c364a..5d80b51c52 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ description = """pkg-config is a helper tool used when compiling applications an gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).""" -toolchain = {'name': 'goalf', 'version' : '1.1.0-no-OFED'} +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://pkgconfig.freedesktop.org/releases/'] diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-4.0.6.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-4.0.6.eb index ca1b0b102a..059a000700 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-4.0.6.eb @@ -9,7 +9,7 @@ description = """pkg-config is a helper tool used when compiling applications an gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).""" -toolchain = {'name': 'ictce', 'version' : '4.0.6'} +toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://pkgconfig.freedesktop.org/releases/'] diff --git a/easybuild/easyconfigs/p/popt/popt-1.14-GCC-4.8.2.eb b/easybuild/easyconfigs/p/popt/popt-1.14-GCC-4.8.2.eb index 46a0db16f7..24c87fbd08 100644 --- a/easybuild/easyconfigs/p/popt/popt-1.14-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/p/popt/popt-1.14-GCC-4.8.2.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] sanity_check_paths = { 'files': ['include/popt.h', - ('lib/libpopt.a', 'lib64/libpopt.a'), - ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], + ('lib/libpopt.a', 'lib64/libpopt.a'), + ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/popt/popt-1.14-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/popt/popt-1.14-iccifort-2015.1.133.eb index 24a941cf28..59c5ad2adf 100644 --- a/easybuild/easyconfigs/p/popt/popt-1.14-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/popt/popt-1.14-iccifort-2015.1.133.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] sanity_check_paths = { 'files': ['include/popt.h', - ('lib/libpopt.a', 'lib64/libpopt.a'), - ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], + ('lib/libpopt.a', 'lib64/libpopt.a'), + ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/popt/popt-1.16-GCC-4.9.2.eb b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-4.9.2.eb index 07519cbd9a..fe0e0481dc 100644 --- a/easybuild/easyconfigs/p/popt/popt-1.16-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-4.9.2.eb @@ -10,17 +10,16 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['http://rpm5.org/files/popt/'] sources = [SOURCE_TAR_GZ] -#see if this fixes the assembly language fauilure +# see if this fixes the assembly language fauilure toolchainopts = {'optarch': False} sanity_check_paths = { 'files': ['include/popt.h', - ('lib/libpopt.a', 'lib64/libpopt.a'), - ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], + ('lib/libpopt.a', 'lib64/libpopt.a'), + ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], 'dirs': [], } maxparallel = 1 moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb index 8346a5cd7a..dacbb816a7 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb index 605259b37f..b69d0d92dd 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb @@ -13,9 +13,8 @@ dependencies = [('popt', '1.16')] sanity_check_paths = { - 'files': ['include/pscom.h', ('lib/libpscom.%s' % SHLIB_EXT, 'lib64/libpscom.%s' % SHLIB_EXT)], - 'dirs': [], + 'files': ['include/pscom.h', ('lib/libpscom.%s' % SHLIB_EXT, 'lib64/libpscom.%s' % SHLIB_EXT)], + 'dirs': [], } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb index 3b463debfc..7da1e4a7f7 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb @@ -13,8 +13,7 @@ sources = ['%(version)s.zip'] dependencies = [('popt', '1.14')] sanity_check_paths = { - 'files': ['include/pscom.h', ('lib/libpscom.%s' % SHLIB_EXT, 'lib64/libpscom.%s' % SHLIB_EXT)], - 'dirs': [], + 'files': ['include/pscom.h', ('lib/libpscom.%s' % SHLIB_EXT, 'lib64/libpscom.%s' % SHLIB_EXT)], + 'dirs': [], } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index d99677edc9..f1eb61bd5b 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -23,9 +23,7 @@ preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset # Build shared libraries configopts = '--with-confset=gcc --enable-shared --enable-static' -dependencies = [('pscom' , '5.0.44-1')] - - +dependencies = [('pscom', '5.0.44-1')] sanity_check_paths = { @@ -44,4 +42,3 @@ sanity_check_paths = { moduleclass = 'mpi' - diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index fc50026e3c..16c0c9ffc3 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -23,7 +23,7 @@ preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset # Build shared libraries configopts = '--with-confset=intel --enable-shared --enable-static --enable-romio --enable-mpe' -dependencies = [('pscom' , '5.0.44-1')] +dependencies = [('pscom', '5.0.44-1')] sanity_check_paths = { @@ -41,4 +41,3 @@ sanity_check_paths = { } moduleclass = 'mpi' - diff --git a/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2-mt.eb b/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2-mt.eb index d7fb1e75ef..f88f324c9e 100644 --- a/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2-mt.eb +++ b/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2-mt.eb @@ -47,4 +47,3 @@ sanity_check_paths = { } moduleclass = 'mpi' - diff --git a/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2.eb b/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2.eb index 9c3dd66c77..21643d2e81 100644 --- a/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/p/psmpi2/psmpi2-5.0.29-GCC-4.8.2.eb @@ -46,4 +46,3 @@ sanity_check_paths = { } moduleclass = 'mpi' - diff --git a/easybuild/easyconfigs/p/pyTables/pyTables-2.4.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/pyTables/pyTables-2.4.0-ictce-4.1.13-Python-2.7.3.eb index c5aa1dcd66..ee64c3384a 100644 --- a/easybuild/easyconfigs/p/pyTables/pyTables-2.4.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pyTables/pyTables-2.4.0-ictce-4.1.13-Python-2.7.3.eb @@ -24,16 +24,16 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('numexpr', '2.0.1', versionsuffix), - ('HDF5', '1.8.10', '-gpfs'), - ('Cython', '0.16', versionsuffix), - ] + (python, pythonver), + ('numexpr', '2.0.1', versionsuffix), + ('HDF5', '1.8.10', '-gpfs'), + ('Cython', '0.16', versionsuffix), +] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['nctoh5', 'ptdump', 'ptrepack']], - 'dirs': ['lib/python%s/site-packages/tables' % pythonshortver] - } + 'files': ['bin/%s' % x for x in ['nctoh5', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%s/site-packages/tables' % pythonshortver] +} options = {'modulename': 'tables'} -- GitLab From e299be700367558b1637c2d803b49d977bed1c4b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:54:59 +0100 Subject: [PATCH 0278/2133] Style fixes with autopep8: r Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb | 3 ++- easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 1 - .../r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-ictce-4.1.13-hybrid-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-ictce-4.1.13-mpi-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-ictce-4.1.13-mt-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-ictce-4.1.13-seq-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb | 2 +- .../r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb | 2 +- .../r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb | 2 +- .../r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb | 2 +- .../r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb | 2 +- .../r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb | 2 +- .../r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb | 2 +- .../r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb | 2 +- .../r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb | 2 +- .../r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb | 2 +- .../r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb | 2 +- .../r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb | 2 +- .../r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb | 2 +- .../r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb | 2 +- .../r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-avx.eb | 2 +- .../r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-avx2.eb | 2 +- .../r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-sse3.eb | 2 +- .../easyconfigs/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb | 6 +++--- easybuild/easyconfigs/r/RNAz/RNAz-2.1-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-4.0.6.eb | 6 +++--- easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-5.3.0.eb | 6 +++--- .../r/ROOT/ROOT-v5.34.01-goalf-1.1.0-no-OFED.eb | 4 ++-- .../easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb | 10 +++++----- .../easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb | 4 ++-- .../easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb | 2 +- .../r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb | 2 +- .../easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb | 2 +- .../r/randrproto/randrproto-1.5.0-intel-2015b.eb | 4 ++-- .../r/renderproto/renderproto-0.11-foss-2014b.eb | 4 ++-- .../r/renderproto/renderproto-0.11-intel-2014b.eb | 4 ++-- .../r/renderproto/renderproto-0.11-intel-2015a.eb | 4 ++-- .../r/renderproto/renderproto-0.11-intel-2015b.eb | 4 ++-- 44 files changed, 63 insertions(+), 63 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb index dd2dee5fb4..95d136f187 100644 --- a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb @@ -32,7 +32,8 @@ ext_options = { exts_list = [ ('pbdMPI', '0.2-5', ext_options), ('pbdSLAP', '0.2-0', ext_options), - ('pbdBASE', '0.2-3', dict(ext_options.items() + [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), + ('pbdBASE', '0.2-3', dict(ext_options.items() + + [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), ('pbdDMAT', '0.2-3', ext_options), ('pbdDEMO', '0.2-0', ext_options), ('pmclust', '0.1-6', ext_options), diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index bcd67f42d0..6eb8bee5eb 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -375,4 +375,3 @@ exts_list = [ ] moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb index 567f46f555..cbe5be6c23 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-hybrid-sse3' +versionsuffix = '-hybrid-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb index 0a2fbab41a..884ad84637 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-mpi-sse3' +versionsuffix = '-mpi-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb index ebf504fd65..3a380bd6de 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-mt-sse3' +versionsuffix = '-mt-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb index 67c58af8a4..02608c18da 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-seq-sse3' +versionsuffix = '-seq-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-hybrid-sse3.eb index 4d4122a29d..d138389b54 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-hybrid-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-hybrid-sse3' +versionsuffix = '-hybrid-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mpi-sse3.eb index bb28e8240e..72d074f334 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mpi-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-mpi-sse3' +versionsuffix = '-mpi-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mt-sse3.eb index 9768fc2a61..d5270c4549 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mt-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-mt-sse3' +versionsuffix = '-mt-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-seq-sse3.eb index 6c06107ea3..2cab68e67d 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-seq-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-seq-sse3' +versionsuffix = '-seq-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb index c8becaa3bb..58fb5bd173 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-hybrid-sse3' +versionsuffix = '-hybrid-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb index e759597ee1..2e5e7cabbc 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-mpi-sse3' +versionsuffix = '-mpi-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb index 4dc53e2ba9..e8060e8191 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-mt-sse3' +versionsuffix = '-mt-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb index b257e16233..adabadb76b 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.2.6' -versionsuffix ='-seq-sse3' +versionsuffix = '-seq-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb index e836b4e2bd..d053b3dc21 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.7.5' -versionsuffix ='-hybrid-sse3' +versionsuffix = '-hybrid-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb index b5fb519230..575001db8d 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.7.5' -versionsuffix ='-mpi-sse3' +versionsuffix = '-mpi-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb index 25df746f3e..a1fec5b741 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.7.5' -versionsuffix ='-mt-sse3' +versionsuffix = '-mt-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb index 46179d71f4..f253cc9c29 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.7.5' -versionsuffix ='-seq-sse3' +versionsuffix = '-seq-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb index e82295aeaa..7eb0b37f64 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.7.5' -versionsuffix ='-hybrid-sse3' +versionsuffix = '-hybrid-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb index dc746f9bc0..0058765fc5 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.7.5' -versionsuffix ='-mpi-sse3' +versionsuffix = '-mpi-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb index 6c8a50bbe3..86dab359ac 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.7.5' -versionsuffix ='-mt-sse3' +versionsuffix = '-mt-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb index 9fb4191bd0..b107d2a11a 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'RAxML' version = '7.7.5' -versionsuffix ='-seq-sse3' +versionsuffix = '-seq-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb index 34e93e35d8..d7d22ad5ae 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'RAxML' version = '8.1.1' -versionsuffix ='-mpi-avx' +versionsuffix = '-mpi-avx' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb index 42ce2e4fdd..dd4462802c 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'RAxML' version = '8.1.1' -versionsuffix ='-mpi-sse3' +versionsuffix = '-mpi-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb index 09ffafe613..d55bca8237 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'RAxML' version = '8.1.1' -versionsuffix ='-mt-avx' +versionsuffix = '-mt-avx' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb index 305c9c94a6..859f2adbb7 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'RAxML' version = '8.1.1' -versionsuffix ='-mt-sse3' +versionsuffix = '-mt-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-avx.eb index 21edb6b264..32f1d767ad 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-avx.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-avx.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'RAxML' version = '8.2.4' -versionsuffix ='-hybrid-avx' +versionsuffix = '-hybrid-avx' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-avx2.eb index 4a164f580e..8ee726adbf 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-avx2.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-avx2.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'RAxML' version = '8.2.4' -versionsuffix ='-hybrid-avx2' +versionsuffix = '-hybrid-avx2' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-sse3.eb index 2bd6afbde9..1f3cc9523c 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-intel-2015b-hybrid-sse3.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'RAxML' version = '8.2.4' -versionsuffix ='-hybrid-sse3' +versionsuffix = '-hybrid-sse3' homepage = 'https://github.com/stamatak/standard-RAxML' description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb index f2f5762dda..5f373bcc46 100644 --- a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb @@ -26,8 +26,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tbi.univie.ac.at/~wash/%s' % name] sanity_check_paths = { - 'files': ['bin/RNAz'], - 'dirs': [] - } + 'files': ['bin/RNAz'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goolf-1.4.10.eb index c2b6fa1b2b..2155ac1e76 100644 --- a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goolf-1.4.10.eb @@ -26,8 +26,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tbi.univie.ac.at/~wash/%s' % name] sanity_check_paths = { - 'files': ['bin/RNAz'], - 'dirs': [] - } + 'files': ['bin/RNAz'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-4.0.6.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-4.0.6.eb index 7db2213126..71400b6f39 100644 --- a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-4.0.6.eb @@ -26,8 +26,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tbi.univie.ac.at/~wash/%s' % name] sanity_check_paths = { - 'files': ['bin/RNAz'], - 'dirs': [] - } + 'files': ['bin/RNAz'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-5.3.0.eb index 32c6bcbc4b..03f3c66bab 100644 --- a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-5.3.0.eb @@ -27,8 +27,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tbi.univie.ac.at/~wash/%s' % name] sanity_check_paths = { - 'files': ['bin/RNAz'], - 'dirs': [] - } + 'files': ['bin/RNAz'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goalf-1.1.0-no-OFED.eb index 304bbf99c8..b1ee5419da 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goalf-1.1.0-no-OFED.eb @@ -6,7 +6,7 @@ description = """The ROOT system provides a set of OO frameworks with all the fu needed to handle and analyze large amounts of data in a very efficient way.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -toolchainopts = {'pic':True} +toolchainopts = {'pic': True} sources = ['%s_%s.source.tar.gz' % (name.lower(), version)] source_urls = ['ftp://root.cern.ch/root/'] @@ -18,7 +18,7 @@ dependencies = [ ('GSL', '1.15'), ('libxml2', '2.8.0', '-%s-%s' % (python, pyver)), (python, pyver), - ] +] # architecture arch = 'linuxx8664gcc' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb index c771b391bb..4e14ff0190 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb @@ -6,7 +6,7 @@ description = """The ROOT system provides a set of OO frameworks with all the fu needed to handle and analyze large amounts of data in a very efficient way.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'pic':True} +toolchainopts = {'pic': True} sources = ['%s_%s.source.tar.gz' % (name.lower(), version)] source_urls = ['ftp://root.cern.ch/root/'] @@ -15,10 +15,10 @@ python = 'Python' pyver = '2.7.3' dependencies = [ - ('GSL', '1.15'), - ('libxml2', '2.8.0', '-%s-%s' % (python, pyver)), - (python, pyver), - ] + ('GSL', '1.15'), + ('libxml2', '2.8.0', '-%s-%s' % (python, pyver)), + (python, pyver), +] # architecture arch = 'linuxx8664gcc' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb index 55aab9105b..6ac9d3d52c 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb @@ -13,7 +13,7 @@ source_urls = ['ftp://root.cern.ch/root/'] patches = [ 'configure_FftwFromMkl_28.patch', 'icc_ifort_v12.patch' - ] +] python = 'Python' pyver = '2.7.3' @@ -22,7 +22,7 @@ dependencies = [ ('GSL', '1.15'), ('libxml2', '2.8.0', '-%s-%s' % (python, pyver)), (python, pyver), - ] +] # architecture arch = 'linuxx8664icc' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb index c0e1e4e91e..a65a733278 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -22,7 +22,7 @@ dependencies = [ ('GSL', '1.15'), ('libxml2', '2.8.0', '-%s-%s' % (python, pyver)), (python, pyver), - ] +] # architecture arch = 'linuxx8664icc' diff --git a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb index d832fcca93..d0bbd7da76 100644 --- a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'RSEQtools' version = '0.6' diff --git a/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb index 21ca0b75f9..515ad4d74a 100644 --- a/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'rSeq' version = '0.2.0' diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb index 2e61ea7155..cb2cc76a3b 100644 --- a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb @@ -12,8 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], - 'dirs' : [], + 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb index f073ec9749..3119cd29b7 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], - 'dirs' : [], + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb index 34ed4ccca7..9d7f0c2a91 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], - 'dirs' : [], + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb index b1d4936121..87042e0e65 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], - 'dirs' : [], + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb index 6d58ade80a..b16c201ac1 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], - 'dirs' : [], + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], } moduleclass = 'devel' -- GitLab From 6a1cf4c3c9891e0eda3346139ce334c09ea88b27 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:55:37 +0100 Subject: [PATCH 0279/2133] Style fixes with autopep8: s Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb | 2 +- .../s/SIBELia/SIBELia-3.0.4-goolf-1.4.10.eb | 1 - .../s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb | 3 ++- .../s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb | 3 ++- .../s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb | 3 ++- .../s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb | 3 ++- .../s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb | 3 ++- .../s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb | 2 +- .../easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb | 2 +- .../s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb | 2 +- .../s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb | 2 +- .../s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb | 2 +- .../s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb | 2 +- .../s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb | 2 +- .../s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb | 2 +- .../s/SPAdes/SPAdes-3.0.0-goolf-1.4.10.eb | 1 - .../s/SPAdes/SPAdes-3.1.0-goolf-1.4.10.eb | 1 - .../s/STREAM/STREAM-5.10-intel-2015a.eb | 2 +- ...0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1.eb | 2 +- ...iqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb | 2 +- ...gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0.eb | 2 +- ....2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...apich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...apich2-1.7.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...mvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 2 +- ...-gmvapich2-1.7.9a2-ACML-5.2.0-gfortran-64bit.eb | 2 +- ...0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...i-1.4.10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...2.0.2-gompi-1.5.12-ATLAS-3.10.1-LAPACK-3.4.2.eb | 2 +- ...mpi-1.5.12-no-OFED-ATLAS-3.10.1-LAPACK-3.4.2.eb | 2 +- ...0.2-gompi-1.5.14-OpenBLAS-0.2.8-LAPACK-3.5.0.eb | 2 +- ...i-1.5.14-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb | 2 +- ....2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 2 +- ...0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb | 2 +- ....2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 2 +- ....0.2-gompi-2014b-OpenBLAS-0.2.9-LAPACK-3.5.0.eb | 2 +- ...2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb | 2 +- ...0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 2 +- ...0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb | 2 +- ...0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb | 2 +- ....2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb | 2 +- ...-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb | 3 +-- ...K-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb | 2 +- .../Scalasca-1.4.3-gompi-1.4.12-no-OFED.eb | 4 ++-- .../easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb | 4 ++-- ...pely-1.2.15-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 14 +++++++------- .../Shapely-1.2.15-goolf-1.4.10-Python-2.7.3.eb | 14 +++++++------- .../Shapely-1.2.15-ictce-4.0.6-Python-2.7.3.eb | 14 +++++++------- .../Shapely-1.2.15-ictce-5.3.0-Python-2.7.3.eb | 14 +++++++------- ...phinx-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 +++--- .../Sphinx-1.1.3-goolf-1.4.10-Python-2.7.3.eb | 6 +++--- .../Sphinx-1.1.3-ictce-4.0.6-Python-2.7.3.eb | 6 +++--- .../Sphinx-1.1.3-ictce-5.3.0-Python-2.7.3.eb | 6 +++--- .../s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb | 6 +++--- .../easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb | 6 +++--- .../easyconfigs/s/Stow/Stow-1.3.3-ictce-4.0.6.eb | 6 +++--- .../easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb | 6 +++--- .../s/Stride/Stride-1.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/s/Stride/Stride-1.0-ictce-5.3.0.eb | 2 +- .../s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb | 4 ++-- ...ools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 +++--- .../setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb | 6 +++--- .../setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb | 6 +++--- .../setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb | 6 +++--- .../s/sparsehash/sparsehash-2.0.2-ictce-4.0.6.eb | 2 +- .../s/sparsehash/sparsehash-2.0.2-ictce-5.3.0.eb | 2 +- 70 files changed, 123 insertions(+), 122 deletions(-) diff --git a/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb b/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb index a74b423aa7..cd91fac4e4 100644 --- a/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb +++ b/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb @@ -39,6 +39,6 @@ sanity_check_paths = { 'dirs': [] } -runtest = 'installcheck' # N.B. the current Makefile contains just a placeholder and is empty +runtest = 'installcheck' # N.B. the current Makefile contains just a placeholder and is empty moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/s/SIBELia/SIBELia-3.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SIBELia/SIBELia-3.0.4-goolf-1.4.10.eb index 2bba2e77c8..5c52477972 100644 --- a/easybuild/easyconfigs/s/SIBELia/SIBELia-3.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SIBELia/SIBELia-3.0.4-goolf-1.4.10.eb @@ -31,4 +31,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb index aaac9462ce..49346a9d1c 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb @@ -26,7 +26,8 @@ configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortve sanity_check_paths = { 'files': ['bin/sip', 'include/sip.h'] + - ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + ['lib/python%s/site-packages/%s' % (pyshortver, x) + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb index f0dcc913e9..e61810f5fd 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb @@ -26,7 +26,8 @@ configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortve sanity_check_paths = { 'files': ['bin/sip', 'include/sip.h'] + - ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + ['lib/python%s/site-packages/%s' % (pyshortver, x) + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb index af473b7d9f..eed3ec9cee 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb @@ -26,7 +26,8 @@ configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortve sanity_check_paths = { 'files': ['bin/sip', 'include/sip.h'] + - ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + ['lib/python%s/site-packages/%s' % (pyshortver, x) + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb index 2fb045fa84..517317038b 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb @@ -26,7 +26,8 @@ configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortve sanity_check_paths = { 'files': ['bin/sip', 'include/sip.h'] + - ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + ['lib/python%s/site-packages/%s' % (pyshortver, x) + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb index 457e09c556..b2e1479cba 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb @@ -26,7 +26,8 @@ configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortve sanity_check_paths = { 'files': ['bin/sip', 'include/sip.h'] + - ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + ['lib/python%s/site-packages/%s' % (pyshortver, x) + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb index a2509710ab..ed0395223c 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb @@ -25,7 +25,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['simread', 'smalt', 'mixreads','readstats']], + 'files': ['bin/%s' % x for x in ['simread', 'smalt', 'mixreads', 'readstats']], 'dirs': [] } diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb index 97b9385894..16d05cf341 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb @@ -25,7 +25,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['simread', 'smalt', 'mixreads','readstats']], + 'files': ['bin/%s' % x for x in ['simread', 'smalt', 'mixreads', 'readstats']], 'dirs': [] } diff --git a/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb b/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb index 8bbd1d0d43..67f7cd27da 100644 --- a/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb +++ b/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'SOAPaligner' version = '2.21' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb index 195190a776..7e9207e3f1 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb @@ -30,7 +30,7 @@ patches = ['SOAPdenovo2-fix-unistd-includes.patch'] # parallel build is broken maxparallel = 1 -files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] +files_to_copy = [(['SOAPdenovo-127mer', 'SOAPdenovo-63mer'], 'bin')] sanity_check_paths = { 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb index c597bc0601..e74ff0cb83 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb @@ -30,7 +30,7 @@ patches = ['SOAPdenovo2-fix-unistd-includes.patch'] # parallel build is broken maxparallel = 1 -files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] +files_to_copy = [(['SOAPdenovo-127mer', 'SOAPdenovo-63mer'], 'bin')] sanity_check_paths = { 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb index 003c593651..6e27e80aad 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb @@ -30,7 +30,7 @@ patches = ['SOAPdenovo2-fix-unistd-includes.patch'] # parallel build is broken maxparallel = 1 -files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] +files_to_copy = [(['SOAPdenovo-127mer', 'SOAPdenovo-63mer'], 'bin')] sanity_check_paths = { 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb index 16d7b49429..d56a8ae4dd 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb @@ -30,7 +30,7 @@ patches = ['SOAPdenovo2-fix-unistd-includes.patch'] # parallel build is broken maxparallel = 1 -files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] +files_to_copy = [(['SOAPdenovo-127mer', 'SOAPdenovo-63mer'], 'bin')] sanity_check_paths = { 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb index 829511351f..4948eef292 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015b.eb @@ -30,7 +30,7 @@ patches = ['SOAPdenovo2-fix-unistd-includes.patch'] # parallel build is broken maxparallel = 1 -files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] +files_to_copy = [(['SOAPdenovo-127mer', 'SOAPdenovo-63mer'], 'bin')] sanity_check_paths = { 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.0.0-goolf-1.4.10.eb index f8b0fa21e0..ab6bd52347 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.0.0-goolf-1.4.10.eb @@ -33,4 +33,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.1.0-goolf-1.4.10.eb index 59c84e5a28..5eb12170f6 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.1.0-goolf-1.4.10.eb @@ -33,4 +33,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb index ede241886d..7984157482 100644 --- a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb @@ -17,7 +17,7 @@ checksums = ['dd2941e3a28ff90a79b571273c10aacf'] skipsteps = ['source'] # 10 million array elements (1000 runs): requires ~224MB of memory -cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " # 100 million array elements (1000 runs): requires ~2.2GiB of memory cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " # 1 billion array elements (1000 runs): requires ~22.4 GiB of memory diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1.eb index 210286f19d..6c10e15771 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1.eb @@ -31,7 +31,7 @@ dependencies = [ (blacslib, blacsver) ] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb index adc0860457..fc37a0988b 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb @@ -21,7 +21,7 @@ blacsn = 'BLACS' blacsv = '1.1' blacs = "-%s-%s" % (blacsn, blacsv) -versionsuffix = "%s%s"% (acml, blacs) +versionsuffix = "%s%s" % (acml, blacs) # both icc and ifort are needed, but ifort is not part of icc 'toolkit' dependencies = [ diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.1-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.1-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0.eb index 269cb64669..f837989fc4 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.1-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.1-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0.eb @@ -26,7 +26,7 @@ dependencies = [ (lapacklib, lapackver) ] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 904f9125ac..ac50d0ef91 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index df6546768d..4f7213c206 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index d0e2892049..abdf8ee538 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 5325489376..18d673bc52 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 9f4ac4da77..7b0e530a27 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 4e2c7a1161..fbd7ceb342 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb index 4792a692ea..cae50d0f3e 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.8.4'))] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.9a2-ACML-5.2.0-gfortran-64bit.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.9a2-ACML-5.2.0-gfortran-64bit.eb index b8ff206dfb..2756603966 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.9a2-ACML-5.2.0-gfortran-64bit.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.9a2-ACML-5.2.0-gfortran-64bit.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blas_lapack_lib, blas_lapack_ver, blas_lapack_suff dependencies = [(blas_lapack_lib, blas_lapack_ver, blas_lapack_suff, True)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 04f36f4b91..a669a672e1 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 8f7ad295d1..0cb313ec9d 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 5e0e14ba2c..a9d14c3010 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-ATLAS-3.10.1-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-ATLAS-3.10.1-LAPACK-3.4.2.eb index 7e8bf14eee..d9714deb73 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-ATLAS-3.10.1-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-ATLAS-3.10.1-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ dependencies = [ (lapacklib, lapackver), ] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-no-OFED-ATLAS-3.10.1-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-no-OFED-ATLAS-3.10.1-LAPACK-3.4.2.eb index 68e8936860..cdbebf7d1b 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-no-OFED-ATLAS-3.10.1-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-no-OFED-ATLAS-3.10.1-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ dependencies = [ (lapacklib, lapackver), ] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-OpenBLAS-0.2.8-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-OpenBLAS-0.2.8-LAPACK-3.5.0.eb index 2a0a7e12ce..17094c0c6f 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-OpenBLAS-0.2.8-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-OpenBLAS-0.2.8-LAPACK-3.5.0.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb index b55976ccac..7815082cf2 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb index a52473e7ff..a53493b9f7 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb index b037ae507c..98a3aca262 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb index 94cfcc38e5..4f12059c03 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.8.4'))] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2014b-OpenBLAS-0.2.9-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2014b-OpenBLAS-0.2.9-LAPACK-3.5.0.eb index 134eb47e4d..f560b92bf9 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2014b-OpenBLAS-0.2.9-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2014b-OpenBLAS-0.2.9-LAPACK-3.5.0.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.8.3'))] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb index e8390ed236..f65260e697 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff, ('GNU', '4.9.2-2.25'))] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0.eb index be40d5d1ed..ed214b72f2 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.2'))] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb index 758c146b83..e17684d2a5 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff, ('GNU', '4.9.3-2.25'))] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb index 1326db5fe2..00ff5f97ba 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.3-2.25'))] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb index 77f58e7b27..fdc1dfd842 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb index ac55389f2d..292ec23d39 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb @@ -23,8 +23,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) dependencies = [(blaslib, blasver, blassuff, comp)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'numlib' - diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb index 325514fe67..243f17e8c7 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s%s" % (blas_lapack_lib, blas_lapack_ver, blas_lapack_suff dependencies = [(blas_lapack_lib, blas_lapack_ver, blas_lapack_suff, True)] -## parallel build tends to fail, so disabling it +# parallel build tends to fail, so disabling it parallel = 1 moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-1.4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-1.4.3-gompi-1.4.12-no-OFED.eb index aad8b175e4..26b61def41 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-1.4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-1.4.3-gompi-1.4.12-no-OFED.eb @@ -27,8 +27,8 @@ dependencies = [ ('OPARI2', '1.0.7'), ('PAPI', '5.2.0'), ('PDT', '3.19'), -# Scalasca cannot handle name changes yet introduced with OTF-1.12.3 -# ('OTF', '1.12.4'), + # Scalasca cannot handle name changes yet introduced with OTF-1.12.3 + # ('OTF', '1.12.4'), ] # http://apps.fz-juelich.de/scalasca/releases/scalasca/1.4/dist/scalasca-1.4.3.tar.gz diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb index 0676f01766..987ce669c8 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb @@ -21,8 +21,8 @@ builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] dependencies = [ ('APR', '1.5.2'), ('APR-util', '1.5.4'), -# ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 87deeb47fe..5221d93273 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -19,14 +19,14 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('setuptools', '0.6c11', versionsuffix), - ('GEOS', '3.3.5'), - ] + (python, pythonversion), + ('setuptools', '0.6c11', versionsuffix), + ('GEOS', '3.3.5'), +] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/site.py' % (pythonshortversion)], - 'dirs': [] - } + 'files': ['lib/python%s/site-packages/site.py' % (pythonshortversion)], + 'dirs': [] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goolf-1.4.10-Python-2.7.3.eb index 758a4009e5..2aecbeae80 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goolf-1.4.10-Python-2.7.3.eb @@ -19,14 +19,14 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('setuptools', '0.6c11', versionsuffix), - ('GEOS', '3.3.5'), - ] + (python, pythonversion), + ('setuptools', '0.6c11', versionsuffix), + ('GEOS', '3.3.5'), +] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/site.py' % (pythonshortversion)], - 'dirs': [] - } + 'files': ['lib/python%s/site-packages/site.py' % (pythonshortversion)], + 'dirs': [] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-4.0.6-Python-2.7.3.eb index b6ecffc690..ad94a62e1c 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-4.0.6-Python-2.7.3.eb @@ -19,14 +19,14 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('setuptools', '0.6c11', versionsuffix), - ('GEOS', '3.3.5'), - ] + (python, pythonversion), + ('setuptools', '0.6c11', versionsuffix), + ('GEOS', '3.3.5'), +] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/site.py' % (pythonshortversion)], - 'dirs': [] - } + 'files': ['lib/python%s/site-packages/site.py' % (pythonshortversion)], + 'dirs': [] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-5.3.0-Python-2.7.3.eb index 8727c7a7cb..1b6cb746c1 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-5.3.0-Python-2.7.3.eb @@ -19,14 +19,14 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('setuptools', '0.6c11', versionsuffix), - ('GEOS', '3.3.5'), - ] + (python, pythonversion), + ('setuptools', '0.6c11', versionsuffix), + ('GEOS', '3.3.5'), +] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/site.py' % (pythonshortversion)], - 'dirs': [] - } + 'files': ['lib/python%s/site-packages/site.py' % (pythonshortversion)], + 'dirs': [] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index b9a94e2e9e..520c4a6f15 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -27,8 +27,8 @@ dependencies = [(python, pyver), runtest = "make test" sanity_check_paths = { - 'files': ["bin/sphinx-%s" % x for x in ["apidoc", "autogen", "build", "quickstart"]], - 'dirs': ["lib/python%s/site-packages/%s-%s-py%s.egg" % (pyshortver, name, version, pyshortver)] - } + 'files': ["bin/sphinx-%s" % x for x in ["apidoc", "autogen", "build", "quickstart"]], + 'dirs': ["lib/python%s/site-packages/%s-%s-py%s.egg" % (pyshortver, name, version, pyshortver)] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goolf-1.4.10-Python-2.7.3.eb index 61173fdddd..d7ce90b557 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goolf-1.4.10-Python-2.7.3.eb @@ -27,8 +27,8 @@ dependencies = [(python, pyver), runtest = "make test" sanity_check_paths = { - 'files': ["bin/sphinx-%s" % x for x in ["apidoc", "autogen", "build", "quickstart"]], - 'dirs': ["lib/python%s/site-packages/%s-%s-py%s.egg" % (pyshortver, name, version, pyshortver)] - } + 'files': ["bin/sphinx-%s" % x for x in ["apidoc", "autogen", "build", "quickstart"]], + 'dirs': ["lib/python%s/site-packages/%s-%s-py%s.egg" % (pyshortver, name, version, pyshortver)] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-4.0.6-Python-2.7.3.eb index 069dffe6d0..9807eeeeb2 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-4.0.6-Python-2.7.3.eb @@ -27,8 +27,8 @@ dependencies = [(python, pyver), runtest = "make test" sanity_check_paths = { - 'files': ["bin/sphinx-%s" % x for x in ["apidoc", "autogen", "build", "quickstart"]], - 'dirs': ["lib/python%s/site-packages/%s-%s-py%s.egg" % (pyshortver, name, version, pyshortver)] - } + 'files': ["bin/sphinx-%s" % x for x in ["apidoc", "autogen", "build", "quickstart"]], + 'dirs': ["lib/python%s/site-packages/%s-%s-py%s.egg" % (pyshortver, name, version, pyshortver)] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-5.3.0-Python-2.7.3.eb index 300df5535f..79877de835 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-5.3.0-Python-2.7.3.eb @@ -27,8 +27,8 @@ dependencies = [(python, pyver), runtest = "make test" sanity_check_paths = { - 'files': ["bin/sphinx-%s" % x for x in ["apidoc", "autogen", "build", "quickstart"]], - 'dirs': ["lib/python%s/site-packages/%s-%s-py%s.egg" % (pyshortver, name, version, pyshortver)] - } + 'files': ["bin/sphinx-%s" % x for x in ["apidoc", "autogen", "build", "quickstart"]], + 'dirs': ["lib/python%s/site-packages/%s-%s-py%s.egg" % (pyshortver, name, version, pyshortver)] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb index 08108a8a47..0d2c3773f8 100644 --- a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb @@ -24,8 +24,8 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sanity_check_paths = { - 'files': ['bin/stow'], - 'dirs': [] - } + 'files': ['bin/stow'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb index bff8348243..df639eb5dc 100644 --- a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb @@ -24,8 +24,8 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['bin/stow'], - 'dirs': [] - } + 'files': ['bin/stow'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-4.0.6.eb b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-4.0.6.eb index 3dacc81151..e7734dc526 100644 --- a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-4.0.6.eb @@ -24,8 +24,8 @@ source_urls = [GNU_SOURCE] toolchain = {'version': '4.0.6', 'name': 'ictce'} sanity_check_paths = { - 'files': ['bin/stow'], - 'dirs': [] - } + 'files': ['bin/stow'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb index 03fc7dd37c..43fedd4e90 100644 --- a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb @@ -25,8 +25,8 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'ictce', 'version': '5.3.0'} sanity_check_paths = { - 'files': ['bin/stow'], - 'dirs': [] - } + 'files': ['bin/stow'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Stride/Stride-1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Stride/Stride-1.0-goolf-1.4.10.eb index 5ab1176c2f..4982431a8c 100644 --- a/easybuild/easyconfigs/s/Stride/Stride-1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Stride/Stride-1.0-goolf-1.4.10.eb @@ -12,7 +12,7 @@ description = "STRIDE is a program to recognize secondary structural elements in toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://ftp.ebi.ac.uk/pub/software/unix/stride/src/'] -sources = ['%(namelower)s.tar.gz' ] +sources = ['%(namelower)s.tar.gz'] files_to_copy = [(['stride'], "bin")] diff --git a/easybuild/easyconfigs/s/Stride/Stride-1.0-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Stride/Stride-1.0-ictce-5.3.0.eb index da61249bcf..1a6fb2182d 100644 --- a/easybuild/easyconfigs/s/Stride/Stride-1.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/Stride/Stride-1.0-ictce-5.3.0.eb @@ -12,7 +12,7 @@ description = "STRIDE is a program to recognize secondary structural elements in toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://ftp.ebi.ac.uk/pub/software/unix/stride/src/'] -sources = ['%(namelower)s.tar.gz' ] +sources = ['%(namelower)s.tar.gz'] files_to_copy = [(['stride'], "bin")] diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb index f5e2b9d7dd..0c7b7b159e 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb @@ -20,12 +20,12 @@ description = """ segemehl is a software to map short sequencer reads to referen toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/'] -sources = ['%s_%s.tar.gz' % (name, version.replace('.','_'))] +sources = ['%s_%s.tar.gz' % (name, version.replace('.', '_'))] files_to_copy = [(["haarz.x", "lack.x", "segemehl.x"], "bin")] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["haarz.x", "lack.x" , "segemehl.x"]], + 'files': ["bin/%s" % x for x in ["haarz.x", "lack.x", "segemehl.x"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 637462ec29..1283db629b 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -22,8 +22,8 @@ py_short_ver = ".".join(pythonversion.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], - 'dirs': [] - } + 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb index 517404e770..a716508465 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb @@ -22,8 +22,8 @@ py_short_ver = ".".join(pythonversion.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], - 'dirs': [] - } + 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb index 62aa6e2bbc..8ec68722c7 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb @@ -22,8 +22,8 @@ py_short_ver = ".".join(pythonversion.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], - 'dirs': [] - } + 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb index 82de605fe3..cc07ddd7a2 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb @@ -22,8 +22,8 @@ py_short_ver = ".".join(pythonversion.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], - 'dirs': [] - } + 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-4.0.6.eb index 0e8273491c..97d974db7a 100644 --- a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-4.0.6.eb @@ -13,7 +13,7 @@ toolchainopts = {'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sparsehash.googlecode.com/files'] -#runtest = "check" # 1/7 tests fails (hashtable_test), so disabling 'make check' for now +# runtest = "check" # 1/7 tests fails (hashtable_test), so disabling 'make check' for now sanity_check_paths = { 'files': ['include/sparsehash/%s' % x for x in ['dense_hash_map', 'dense_hash_set', 'sparse_hash_map', diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-5.3.0.eb index ef04dcc09e..dc0162d6b6 100644 --- a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ toolchainopts = {'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sparsehash.googlecode.com/files'] -#runtest = "check" # 1/7 tests fails (hashtable_test), so disabling 'make check' for now +# runtest = "check" # 1/7 tests fails (hashtable_test), so disabling 'make check' for now sanity_check_paths = { 'files': ['include/sparsehash/%s' % x for x in ['dense_hash_map', 'dense_hash_set', 'sparse_hash_map', -- GitLab From 47c6d7213157326876cbc52b6205cb1ef3426bf0 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:56:34 +0100 Subject: [PATCH 0280/2133] Style fixes with autopep8: tuv Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb | 3 ++- .../TiCCutils-0.3-goalf-1.1.0-no-OFED.eb | 2 +- .../t/TiCCutils/TiCCutils-0.3-goolf-1.4.10.eb | 2 +- .../t/TiCCutils/TiCCutils-0.3-ictce-4.1.13.eb | 2 +- .../t/TiCCutils/TiCCutils-0.3-ictce-5.3.0.eb | 2 +- .../t/TiCCutils/TiCCutils-0.7-intel-2015b.eb | 2 +- .../TiMBL/TiMBL-6.4.3-goalf-1.1.0-no-OFED.eb | 2 +- .../t/TiMBL/TiMBL-6.4.3-goolf-1.4.10.eb | 2 +- .../t/TiMBL/TiMBL-6.4.3-ictce-4.1.13.eb | 2 +- .../t/TiMBL/TiMBL-6.4.3-ictce-5.3.0.eb | 2 +- .../t/TiMBL/TiMBL-6.4.6-intel-2015b.eb | 2 +- .../TinySVM-0.09-goalf-1.1.0-no-OFED.eb | 2 +- .../t/TinySVM/TinySVM-0.09-goolf-1.4.10.eb | 2 +- .../t/TinySVM/TinySVM-0.09-ictce-4.1.13.eb | 2 +- .../t/TinySVM/TinySVM-0.09-ictce-5.3.0.eb | 2 +- .../Tornado-2012.09.06-goalf-1.1.0-no-OFED.eb | 2 +- ...0.12.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 10 ++++----- ...linos-10.12.2-goolf-1.4.10-Python-2.7.3.eb | 16 +++++++------- ...ilinos-10.12.2-ictce-4.0.6-Python-2.7.3.eb | 10 ++++----- ...ilinos-10.12.2-ictce-5.3.0-Python-2.7.3.eb | 10 ++++----- .../Trim_Galore-0.3.7-goolf-1.4.10.eb | 4 ++-- .../Trinity-2012-10-05-goalf-1.1.0-no-OFED.eb | 20 ++++++++--------- .../Trinity-2012-10-05-goolf-1.4.10.eb | 22 +++++++++---------- .../Trinity-2012-10-05-ictce-3.2.2.u3.eb | 22 +++++++++---------- .../Trinity/Trinity-2012-10-05-ictce-5.3.0.eb | 22 +++++++++---------- .../t/tclcl/tclcl-1.20-goalf-1.1.0-no-OFED.eb | 2 +- .../t/tclcl/tclcl-1.20-goolf-1.4.10.eb | 2 +- .../t/tclcl/tclcl-1.20-ictce-5.3.0.eb | 2 +- .../t/texinfo/texinfo-5.2-GCC-4.8.2.eb | 10 ++++----- ...-2.0.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 10 ++++----- .../UFC-2.0.5-goolf-1.4.10-Python-2.7.3.eb | 10 ++++----- .../UFC/UFC-2.0.5-ictce-4.0.6-Python-2.7.3.eb | 10 ++++----- .../UFC/UFC-2.0.5-ictce-5.3.0-Python-2.7.3.eb | 10 ++++----- ...-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 ++--- .../UFL-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 6 ++--- .../UFL/UFL-1.0.0-ictce-4.0.6-Python-2.7.3.eb | 6 ++--- .../UFL/UFL-1.0.0-ictce-5.3.0-Python-2.7.3.eb | 6 ++--- .../util-linux-2.22.2-goalf-1.1.0-no-OFED.eb | 2 +- .../util-linux-2.22.2-goolf-1.4.10.eb | 2 +- .../util-linux-2.22.2-ictce-4.1.13.eb | 2 +- .../util-linux-2.22.2-ictce-5.3.0.eb | 2 +- .../util-linux-2.22.2-ictce-5.5.0.eb | 2 +- .../util-linux-2.22.2-intel-2014b.eb | 4 ++-- .../util-linux/util-linux-2.24-ictce-5.5.0.eb | 2 +- .../util-linux-2.24.1-ictce-5.5.0.eb | 2 +- .../util-linux-2.26.1-foss-2015a.eb | 2 +- .../util-linux-2.26.1-intel-2015a.eb | 2 +- .../util-linux-2.26.2-intel-2015a.eb | 2 +- .../util-linux-2.27.1-intel-2015b.eb | 2 +- ...-0.1.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 ++--- ...C-tools-0.1.2-ictce-4.1.13-Python-2.7.3.eb | 6 ++--- ...SC-tools-0.1.2-ictce-5.3.0-Python-2.7.3.eb | 6 ++--- .../v/VTK/VTK-5.10.1-goalf-1.1.0-no-OFED.eb | 6 ++--- .../v/VTK/VTK-5.10.1-ictce-4.0.6.eb | 6 ++--- .../v/VTK/VTK-5.10.1-ictce-5.3.0.eb | 6 ++--- .../easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb | 3 ++- .../easyconfigs/v/Vampir/Vampir-8.4.1.eb | 3 ++- .../VampirServer-8.4.1-gompi-2015a.eb | 3 ++- .../ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb | 12 +++++----- .../ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 2 +- .../ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb | 12 +++++----- .../ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 12 +++++----- .../ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 5 ++--- .../easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb | 4 ++-- ...-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 ++--- .../Viper-1.0.0-ictce-4.0.6-Python-2.7.3.eb | 6 ++--- .../Viper-1.0.0-ictce-5.3.0-Python-2.7.3.eb | 6 ++--- ...vincent-0.4.4-intel-2015a-Python-2.7.10.eb | 2 +- ...vincent-0.4.4-intel-2015b-Python-2.7.10.eb | 2 +- 69 files changed, 196 insertions(+), 193 deletions(-) diff --git a/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb b/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb index 9fc79c204d..35f352db69 100644 --- a/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb +++ b/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb @@ -11,7 +11,8 @@ easyblock = 'ConfigureMake' name = 'TCC' version = '0.9.26' -# altversions = ['0.9.21', '0.9.22', '0.9.23', '0.9.24', '0.9.25', '0.9.26'] # older versions may require more special handling +# altversions = ['0.9.21', '0.9.22', '0.9.23', '0.9.24', '0.9.25', +# '0.9.26'] # older versions may require more special handling homepage = 'http://bellard.org/tcc/' description = """The Tiny C Compiler (aka TCC, tCc, or TinyCC) is an x86 and x86-64 C compiler diff --git a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-goalf-1.1.0-no-OFED.eb index f64c40563e..0a31dc00cb 100644 --- a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-goalf-1.1.0-no-OFED.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'TiCCutils' version = '0.3' -homepage = 'http://software.ticc.uvt.nl/' # no real homepage found +homepage = 'http://software.ticc.uvt.nl/' # no real homepage found description = """TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and Centre for Dutch Language and Speech at University of Antwerp.""" diff --git a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-goolf-1.4.10.eb index 445f99bec6..1a4e06f1c9 100644 --- a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-goolf-1.4.10.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'TiCCutils' version = '0.3' -homepage = 'http://software.ticc.uvt.nl/' # no real homepage found +homepage = 'http://software.ticc.uvt.nl/' # no real homepage found description = """TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and Centre for Dutch Language and Speech at University of Antwerp.""" diff --git a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-ictce-4.1.13.eb b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-ictce-4.1.13.eb index 70bc5a288d..c735eaf222 100644 --- a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-ictce-4.1.13.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'TiCCutils' version = '0.3' -homepage = 'http://software.ticc.uvt.nl/' # no real homepage found +homepage = 'http://software.ticc.uvt.nl/' # no real homepage found description = """TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and Centre for Dutch Language and Speech at University of Antwerp.""" diff --git a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-ictce-5.3.0.eb index a5a1f3ba0c..0dcf061046 100644 --- a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.3-ictce-5.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'TiCCutils' version = '0.3' -homepage = 'http://software.ticc.uvt.nl/' # no real homepage found +homepage = 'http://software.ticc.uvt.nl/' # no real homepage found description = """TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and Centre for Dutch Language and Speech at University of Antwerp.""" diff --git a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.7-intel-2015b.eb b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.7-intel-2015b.eb index d62879bb69..563e538143 100644 --- a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.7-intel-2015b.eb +++ b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.7-intel-2015b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'TiCCutils' version = '0.7' -homepage = 'http://software.ticc.uvt.nl/' # no real homepage found +homepage = 'http://software.ticc.uvt.nl/' # no real homepage found description = """TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and Centre for Dutch Language and Speech at University of Antwerp.""" diff --git a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-goalf-1.1.0-no-OFED.eb index efab901860..8f1566ed45 100644 --- a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://software.ticc.uvt.nl/'] dependencies = [ - ('TiCCutils' , '0.3'), + ('TiCCutils', '0.3'), ('libxml2', '2.9.0'), ] diff --git a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-goolf-1.4.10.eb index 9db7b9cd71..4c496b94e6 100644 --- a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-goolf-1.4.10.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://software.ticc.uvt.nl/'] dependencies = [ - ('TiCCutils' , '0.3'), + ('TiCCutils', '0.3'), ('libxml2', '2.9.0'), ] diff --git a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-ictce-4.1.13.eb b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-ictce-4.1.13.eb index ef78059fdf..85caf06073 100644 --- a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-ictce-4.1.13.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://software.ticc.uvt.nl/'] dependencies = [ - ('TiCCutils' , '0.3'), + ('TiCCutils', '0.3'), ('libxml2', '2.9.0'), ] diff --git a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-ictce-5.3.0.eb b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-ictce-5.3.0.eb index 72a8eb72c8..4a0a138713 100644 --- a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.3-ictce-5.3.0.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://software.ticc.uvt.nl/'] dependencies = [ - ('TiCCutils' , '0.3'), + ('TiCCutils', '0.3'), ('libxml2', '2.9.0'), ] diff --git a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.6-intel-2015b.eb b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.6-intel-2015b.eb index 9f42760123..d47e571a90 100644 --- a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.6-intel-2015b.eb +++ b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.6-intel-2015b.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://software.ticc.uvt.nl/'] dependencies = [ - ('TiCCutils' , '0.7'), + ('TiCCutils', '0.7'), ('libxml2', '2.9.2'), ] diff --git a/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-goalf-1.1.0-no-OFED.eb index 456eed6b56..1a655e2f36 100644 --- a/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-goalf-1.1.0-no-OFED.eb @@ -15,7 +15,7 @@ toolchainopts = {'optarch': True, 'pic': True, 'opt': True, 'unroll': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://chasen.org/~taku/software/TinySVM/src'] -#original CXXFLAGS: -Wall -O9 -funroll-all-loops -finline -ffast-math +# original CXXFLAGS: -Wall -O9 -funroll-all-loops -finline -ffast-math buildopts = 'CXXFLAGS="$CXXFLAGS -Wall -funroll-all-loops -finline -ffast-math"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-goolf-1.4.10.eb b/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-goolf-1.4.10.eb index 3b1c60d110..2a3ee4cd04 100644 --- a/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-goolf-1.4.10.eb @@ -15,7 +15,7 @@ toolchainopts = {'optarch': True, 'pic': True, 'opt': True, 'unroll': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://chasen.org/~taku/software/TinySVM/src'] -#original CXXFLAGS: -Wall -O9 -funroll-all-loops -finline -ffast-math +# original CXXFLAGS: -Wall -O9 -funroll-all-loops -finline -ffast-math buildopts = 'CXXFLAGS="$CXXFLAGS -Wall -funroll-all-loops -finline -ffast-math"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-ictce-4.1.13.eb b/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-ictce-4.1.13.eb index 7676e956fa..4191830cf2 100644 --- a/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-ictce-4.1.13.eb @@ -15,7 +15,7 @@ toolchainopts = {'optarch': True, 'pic': True, 'opt': True, 'unroll': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://chasen.org/~taku/software/TinySVM/src'] -#original CXXFLAGS: -Wall -O9 -funroll-all-loops -finline -ffast-math +# original CXXFLAGS: -Wall -O9 -funroll-all-loops -finline -ffast-math buildopts = 'CXXFLAGS="$CXXFLAGS -Wall -funroll-all-loops -finline"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-ictce-5.3.0.eb b/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-ictce-5.3.0.eb index 7c112ec105..3eb47571e1 100644 --- a/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/TinySVM/TinySVM-0.09-ictce-5.3.0.eb @@ -15,7 +15,7 @@ toolchainopts = {'optarch': True, 'pic': True, 'opt': True, 'unroll': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://chasen.org/~taku/software/TinySVM/src'] -#original CXXFLAGS: -Wall -O9 -funroll-all-loops -finline -ffast-math +# original CXXFLAGS: -Wall -O9 -funroll-all-loops -finline -ffast-math buildopts = 'CXXFLAGS="$CXXFLAGS -Wall -funroll-all-loops -finline"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/Tornado/Tornado-2012.09.06-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tornado/Tornado-2012.09.06-goalf-1.1.0-no-OFED.eb index 3ad1ac0bbd..7e0e189b7c 100644 --- a/easybuild/easyconfigs/t/Tornado/Tornado-2012.09.06-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/Tornado/Tornado-2012.09.06-goalf-1.1.0-no-OFED.eb @@ -4,7 +4,7 @@ version = '2012.09.06' homepage = 'http://www.dhigroup.com/' description = """Tornado is a new kernel for modelling and virtual experimentation (i.e. any evaluation of a model) in the domain of water quality management""" - + toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index b287384487..4db1cfdda1 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -18,11 +18,11 @@ patches = ['fix-parmetis.patch'] # order matters! # ParMETIS needs to go after SCOTCH (because of incldue dirs) dependencies = [ - ('Boost', '1.49.0', versionsuffix ), - ('SCOTCH', '5.1.12b_esmumps'), - ('SuiteSparse', '3.7.0', '-withparmetis'), - ('ParMETIS', '4.0.2') - ] + ('Boost', '1.49.0', versionsuffix), + ('SCOTCH', '5.1.12b_esmumps'), + ('SuiteSparse', '3.7.0', '-withparmetis'), + ('ParMETIS', '4.0.2') +] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-goolf-1.4.10-Python-2.7.3.eb index 1ec0f27b13..ec1d8d6521 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-goolf-1.4.10-Python-2.7.3.eb @@ -14,18 +14,18 @@ source_urls = ['http://trilinos.sandia.gov/download/files/'] sources = ['%s-%s-Source.tar.gz' % (name.lower(), version)] patches = [ - 'fix-parmetis.patch', - 'Trilinos_GCC-4.7.patch', - ] + 'fix-parmetis.patch', + 'Trilinos_GCC-4.7.patch', +] # order matters! # ParMETIS needs to go after SCOTCH (because of incldue dirs) dependencies = [ - ('Boost', '1.49.0', versionsuffix ), - ('SCOTCH', '5.1.12b_esmumps'), - ('SuiteSparse', '3.7.0', '-withparmetis'), - ('ParMETIS', '4.0.2') - ] + ('Boost', '1.49.0', versionsuffix), + ('SCOTCH', '5.1.12b_esmumps'), + ('SuiteSparse', '3.7.0', '-withparmetis'), + ('ParMETIS', '4.0.2') +] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-4.0.6-Python-2.7.3.eb index fea45f6e5c..b9ba5e4b73 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-4.0.6-Python-2.7.3.eb @@ -18,11 +18,11 @@ patches = ['fix-parmetis.patch'] # order matters! # ParMETIS needs to go after SCOTCH (because of incldue dirs) dependencies = [ - ('Boost', '1.49.0', versionsuffix ), - ('SCOTCH', '5.1.12b_esmumps'), - ('SuiteSparse', '3.7.0', '-withparmetis'), - ('ParMETIS', '4.0.2') - ] + ('Boost', '1.49.0', versionsuffix), + ('SCOTCH', '5.1.12b_esmumps'), + ('SuiteSparse', '3.7.0', '-withparmetis'), + ('ParMETIS', '4.0.2') +] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-5.3.0-Python-2.7.3.eb index 84613e0ab2..4ee95fa909 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-10.12.2-ictce-5.3.0-Python-2.7.3.eb @@ -19,11 +19,11 @@ patches = ['fix-parmetis.patch'] # order matters! # ParMETIS needs to go after SCOTCH (because of incldue dirs) dependencies = [ - ('Boost', '1.49.0', versionsuffix ), - ('SCOTCH', '5.1.12b_esmumps'), - ('SuiteSparse', '3.7.0', '-withparmetis'), - ('ParMETIS', '4.0.2') - ] + ('Boost', '1.49.0', versionsuffix), + ('SCOTCH', '5.1.12b_esmumps'), + ('SuiteSparse', '3.7.0', '-withparmetis'), + ('ParMETIS', '4.0.2') +] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index 53e79949f3..5b029bff07 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -16,8 +16,8 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.10.1'), - ('cutadapt', '1.5', '-Python-2.7.10'), + ('FastQC', '0.10.1'), + ('cutadapt', '1.5', '-Python-2.7.10'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goalf-1.1.0-no-OFED.eb index 24e51d7fbb..c40d2edf57 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goalf-1.1.0-no-OFED.eb @@ -13,21 +13,21 @@ source_urls = [('http://sourceforge.net/projects/trinityrnaseq/files', 'download sources = ['trinityrnaseq_r%s.tgz' % version] patches = [ - 'chrysalis_commandline_noconsts_2012-10-05.patch', - 'cmd_forker_taskset_2012-10-05.patch', - 'trinitypl_increase_max_cpu_2012-10-05.patch', - 'rsem-plugin_makefile-cxx.patch', - ] + 'chrysalis_commandline_noconsts_2012-10-05.patch', + 'cmd_forker_taskset_2012-10-05.patch', + 'trinitypl_increase_max_cpu_2012-10-05.patch', + 'rsem-plugin_makefile-cxx.patch', +] java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', True), - ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), - ('ncurses', '5.9'), - ('zlib', '1.2.7'), - ] + (java, javaver, '', True), + ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), + ('ncurses', '5.9'), + ('zlib', '1.2.7'), +] bwapluginver = "0.5.7" RSEMmod = True diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb index 3a3bdebbaa..e966db8b0a 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb @@ -13,22 +13,22 @@ source_urls = [('http://sourceforge.net/projects/trinityrnaseq/files', 'download sources = ['trinityrnaseq_r%s.tgz' % version] patches = [ - 'chrysalis_commandline_noconsts_2012-10-05.patch', - 'cmd_forker_taskset_2012-10-05.patch', - 'trinitypl_increase_max_cpu_2012-10-05.patch', - 'rsem-plugin_makefile-cxx.patch', - 'trinity_jellyfish-GCC-4.7.patch', - ] + 'chrysalis_commandline_noconsts_2012-10-05.patch', + 'cmd_forker_taskset_2012-10-05.patch', + 'trinitypl_increase_max_cpu_2012-10-05.patch', + 'rsem-plugin_makefile-cxx.patch', + 'trinity_jellyfish-GCC-4.7.patch', +] java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', True), - ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), - ('ncurses', '5.9'), - ('zlib', '1.2.7'), - ] + (java, javaver, '', True), + ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), + ('ncurses', '5.9'), + ('zlib', '1.2.7'), +] bwapluginver = "0.5.7" RSEMmod = True diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-ictce-3.2.2.u3.eb index d7180a3903..62366fe15c 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-ictce-3.2.2.u3.eb @@ -13,22 +13,22 @@ source_urls = [('http://sourceforge.net/projects/trinityrnaseq/files', 'download sources = ['trinityrnaseq_r%s.tgz' % version] patches = [ - 'chrysalis_commandline_noconsts_2012-10-05.patch', - 'cmd_forker_taskset_2012-10-05.patch', - 'trinitypl_increase_max_cpu_2012-10-05.patch', - 'rsem-plugin_makefile-cxx.patch', - 'trinity_ictce-no-jellyfish.patch', - ] + 'chrysalis_commandline_noconsts_2012-10-05.patch', + 'cmd_forker_taskset_2012-10-05.patch', + 'trinitypl_increase_max_cpu_2012-10-05.patch', + 'rsem-plugin_makefile-cxx.patch', + 'trinity_ictce-no-jellyfish.patch', +] java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', True), - ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), - ('ncurses', '5.9'), - ('zlib', '1.2.7'), - ] + (java, javaver, '', True), + ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), + ('ncurses', '5.9'), + ('zlib', '1.2.7'), +] bwapluginver = "0.5.7" RSEMmod = True diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb index 76aac8d334..7f5d579222 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb @@ -14,22 +14,22 @@ source_urls = [('http://sourceforge.net/projects/trinityrnaseq/files', 'download sources = ['trinityrnaseq_r%s.tgz' % version] patches = [ - 'chrysalis_commandline_noconsts_2012-10-05.patch', - 'cmd_forker_taskset_2012-10-05.patch', - 'trinitypl_increase_max_cpu_2012-10-05.patch', - 'rsem-plugin_makefile-cxx.patch', - 'trinity_ictce-no-jellyfish.patch', - ] + 'chrysalis_commandline_noconsts_2012-10-05.patch', + 'cmd_forker_taskset_2012-10-05.patch', + 'trinitypl_increase_max_cpu_2012-10-05.patch', + 'rsem-plugin_makefile-cxx.patch', + 'trinity_ictce-no-jellyfish.patch', +] java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', True), - ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), - ('ncurses', '5.9'), - ('zlib', '1.2.7'), - ] + (java, javaver, '', True), + ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), + ('ncurses', '5.9'), + ('zlib', '1.2.7'), +] bwapluginver = "0.5.7" RSEMmod = True diff --git a/easybuild/easyconfigs/t/tclcl/tclcl-1.20-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/tclcl/tclcl-1.20-goalf-1.1.0-no-OFED.eb index ae48804dd3..5988030758 100644 --- a/easybuild/easyconfigs/t/tclcl/tclcl-1.20-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/tclcl/tclcl-1.20-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://prdownloads.sourceforge.net/otcl-tclcl'] tcl_ver = '8.5.12' dependencies = [ - ('Tcl',tcl_ver), + ('Tcl', tcl_ver), ('Tk', tcl_ver), ('otcl', '1.14'), ] diff --git a/easybuild/easyconfigs/t/tclcl/tclcl-1.20-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tclcl/tclcl-1.20-goolf-1.4.10.eb index 76b89b4e3d..0fa1db9859 100644 --- a/easybuild/easyconfigs/t/tclcl/tclcl-1.20-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/tclcl/tclcl-1.20-goolf-1.4.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://prdownloads.sourceforge.net/otcl-tclcl'] tcl_ver = '8.5.12' dependencies = [ - ('Tcl',tcl_ver), + ('Tcl', tcl_ver), ('Tk', tcl_ver), ('otcl', '1.14'), ] diff --git a/easybuild/easyconfigs/t/tclcl/tclcl-1.20-ictce-5.3.0.eb b/easybuild/easyconfigs/t/tclcl/tclcl-1.20-ictce-5.3.0.eb index 70183e7b6f..7009190de2 100644 --- a/easybuild/easyconfigs/t/tclcl/tclcl-1.20-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/tclcl/tclcl-1.20-ictce-5.3.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://prdownloads.sourceforge.net/otcl-tclcl'] tcl_ver = '8.5.12' dependencies = [ - ('Tcl',tcl_ver), + ('Tcl', tcl_ver), ('Tk', tcl_ver), ('otcl', '1.14'), ] diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb index 7e2b9ee6aa..e8a270b38c 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb @@ -17,11 +17,11 @@ preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " # This will overwrite a users $TEXMFHOME so this module is best used as a build dependency modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} -modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable \\$TEXMFHOME.\n" -modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" -modloadmsg += "new \\$TEXMFHOME to your custom directory and reset the value of \\$TEXMFHOME to point to that space:\n" -modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" -modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable \\$TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new \\$TEXMFHOME to your custom directory and reset the value of \\$TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" sanity_check_paths = { 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf', 'texmf/tex/texinfo/texinfo.tex'], diff --git a/easybuild/easyconfigs/u/UFC/UFC-2.0.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/u/UFC/UFC-2.0.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb index d5b5101177..764f2be10b 100644 --- a/easybuild/easyconfigs/u/UFC/UFC-2.0.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/u/UFC/UFC-2.0.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -17,11 +17,11 @@ pythonversion = '2.7.3' versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('Boost', '1.49.0', versionsuffix), - ('Instant', '1.0.0', versionsuffix), - ('SWIG', '2.0.4', versionsuffix), - ] + (python, pythonversion), + ('Boost', '1.49.0', versionsuffix), + ('Instant', '1.0.0', versionsuffix), + ('SWIG', '2.0.4', versionsuffix), +] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/u/UFC/UFC-2.0.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/u/UFC/UFC-2.0.5-goolf-1.4.10-Python-2.7.3.eb index 10b9d9e61d..47c5ff4491 100644 --- a/easybuild/easyconfigs/u/UFC/UFC-2.0.5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/u/UFC/UFC-2.0.5-goolf-1.4.10-Python-2.7.3.eb @@ -17,11 +17,11 @@ pythonversion = '2.7.3' versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('Boost', '1.49.0', versionsuffix), - ('Instant', '1.0.0', versionsuffix), - ('SWIG', '2.0.4', versionsuffix), - ] + (python, pythonversion), + ('Boost', '1.49.0', versionsuffix), + ('Instant', '1.0.0', versionsuffix), + ('SWIG', '2.0.4', versionsuffix), +] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/u/UFC/UFC-2.0.5-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/u/UFC/UFC-2.0.5-ictce-4.0.6-Python-2.7.3.eb index ea960b2f02..0a5f724b73 100644 --- a/easybuild/easyconfigs/u/UFC/UFC-2.0.5-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/u/UFC/UFC-2.0.5-ictce-4.0.6-Python-2.7.3.eb @@ -17,11 +17,11 @@ pythonversion = '2.7.3' versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('Boost', '1.49.0', versionsuffix), - ('Instant', '1.0.0', versionsuffix), - ('SWIG', '2.0.4', versionsuffix), - ] + (python, pythonversion), + ('Boost', '1.49.0', versionsuffix), + ('Instant', '1.0.0', versionsuffix), + ('SWIG', '2.0.4', versionsuffix), +] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/u/UFC/UFC-2.0.5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/u/UFC/UFC-2.0.5-ictce-5.3.0-Python-2.7.3.eb index 2be9be92da..4998756c2e 100644 --- a/easybuild/easyconfigs/u/UFC/UFC-2.0.5-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/u/UFC/UFC-2.0.5-ictce-5.3.0-Python-2.7.3.eb @@ -18,11 +18,11 @@ pythonversion = '2.7.3' versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ - (python, pythonversion), - ('Boost', '1.49.0', versionsuffix), - ('Instant', '1.0.0', versionsuffix), - ('SWIG', '2.0.4', versionsuffix), - ] + (python, pythonversion), + ('Boost', '1.49.0', versionsuffix), + ('Instant', '1.0.0', versionsuffix), + ('SWIG', '2.0.4', versionsuffix), +] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 9bd8667afb..806978a044 100644 --- a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -23,8 +23,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], - 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] - } + 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], + 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] +} moduleclass = 'cae' diff --git a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 4177e70f06..44bbfb4a06 100644 --- a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -23,8 +23,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], - 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] - } + 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], + 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] +} moduleclass = 'cae' diff --git a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-4.0.6-Python-2.7.3.eb index 55688fcbe6..0d8f8edb49 100644 --- a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-4.0.6-Python-2.7.3.eb @@ -23,8 +23,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], - 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] - } + 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], + 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] +} moduleclass = 'cae' diff --git a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-5.3.0-Python-2.7.3.eb index fcb84880d3..30a212235a 100644 --- a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-5.3.0-Python-2.7.3.eb @@ -24,8 +24,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], - 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] - } + 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], + 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] +} moduleclass = 'cae' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goalf-1.1.0-no-OFED.eb index 5c2f9f5f7c..5e621327c3 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goalf-1.1.0-no-OFED.eb @@ -22,7 +22,7 @@ configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb index 80fbeb975f..75238f2124 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb @@ -22,7 +22,7 @@ configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-4.1.13.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-4.1.13.eb index f9d273f24a..dadb7261d1 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-4.1.13.eb @@ -22,7 +22,7 @@ configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb index aa973159c7..ed49a78c1e 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb @@ -22,7 +22,7 @@ configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb index a3c1598357..43d67f412c 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb @@ -22,7 +22,7 @@ configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb index bfe2f53f72..df0a957cf2 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb @@ -8,7 +8,7 @@ description = """Set of Linux utilities""" toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['%s/v%s'%(homepage,'.'.join(version.split('.')[0:2]) )] +source_urls = ['%s/v%s' % (homepage, '.'.join(version.split('.')[0:2]))] sources = [SOURCELOWER_TAR_GZ] # disable account related utilities (they need OS dependant pam-devel files) @@ -22,7 +22,7 @@ configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb index c583476f42..be21e2d15b 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb @@ -22,7 +22,7 @@ configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb index ba35f12734..f71360b39b 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb @@ -24,7 +24,7 @@ configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/complet dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb index dc874b1a62..61d17ba4f2 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb @@ -26,7 +26,7 @@ configopts += "--without-python " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb index b640735411..c339492021 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb @@ -26,7 +26,7 @@ configopts += "--without-python " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb index 0d1eb341d5..dae5a4f297 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb @@ -26,7 +26,7 @@ configopts += "--without-python " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb index 43293be3b6..98645a6d82 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb @@ -26,7 +26,7 @@ configopts += "--without-python " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 2f4453a352..31f3ed4ec2 100644 --- a/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -7,9 +7,9 @@ description = """VSC-tools is a set of Python libraries and scripts that are com toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [ - 'vsc-base-0.95.tar.gz', - 'vsc-mympirun-3.0.5.tar.gz', - ] + 'vsc-base-0.95.tar.gz', + 'vsc-mympirun-3.0.5.tar.gz', +] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-ictce-4.1.13-Python-2.7.3.eb index efba5e0d07..cbae339789 100644 --- a/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-ictce-4.1.13-Python-2.7.3.eb @@ -7,9 +7,9 @@ description = """VSC-tools is a set of Python libraries and scripts that are com toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [ - 'vsc-base-0.95.tar.gz', - 'vsc-mympirun-3.0.5.tar.gz', - ] + 'vsc-base-0.95.tar.gz', + 'vsc-mympirun-3.0.5.tar.gz', +] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-ictce-5.3.0-Python-2.7.3.eb index 36fb089f67..4142cd2fe3 100644 --- a/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/v/VSC-tools/VSC-tools-0.1.2-ictce-5.3.0-Python-2.7.3.eb @@ -8,9 +8,9 @@ description = """VSC-tools is a set of Python libraries and scripts that are com toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [ - 'vsc-base-0.95.tar.gz', - 'vsc-mympirun-3.0.5.tar.gz', - ] + 'vsc-base-0.95.tar.gz', + 'vsc-mympirun-3.0.5.tar.gz', +] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/v/VTK/VTK-5.10.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/v/VTK/VTK-5.10.1-goalf-1.1.0-no-OFED.eb index 8f65a96e35..d0373056bb 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-5.10.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-5.10.1-goalf-1.1.0-no-OFED.eb @@ -36,8 +36,8 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} builddependencies = [('CMake', '2.8.4')] sanity_check_paths = { - 'files': ['bin/vtkEncodeString'], - 'dirs': ['lib/vtk-%s' % vermajor, 'include/vtk-%s' % vermajor] - } + 'files': ['bin/vtkEncodeString'], + 'dirs': ['lib/vtk-%s' % vermajor, 'include/vtk-%s' % vermajor] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-4.0.6.eb b/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-4.0.6.eb index 286f9e74f0..2a354f444a 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-4.0.6.eb @@ -36,8 +36,8 @@ toolchain = {'version': '4.0.6', 'name': 'ictce'} builddependencies = [('CMake', '2.8.4')] sanity_check_paths = { - 'files': ['bin/vtkEncodeString'], - 'dirs': ['lib/vtk-%s' % vermajor, 'include/vtk-%s' % vermajor] - } + 'files': ['bin/vtkEncodeString'], + 'dirs': ['lib/vtk-%s' % vermajor, 'include/vtk-%s' % vermajor] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-5.3.0.eb b/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-5.3.0.eb index 3d9b76d1f1..45d8b25c17 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-5.3.0.eb @@ -36,8 +36,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} builddependencies = [('CMake', '2.8.4')] sanity_check_paths = { - 'files': ['bin/vtkEncodeString'], - 'dirs': ['lib/vtk-%s' % vermajor, 'include/vtk-%s' % vermajor] - } + 'files': ['bin/vtkEncodeString'], + 'dirs': ['lib/vtk-%s' % vermajor, 'include/vtk-%s' % vermajor] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb index 44f692903f..4ebcf299af 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb @@ -30,7 +30,8 @@ sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] # Adjust this variable to point to the location of your Vampir license file license_file = '/example/licenses/path/vampir.license' -install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" +install_cmd = "./" + sources[0] + \ + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb index 5596a89f02..80a6746a4c 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb @@ -33,7 +33,8 @@ checksums = [ # Adjust this variable to point to the location of your Vampir license file license_file = '/example/licenses/path/vampir.license' -install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" +install_cmd = "./" + sources[0] + \ + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb index 09d9d1ef44..0d946c3eca 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -34,7 +34,8 @@ checksums = [ # Adjust this variable to point to the location of your Vampir license file license_file = '/example/licenses/path/vampir.license' -install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" +install_cmd = "./" + sources[0] + \ + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf", "lib/vampirserver-driver.%s" % SHLIB_EXT], diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb index 3f61b94705..7c6cf538ad 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb @@ -32,13 +32,13 @@ configopts = '--without-perl' #preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { - 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', - 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', - 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', 'aliduplex', 'Lalifold', '2Dfold', 'parconv', 'PKplex', 'plex', 'snoop', 'forester']] + - ['bin/Kinfold'], - 'dirs': [] - } + ['bin/Kinfold'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 6f92dee837..327bd773eb 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -37,7 +37,7 @@ sanity_check_paths = { 'paln', 'duplex', 'alifold', 'plfold', 'up', 'aliduplex', 'Lalifold', '2Dfold', 'parconv', 'PKplex', 'plex', 'snoop', 'forester']] + - ['bin/Kinfold'], + ['bin/Kinfold'], 'dirs': [], } diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb index 68de4eec04..9c115491a3 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb @@ -34,13 +34,13 @@ configopts = '--without-perl' #preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { - 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', - 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', - 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', 'aliduplex', 'Lalifold', '2Dfold', 'parconv', 'PKplex', 'plex', 'snoop', 'forester']] + - ['bin/Kinfold'], - 'dirs': [] - } + ['bin/Kinfold'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index 14f9815f66..b0f11b9ddd 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -35,13 +35,13 @@ configopts = '--without-perl' #preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { - 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', - 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', - 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', 'aliduplex', 'Lalifold', '2Dfold', 'parconv', 'PKplex', 'plex', 'snoop', 'forester']] + - ['bin/Kinfold'], - 'dirs': [] - } + ['bin/Kinfold'], + 'dirs': [] +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index 281ecf7b59..d9a8ebec92 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -19,7 +19,7 @@ homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" -toolchain = {'name': 'ictce', 'version': '5.5.0' } +toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] @@ -39,9 +39,8 @@ sanity_check_paths = { 'paln', 'duplex', 'alifold', 'plfold', 'up', 'aliduplex', 'Lalifold', '2Dfold', 'parconv', 'PKplex', 'plex', 'snoop', 'forester']] + - ['bin/Kinfold'], + ['bin/Kinfold'], 'dirs': [], } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb index 9ed98058b9..824152274f 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb @@ -22,12 +22,12 @@ sources = [SOURCELOWER_TAR_BZ2] dependencies = [ ('Python', '2.7.5'), ('Perl', '5.16.3') - ] +] configopts = '--with-features=huge --enable-pythoninterp=yes --enable-perlinterp=yes' sanity_check_paths = { - 'files': ['bin/vim','bin/vimdiff'], + 'files': ['bin/vim', 'bin/vimdiff'], 'dirs': [], } diff --git a/easybuild/easyconfigs/v/Viper/Viper-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/v/Viper/Viper-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index ba86942900..66555db5aa 100644 --- a/easybuild/easyconfigs/v/Viper/Viper-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/v/Viper/Viper-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -26,8 +26,8 @@ dependencies = [(python, pythonversion)] options = {'modulename': 'os'} sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/python%s/site-packages/viper' % pythonshortversion] - } + 'files': [], + 'dirs': ['bin', 'lib/python%s/site-packages/viper' % pythonshortversion] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-4.0.6-Python-2.7.3.eb index 45f56436e0..031d7e98f1 100644 --- a/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-4.0.6-Python-2.7.3.eb @@ -26,8 +26,8 @@ dependencies = [(python, pythonversion)] options = {'modulename': 'os'} sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/python%s/site-packages/viper' % pythonshortversion] - } + 'files': [], + 'dirs': ['bin', 'lib/python%s/site-packages/viper' % pythonshortversion] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-5.3.0-Python-2.7.3.eb index 144a9dcc46..5c807c96fb 100644 --- a/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-5.3.0-Python-2.7.3.eb @@ -27,8 +27,8 @@ dependencies = [(python, pythonversion)] options = {'modulename': 'os'} sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/python%s/site-packages/viper' % pythonshortversion] - } + 'files': [], + 'dirs': ['bin', 'lib/python%s/site-packages/viper' % pythonshortversion] +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/vincent/vincent-0.4.4-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/v/vincent/vincent-0.4.4-intel-2015a-Python-2.7.10.eb index f23a488554..0c1009a3ab 100644 --- a/easybuild/easyconfigs/v/vincent/vincent-0.4.4-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/v/vincent/vincent-0.4.4-intel-2015a-Python-2.7.10.eb @@ -10,7 +10,7 @@ description = """Vincent takes Python data structures (tuples, lists, dicts, and toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = [PYPI_SOURCE] +source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/v/vincent/vincent-0.4.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/v/vincent/vincent-0.4.4-intel-2015b-Python-2.7.10.eb index 3ee6bac253..c16f8a1ce6 100644 --- a/easybuild/easyconfigs/v/vincent/vincent-0.4.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/v/vincent/vincent-0.4.4-intel-2015b-Python-2.7.10.eb @@ -10,7 +10,7 @@ description = """Vincent takes Python data structures (tuples, lists, dicts, and toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = [PYPI_SOURCE] +source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' -- GitLab From 8c697aa9edc1f3985cdfd12945dea864e3b41186 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 28 Jan 2016 14:57:36 +0100 Subject: [PATCH 0281/2133] Style fixes with autopep8: x Generated by: find -name '*.eb' -print0 | xargs -0 autopep8 --max-line-length=120 -i -v --- .../XCrySDen-1.5.53-goalf-1.1.0-no-OFED.eb | 8 ++++---- .../x/XCrySDen/XCrySDen-1.5.53-ictce-4.0.6.eb | 8 ++++---- .../x/XCrySDen/XCrySDen-1.5.53-ictce-5.3.0.eb | 8 ++++---- ...eyboardConfig-2.16-intel-2015b-Python-2.7.11.eb | 4 ++-- .../XKeyboardConfig-2.16-intel-2015b.eb | 4 ++-- .../Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb | 2 +- .../x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb | 4 ++-- .../x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb | 4 ++-- .../x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb | 4 ++-- .../x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb | 4 ++-- .../x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb | 4 ++-- .../xcb-proto-1.10-foss-2014b-Python-2.7.8.eb | 2 +- .../xcb-proto-1.10-intel-2014b-Python-2.7.8.eb | 2 +- .../xcb-proto-1.11-goolf-1.5.14-Python-2.7.9.eb | 2 +- .../xcb-proto-1.11-intel-2015a-Python-2.7.10.eb | 2 +- .../xcb-proto-1.11-intel-2015a-Python-2.7.9.eb | 2 +- .../xcb-proto-1.11-intel-2015b-Python-2.7.10.eb | 2 +- .../xcb-proto-1.11-intel-2015b-Python-2.7.11.eb | 2 +- ...b-proto-1.7-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 8 ++++---- .../xcb-proto-1.7-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../xcb-proto-1.7-goolf-1.5.14-Python-2.7.3.eb | 2 +- .../xcb-proto-1.7-ictce-4.0.6-Python-2.7.3.eb | 8 ++++---- .../xcb-proto-1.7-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../xcb-proto-1.7-ictce-5.3.0-Python-2.7.3.eb | 8 ++++---- .../xcb-proto-1.7-intel-2014b-Python-2.7.8.eb | 2 +- ...b-util-image-0.4.0-intel-2015b-Python-2.7.11.eb | 2 +- .../xcb-util-image-0.4.0-intel-2015b.eb | 2 +- ...util-keysyms-0.4.0-intel-2015b-Python-2.7.11.eb | 2 +- .../xcb-util-keysyms-0.4.0-intel-2015b.eb | 2 +- ...l-renderutil-0.3.9-intel-2015b-Python-2.7.11.eb | 2 +- .../xcb-util-renderutil-0.3.9-intel-2015b.eb | 2 +- .../xcb-util-wm-0.4.1-intel-2015b-Python-2.7.11.eb | 2 +- .../x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b.eb | 2 +- .../xcb-util-0.4.0-intel-2015b-Python-2.7.11.eb | 2 +- .../x/xcb-util/xcb-util-0.4.0-intel-2015b.eb | 2 +- .../x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb | 8 ++++---- .../x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb | 8 ++++---- .../x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb | 8 ++++---- .../x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb | 8 ++++---- .../x/xextproto/xextproto-7.2.1-intel-2014b.eb | 8 ++++---- .../x/xextproto/xextproto-7.3.0-foss-2014b.eb | 8 ++++---- .../x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb | 8 ++++---- .../x/xextproto/xextproto-7.3.0-intel-2014b.eb | 8 ++++---- .../x/xextproto/xextproto-7.3.0-intel-2015a.eb | 8 ++++---- .../x/xextproto/xextproto-7.3.0-intel-2015b.eb | 8 ++++---- .../xineramaproto-1.2.1-foss-2014b.eb | 4 ++-- .../xineramaproto-1.2.1-intel-2014b.eb | 4 ++-- .../xineramaproto-1.2.1-intel-2015b.eb | 4 ++-- .../x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb | 14 +++++++------- .../x/xproto/xproto-7.0.23-goolf-1.4.10.eb | 12 ++++++------ .../x/xproto/xproto-7.0.23-goolf-1.5.14.eb | 12 ++++++------ .../x/xproto/xproto-7.0.23-ictce-4.0.6.eb | 14 +++++++------- .../x/xproto/xproto-7.0.23-ictce-4.1.13.eb | 8 ++++---- .../x/xproto/xproto-7.0.23-ictce-5.3.0.eb | 14 +++++++------- .../x/xproto/xproto-7.0.26-foss-2014b.eb | 12 ++++++------ .../x/xproto/xproto-7.0.26-intel-2014b.eb | 12 ++++++------ .../x/xproto/xproto-7.0.27-goolf-1.5.14.eb | 12 ++++++------ .../x/xproto/xproto-7.0.27-intel-2015a.eb | 12 ++++++------ .../x/xproto/xproto-7.0.28-intel-2015b.eb | 12 ++++++------ .../x/xtrans/xtrans-1.2-goolf-1.4.10.eb | 6 +++--- .../x/xtrans/xtrans-1.2-goolf-1.5.14.eb | 6 +++--- .../x/xtrans/xtrans-1.2-ictce-4.1.13.eb | 6 +++--- .../easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb | 6 +++--- .../x/xtrans/xtrans-1.2.6-foss-2014b.eb | 6 +++--- .../x/xtrans/xtrans-1.3.4-intel-2014b.eb | 6 +++--- .../x/xtrans/xtrans-1.3.4-intel-2015a.eb | 6 +++--- .../x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb | 6 +++--- .../x/xtrans/xtrans-1.3.5-intel-2015a.eb | 6 +++--- .../x/xtrans/xtrans-1.3.5-intel-2015b.eb | 6 +++--- 69 files changed, 203 insertions(+), 203 deletions(-) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-goalf-1.1.0-no-OFED.eb index a68cdcecf8..29c6323d63 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-goalf-1.1.0-no-OFED.eb @@ -16,10 +16,10 @@ patches = ['XCrySDen_no-bwidget.patch'] tcltk_ver = '8.5.12' dependencies = [ - ('Tcl', tcltk_ver), - ('Tk', tcltk_ver), - ('Mesa', '7.11.2', '-Python-2.7.3'), - ] + ('Tcl', tcltk_ver), + ('Tk', tcltk_ver), + ('Mesa', '7.11.2', '-Python-2.7.3'), +] osdependencies = ['libXmu-devel'] diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-ictce-4.0.6.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-ictce-4.0.6.eb index 75e7ae09d8..bba359b7d7 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-ictce-4.0.6.eb @@ -15,10 +15,10 @@ patches = ['XCrySDen_no-bwidget.patch'] tcltk_ver = '8.5.12' dependencies = [ - ('Tcl', tcltk_ver), - ('Tk', tcltk_ver), - ('Mesa', '7.11.2', '-Python-2.7.3'), - ] + ('Tcl', tcltk_ver), + ('Tk', tcltk_ver), + ('Mesa', '7.11.2', '-Python-2.7.3'), +] osdependencies = ['libXmu-devel'] diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-ictce-5.3.0.eb index 6c009ea47a..a6b6321356 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.5.53-ictce-5.3.0.eb @@ -16,10 +16,10 @@ patches = ['XCrySDen_no-bwidget.patch'] tcltk_ver = '8.5.12' dependencies = [ - ('Tcl', tcltk_ver), - ('Tk', tcltk_ver), - ('Mesa', '7.11.2', '-Python-2.7.3'), - ] + ('Tcl', tcltk_ver), + ('Tk', tcltk_ver), + ('Mesa', '7.11.2', '-Python-2.7.3'), +] osdependencies = ['libXmu-devel'] diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.16-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.16-intel-2015b-Python-2.7.11.eb index 6a5ccd4d2e..313bc69227 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.16-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.16-intel-2015b-Python-2.7.11.eb @@ -13,7 +13,7 @@ description = """The non-arch keyboard configuration database for X Window. toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://ftp.x.org/pub/individual/data/xkeyboard-config/'] +source_urls = ['http://ftp.x.org/pub/individual/data/xkeyboard-config/'] sources = ['xkeyboard-config-%(version)s.tar.bz2'] builddependencies = [ @@ -26,7 +26,7 @@ dependencies = [ ('libX11', '1.6.3', '-Python-2.7.11'), ] -#see http://www.linuxfromscratch.org/blfs/view/svn/x/xkeyboard-config.html +# see http://www.linuxfromscratch.org/blfs/view/svn/x/xkeyboard-config.html configopts = '--with-xkb-rules-symlink=xorg ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.16-intel-2015b.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.16-intel-2015b.eb index 2f437613fc..713916a02a 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.16-intel-2015b.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.16-intel-2015b.eb @@ -12,7 +12,7 @@ description = """The non-arch keyboard configuration database for X Window. toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://ftp.x.org/pub/individual/data/xkeyboard-config/'] +source_urls = ['http://ftp.x.org/pub/individual/data/xkeyboard-config/'] sources = ['xkeyboard-config-%(version)s.tar.bz2'] builddependencies = [ @@ -25,7 +25,7 @@ dependencies = [ ('libX11', '1.6.3', '-Python-2.7.10'), ] -#see http://www.linuxfromscratch.org/blfs/view/svn/x/xkeyboard-config.html +# see http://www.linuxfromscratch.org/blfs/view/svn/x/xkeyboard-config.html configopts = '--with-xkb-rules-symlink=xorg ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb index d9881b2ef7..ec08bd48fa 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -4,7 +4,7 @@ versionsuffix = '-with-incl-deps' homepage = 'http://xmipp.cnb.csic.es/' description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." - + source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] sources = ['Xmipp-%(version)s-src.tar.gz'] diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb index f4bfeba75e..93be023dae 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb @@ -12,8 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] sanity_check_paths = { - 'files' : ['include/X11/bitmaps/gray'], - 'dirs' : [] + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb index 73f42d4735..7edd725bb8 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb @@ -11,8 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] sanity_check_paths = { - 'files' : ['include/X11/bitmaps/gray'], - 'dirs' : [] + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb index 524c55782b..38732656c2 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb @@ -12,8 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] sanity_check_paths = { - 'files' : ['include/X11/bitmaps/gray'], - 'dirs' : [] + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb index e352b3479d..f7d2e42a4b 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb @@ -12,8 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] sanity_check_paths = { - 'files' : ['include/X11/bitmaps/gray'], - 'dirs' : [] + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb index 159e636639..7c6cc82582 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb @@ -12,8 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] sanity_check_paths = { - 'files' : ['include/X11/bitmaps/gray'], - 'dirs' : [] + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.10-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.10-foss-2014b-Python-2.7.8.eb index ffd6717735..56c11b1259 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.10-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.10-foss-2014b-Python-2.7.8.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'foss', 'version': '2014b'} diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.10-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.10-intel-2014b-Python-2.7.8.eb index 1f1ee49c72..4e713d1007 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.10-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.10-intel-2014b-Python-2.7.8.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-goolf-1.5.14-Python-2.7.9.eb index 5321244281..5aabb670dd 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-goolf-1.5.14-Python-2.7.9.eb @@ -9,7 +9,7 @@ description = """The X protocol C-language Binding (XCB) is a replacement for Xl toolchain = {'name': 'goolf', 'version': '1.5.14'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb index 32ea56a932..d27f91cf2b 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.9.eb index 38f0fd5a88..7dd5fbf8e3 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.9.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015b-Python-2.7.10.eb index a52aa643f5..be9444a25e 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015b-Python-2.7.10.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015b-Python-2.7.11.eb index 750bbbc4cd..47d245e6de 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015b-Python-2.7.11.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 01ca8890f3..6664f94fac 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} @@ -20,8 +20,8 @@ dependencies = [(python, pyver)] pyshortver = '.'.join(pyver.split('.')[0:2]) sanity_check_paths = { - 'files': ['lib/pkgconfig/xcb-proto.pc'], - 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] - } + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.4.10-Python-2.7.3.eb index 49ac560a5b..0d23ddbe58 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.4.10-Python-2.7.3.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.3.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.3.eb index ba3ec86dfd..da6b2762c1 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.3.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.3.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.5.14'} diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.0.6-Python-2.7.3.eb index fb6b5dd346..2af6f49473 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.0.6-Python-2.7.3.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '4.0.6'} @@ -20,8 +20,8 @@ dependencies = [(python, pyver)] pyshortver = '.'.join(pyver.split('.')[0:2]) sanity_check_paths = { - 'files': ['lib/pkgconfig/xcb-proto.pc'], - 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] - } + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.1.13-Python-2.7.3.eb index 673f729a0b..6bd488684d 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-4.1.13-Python-2.7.3.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-5.3.0-Python-2.7.3.eb index 153a7de496..d0f7ea4159 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-ictce-5.3.0-Python-2.7.3.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] @@ -21,8 +21,8 @@ dependencies = [(python, pyver)] pyshortver = '.'.join(pyver.split('.')[0:2]) sanity_check_paths = { - 'files': ['lib/pkgconfig/xcb-proto.pc'], - 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] - } + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2014b-Python-2.7.8.eb index e1af44f569..d4f3a149df 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2014b-Python-2.7.8.eb @@ -7,7 +7,7 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b-Python-2.7.11.eb index 360cb404a5..83c4d8a05b 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b-Python-2.7.11.eb @@ -9,7 +9,7 @@ description = """The xcb-util-image package provides additional extensions to th toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb index 4f85a1627f..933c8b66d8 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb @@ -8,7 +8,7 @@ description = """The xcb-util-image package provides additional extensions to th toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2015b-Python-2.7.11.eb index 2fb24a7013..8a78eed400 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2015b-Python-2.7.11.eb @@ -10,7 +10,7 @@ description = """The xcb-util-keysyms package contains a library for toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2015b.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2015b.eb index 4854d896a1..72d3c0d7bc 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = """The xcb-util-keysyms package contains a library for toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2015b-Python-2.7.11.eb index 5ab8e229a6..1254207ef5 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2015b-Python-2.7.11.eb @@ -9,7 +9,7 @@ description = """The xcb-util-renderutil package provides additional extensions toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2015b.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2015b.eb index bf0147fea6..561b237980 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2015b.eb @@ -8,7 +8,7 @@ description = """The xcb-util-renderutil package provides additional extensions toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b-Python-2.7.11.eb index a3589e6112..3958944410 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b-Python-2.7.11.eb @@ -9,7 +9,7 @@ description = """The xcb-util-wm package contains libraries which provide client toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b.eb index 0ee7ac8271..147e33bc0c 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b.eb @@ -8,7 +8,7 @@ description = """The xcb-util-wm package contains libraries which provide client toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2015b-Python-2.7.11.eb index a893851869..0587deb544 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2015b-Python-2.7.11.eb @@ -10,7 +10,7 @@ description = """The xcb-util package provides additional extensions to the XCB toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2015b.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2015b.eb index 8fd3b74ca5..a6a5649a3c 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = """The xcb-util package provides additional extensions to the XCB toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb index 3418593f36..d4118dc48c 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb @@ -15,10 +15,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb index 3c2320e860..6e6a5a03b2 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb @@ -15,10 +15,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb index 447dc3ac65..054bc51cbe 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb @@ -14,10 +14,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb index 6256b4a10c..4f5a5e2a0d 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb @@ -14,10 +14,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb index d79aece7ee..829a1e95f8 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb @@ -14,10 +14,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb index bfc2d59685..0c9b21f3fb 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb @@ -14,10 +14,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb index 19c9e6fc6f..18ab59d5ae 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb @@ -14,10 +14,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb index d03ad18e50..673a0e5e21 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb @@ -14,10 +14,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb index 01075a73cf..494a482b64 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb @@ -14,10 +14,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb index 983804175f..6c19b3821e 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb @@ -14,10 +14,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] ], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb index 83415bc67b..b0ee431324 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb @@ -12,8 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/extensions/panoramiXproto.h'], - 'dirs' : [] + 'files': ['include/X11/extensions/panoramiXproto.h'], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb index 16a5aa8610..797b75e5e7 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb @@ -12,8 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/extensions/panoramiXproto.h'], - 'dirs' : [] + 'files': ['include/X11/extensions/panoramiXproto.h'], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb index 75a6e48c10..e96e89759a 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb @@ -12,8 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/extensions/panoramiXproto.h'], - 'dirs' : [] + 'files': ['include/X11/extensions/panoramiXproto.h'], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb index 0b9f7d0f3f..f6c2e0c627 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb @@ -13,12 +13,12 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] - } + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb index e7dc372ce2..241268e4a6 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb @@ -13,12 +13,12 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb index 4a07188aa9..ab202e5075 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb @@ -13,12 +13,12 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb index 0b738cf50c..e0f4abf144 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb @@ -13,12 +13,12 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] - } + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb index 5f36cfb20c..884e64e8dd 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb @@ -14,10 +14,10 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb index 90b584a81e..8f17ba5d45 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb @@ -14,12 +14,12 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] - } + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb index 14e0666049..bdb6d9e8c7 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb @@ -13,12 +13,12 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb index f620518aca..74b305ce8c 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb @@ -13,12 +13,12 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb index 818673c9f9..4ec0e6221a 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb @@ -13,12 +13,12 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb index 4093d23e90..f9bd7118c8 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb @@ -13,12 +13,12 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb index 08bc258df3..d3de936da4 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb @@ -13,12 +13,12 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb index 6676a3761d..d4d9f7b97d 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb @@ -15,12 +15,12 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'files': ['include/X11/Xtrans/%s' % x for x in [ 'transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' - ] + ] ], - 'dirs' : [] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb index 55dfe1aab5..a2a0755c9f 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb @@ -15,12 +15,12 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'files': ['include/X11/Xtrans/%s' % x for x in [ 'transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' - ] + ] ], - 'dirs' : [] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb index ae5d033d58..e0801c0268 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb @@ -14,12 +14,12 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'files': ['include/X11/Xtrans/%s' % x for x in [ 'transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' - ] + ] ], - 'dirs' : [] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb index c4c078f4c4..90167fba75 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb @@ -15,12 +15,12 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'files': ['include/X11/Xtrans/%s' % x for x in [ 'transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' - ] + ] ], - 'dirs' : [] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb index 825d041de5..70ff99da7d 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb @@ -15,12 +15,12 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'files': ['include/X11/Xtrans/%s' % x for x in [ 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' - ] + ] ], - 'dirs' : [] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb index d17e971313..ec215c7fbf 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb @@ -15,12 +15,12 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'files': ['include/X11/Xtrans/%s' % x for x in [ 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c' - ] + ] ], - 'dirs' : [] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb index dc21e51c71..1793db7b6f 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb @@ -15,12 +15,12 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'files': ['include/X11/Xtrans/%s' % x for x in [ 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c' - ] + ] ], - 'dirs' : [] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb index 2286309947..9f200617fa 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb @@ -15,12 +15,12 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'files': ['include/X11/Xtrans/%s' % x for x in [ 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c' - ] + ] ], - 'dirs' : [] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb index ef00169dc4..06cbd1c8ee 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb @@ -15,12 +15,12 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'files': ['include/X11/Xtrans/%s' % x for x in [ 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c' - ] + ] ], - 'dirs' : [] + 'dirs': [] } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb index 94ae99a09d..886f7c9bbf 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb @@ -15,12 +15,12 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'files': ['include/X11/Xtrans/%s' % x for x in [ 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c' - ] + ] ], - 'dirs' : [] + 'dirs': [] } moduleclass = 'devel' -- GitLab From 6a252dac482f19fb8afd64954d97ad8b0a58a9ff Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 29 Jan 2016 14:51:18 +0100 Subject: [PATCH 0282/2133] updated ebs for new cray TC using dependency pinning --- .../j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb | 21 ---- .../l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb | 24 ---- .../libreadline-6.3-CrayGNU-5.2.40.eb | 30 ----- .../l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb | 32 ----- .../m/M4/M4-1.4.17-CrayGNU-5.2.40.eb | 23 ---- .../n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb | 22 ---- .../n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 36 ------ ...numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb | 26 ---- .../Python-2.7.9-CrayGNU-5.2.40-bare.eb | 39 ------ .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 115 ------------------ .../s/Szip/Szip-2.1-CrayGNU-5.2.40.eb | 23 ---- ...cipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb | 19 --- .../s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb | 22 ---- .../t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb | 39 ------ .../w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb | 41 ------- .../z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb | 22 ---- 16 files changed, 534 deletions(-) delete mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb delete mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb deleted file mode 100644 index cef32fd43d..0000000000 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'JasPer' -version = '1.900.1' - -homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' -description = """The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_ZIP] -source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] - -sanity_check_paths = { - 'files': ["bin/jasper", "lib/libjasper.a"], - 'dirs': ["include"], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb deleted file mode 100644 index 4f2df44352..0000000000 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'Libint' -version = '1.1.4' - -homepage = 'https://sourceforge.net/p/libint/' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'opt': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') - -configopts = "--enable-deriv --enable-r12" - -sanity_check_paths = { - 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + - ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + - ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb deleted file mode 100644 index 18966e6606..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '6.3' - -homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' -description = """The GNU Readline library provides a set of functions for use by applications that - allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. - The Readline library includes additional functions to maintain a list of previously-entered command lines, - to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '5.9')] - -# for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" - -sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb deleted file mode 100644 index 80df7f4320..0000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '2.2.1' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'opt': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] - -configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' - -# From the libxc mailing list -# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -# a fully working testsuite soon (unless someone wants to volunteer to do -# it, of course ) In the meantime, unless the majority of the tests -# fail, your build should be fine. -#runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc.a'], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb deleted file mode 100644 index d1ac7167dc..0000000000 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'M4' -version = '1.4.17' - -homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -configopts = "--enable-cxx" - -sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb deleted file mode 100644 index 292a68dda4..0000000000 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'NFFT' -version = '3.3.0' - -homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' -description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine - library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more - dimensions, of arbitrary input size, and of complex data.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = { 'dynamic': True } - -source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb deleted file mode 100644 index 6f00fdbd51..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'optarch': True, 'shared': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['ncurses-%(version)s_configure_darwin.patch'] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb deleted file mode 100644 index 7d81f886bc..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'numpy' -version = '1.9.2' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['numpy-1.8.0-mkl.patch'] - -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb deleted file mode 100644 index 3fafaaa920..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'Python' -version = '2.7.9' -versionsuffix = '-bare' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True, 'opt': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -# bare installation: no extensions included -exts_list = [] - -buildopts = 'LINKCC="$CC -dynamic"' - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb deleted file mode 100644 index 186e5f94df..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,115 +0,0 @@ -name = 'Python' -version = '2.7.9' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.9.1' -scipyversion = '0.14.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -buildopts = 'LINKCC="$CC -dynamic"' - -# order is important! -# package versions updated Jan 19th 2015 -exts_list = [ - ('setuptools', '11.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.4.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.13', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), -] - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb deleted file mode 100644 index 821b800cb6..0000000000 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1' - -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' -description = "Szip compression software, providing lossless compression of scientific data" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True, 'dynamic': True} - -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb deleted file mode 100644 index adb35688b3..0000000000 --- a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'scipy' -version = '0.15.1' -versionsuffix = '-Python-2.7.9' - -homepage = 'http://www.scipy.org' -description = """SciPy is a collection of mathematical algorithms and convenience - functions built on the Numpy extension for Python.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True} - -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('numpy', '1.9.2', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb deleted file mode 100644 index f3db34a07a..0000000000 --- a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'spglib' -version = '1.7.3' - -homepage = 'http://spglib.sourceforge.net/' -description = """Spglib is a C library for finding and handling crystal symmetries.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'dynamic': True, } - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -start_dir = '%(name)s-%(version)s' - -sanity_check_paths = { - 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], - 'dirs': ['include/spglib'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb deleted file mode 100644 index 171465e133..0000000000 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,39 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -# Authors:: Valentin Plugaru -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html -## -easyblock = 'ConfigureMake' - -name = 'tcsh' -version = '6.18.01' - -homepage = 'http://www.tcsh.org' -description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). - It is a command language interpreter usable both as an interactive login shell and a shell script command - processor. It includes a command-line editor, programmable word completion, spelling correction, a history - mechanism, job control and a C-like syntax.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'dynamic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.astron.com/pub/%(namelower)s', - 'ftp://ftp.astron.com/pub/%(namelower)s/old', -] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/tcsh"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb deleted file mode 100644 index 4f97a28683..0000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb +++ /dev/null @@ -1,41 +0,0 @@ -name = 'WRF' -version = '3.6.1' - -homepage = 'http://www.wrf-model.org' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -sources = ['%(name)sV%(version)s.TAR.gz'] -source_urls = [ - 'http://www2.mmm.ucar.edu/wrf/src/', - 'http://www.mmm.ucar.edu/wrf/src/', -] - -# csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] - -dependencies = [ - ('JasPer', '1.900.1'), - ('cray-netcdf/4.3.2', EXTERNAL_MODULE), - ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), -] - -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-3.6.1_known_problems.patch', - 'WRF_tests_limit-runtimes.patch', -] - -# limit parallel build to 20 -maxparallel = 20 - -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -runtest = False - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb deleted file mode 100644 index 942056eae5..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.8' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True, 'dynamic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' -- GitLab From 4899a5bdbf2e3b8601a8d544e41aa492689cd3a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Jan 2016 16:45:41 +0200 Subject: [PATCH 0283/2133] add easyconfig netCDF-4.4.0-intel-2016a.eb --- .../n/netCDF/netCDF-4.4.0-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb new file mode 100644 index 0000000000..2818683dd7 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb @@ -0,0 +1,33 @@ +name = 'netCDF' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.47.0'), +] + +builddependencies = [ + ('CMake', '3.4.3'), + ('Doxygen', '1.8.11'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From 031740aadc9aca300f7f4d6cc78b6be74eed50fe Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Fri, 29 Jan 2016 16:23:56 +0100 Subject: [PATCH 0284/2133] rpmrebuild easyconfig --- .../r/rpmrebuild/rpmrebuild-2.11.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb diff --git a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb new file mode 100644 index 0000000000..742b46640d --- /dev/null +++ b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Forschungszentrum Juelich GmbH +# Authors:: Damian Alvarez +# License:: MIT/GPL +# $Id$ +## + +easyblock = "Tarball" + +name = "rpmrebuild" +version = "2.11" + +homepage = 'http://rpmrebuild.sourceforge.net/' +description = """rpmrebuild is a tool to build an RPM file from a package that has already been + installed in a basic use""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s-%s.tar.gz' % (name.lower(), version)] + +modextrapaths = {'PATH': ['']} +modextravars = {'RPMREBUILD_ROOT_DIR': '%(installdir)s'} + +sanity_check_paths = { + 'files': ["rpmrebuild"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 7182df87e936e54ad1cf71550f8e540d87b6d5d9 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 10:23:57 +1300 Subject: [PATCH 0285/2133] New easyconfig for bzip2 with ictce 5.4.0 toolchain --- .../b/bzip2/bzip2-1.0.6-ictce-5.4.0.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.4.0.eb new file mode 100644 index 0000000000..705ab72be8 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.4.0.eb @@ -0,0 +1,16 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + + +toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' -- GitLab From 31b40488802ddd65bb8e84d62028344e8a0af057 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 10:34:47 +1300 Subject: [PATCH 0286/2133] Doxygen versions needed for GRASS and Amber --- .../d/Doxygen/Doxygen-1.8.1.1-ictce-5.4.0.eb | 18 ++++++++++++++++++ .../d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb | 18 ++++++++++++++++++ .../d/Doxygen/Doxygen-1.8.11-foss-2015a.eb | 19 +++++++++++++++++++ 3 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.4.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.4.0.eb new file mode 100644 index 0000000000..bb65203341 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.4.0.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.1.1' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb new file mode 100644 index 0000000000..3b682b018a --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.11' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.3'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb new file mode 100644 index 0000000000..1db648e43d --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.11' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.1'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' -- GitLab From bc9fead26aeaecf135d15d25423c0d3d23c3a9ab Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 11:04:25 +1300 Subject: [PATCH 0287/2133] libreadline for ictce-5.4.0 toolchain --- .../libreadline-6.2-ictce-5.4.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb new file mode 100644 index 0000000000..8003f03676 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.2' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' -- GitLab From cb61df5a1ab9bd529a6a7c00126732ab1d42e89d Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 12:55:06 +1300 Subject: [PATCH 0288/2133] EasyConfig for Yasm 1.3.0 with foss-2015a toolchain --- .../y/Yasm/Yasm-1.3.0-foss-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2015a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2015a.eb new file mode 100644 index 0000000000..90c83cfb4e --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2015a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 0dc3d69ac46e840d90f09e788601462050a0b80b Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 12:58:41 +1300 Subject: [PATCH 0289/2133] New EasyConfig for NASM 2.11.08 with FOSS 2015a toolchain --- .../n/NASM/NASM-2.11.08-foss-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015a.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015a.eb new file mode 100644 index 0000000000..54389e3415 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 223b9aa4fecfa5349d34b36b52f71fad18c93d10 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:01:04 +1300 Subject: [PATCH 0290/2133] New EasyConfig for Bison 3.0.4 with the foss-2015a toolchain --- .../b/Bison/Bison-3.0.4-foss-2015a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2015a.eb new file mode 100644 index 0000000000..b4eb8b2471 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From d4dbf8431a813623d80d28f9c77fc69ee0866044 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:04:58 +1300 Subject: [PATCH 0291/2133] New EasyConfig for CMake 3.4.1 with the foss-2015a toolchain --- .../c/CMake/CMake-3.4.1-foss-2015a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb new file mode 100644 index 0000000000..4f9c1dcfa2 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From e69e7d6b4cd7108b22cee3bd9ab6043c20cba9ab Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:11:19 +1300 Subject: [PATCH 0292/2133] New EasyConfig for GMP 6.1.0 with the foss-2015a toolchain --- .../easyconfigs/g/GMP/GMP-6.1.0-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2015a.eb new file mode 100644 index 0000000000..7ddae5e22f --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 557eef83b66c2d5736f3fafaed667c1757602eed Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:13:18 +1300 Subject: [PATCH 0293/2133] New EasyConfig for SQLite 3.10.0 with the foss-2015a toolchain --- .../s/SQLite/SQLite-3.10.0-foss-2015a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb new file mode 100644 index 0000000000..be167b2761 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.10.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2016/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 211f01fa7f70ea35690afaaf76f2bc4e34563c5c Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:17:46 +1300 Subject: [PATCH 0294/2133] New EasyConfig for PROJ 4.9.1 with the foss-2015a toolchain --- .../p/PROJ/PROJ-4.9.1-foss-2015a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb new file mode 100644 index 0000000000..ce218bd9f2 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.1' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 9477dd6d220920ddb4587e22ad4b2704fb534d82 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:20:44 +1300 Subject: [PATCH 0295/2133] New EasyConfig for cURL 7.46.0 with the foss-2015a toolchain --- .../c/cURL/cURL-7.46.0-foss-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.46.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.46.0-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-foss-2015a.eb new file mode 100644 index 0000000000..db4a8f5826 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-foss-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.46.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From 01925369ffe450b9ad49d29ab3e3e205e61819e5 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:22:57 +1300 Subject: [PATCH 0296/2133] New EasyConfig for HDF5 1.8.16 with the foss-2015a toolchain --- .../h/HDF5/HDF5-1.8.16-foss-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb new file mode 100644 index 0000000000..25e05e8e27 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.16' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From e6645eb9be02116f4cb21c86790b1f5a6884208c Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:25:46 +1300 Subject: [PATCH 0297/2133] New EasyConfig for libpng 1.6.20 with the foss-2015a toolchain --- .../l/libpng/libpng-1.6.20-foss-2015a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.20-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.20-foss-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.20-foss-2015a.eb new file mode 100644 index 0000000000..94bb4e0c8f --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.20-foss-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.20' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' -- GitLab From 4f288d7294f8b81873e560d101f9fae05042f13e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:28:26 +1300 Subject: [PATCH 0298/2133] New EasyConfig for LibTIFF 4.0.6 with the foss-2015a toolchain --- .../l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb new file mode 100644 index 0000000000..68f9ad3dc9 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.6' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From beeb231bae77b1e47ed533fa1cd5526cba494146 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:30:55 +1300 Subject: [PATCH 0299/2133] New EasyConfig for x264 20160114 with the foss-2015a toolchain --- .../x/x264/x264-20160114-foss-2015a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/x/x264/x264-20160114-foss-2015a.eb diff --git a/easybuild/easyconfigs/x/x264/x264-20160114-foss-2015a.eb b/easybuild/easyconfigs/x/x264/x264-20160114-foss-2015a.eb new file mode 100644 index 0000000000..eddd9ff8e0 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160114-foss-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160114' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['ftp://ftp.videolan.org/pub/videolan/x264/snapshots/'] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 05eb25ecc272856e06af42ef6d36acfa148c6e59 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:34:45 +1300 Subject: [PATCH 0300/2133] New EasyConfig for freetype2.6.2 with the foss-2015a toolchain --- .../f/freetype/freetype-2.6.2-foss-2015a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb new file mode 100644 index 0000000000..32c4b9ab5c --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.20')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' -- GitLab From 052e8f3b1aba9bd2a231f9bc49624500efc01db2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:37:38 +1300 Subject: [PATCH 0301/2133] New EasyConfig for KEALib 1.4.4 with the foss-2015a toolchain --- .../k/KEALib/KEALib-1.4.4-foss-2015a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/k/KEALib/KEALib-1.4.4-foss-2015a.eb diff --git a/easybuild/easyconfigs/k/KEALib/KEALib-1.4.4-foss-2015a.eb b/easybuild/easyconfigs/k/KEALib/KEALib-1.4.4-foss-2015a.eb new file mode 100644 index 0000000000..81322d46f5 --- /dev/null +++ b/easybuild/easyconfigs/k/KEALib/KEALib-1.4.4-foss-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'KEALib' +version = '1.4.4' + +homepage = 'http://www.kealib.org' +description = """KEALib provides an implementation of the GDAL data model. The +format supports raster attribute tables, image pyramids, meta-data and in-built +statistics while also handling very large files and compression throughout. +Based on the HDF5 standard, it also provides a base from which other formats +can be derived and is a good choice for long term data archiving. An +independent software library (libkea) provides complete access to the KEA image +format and a GDAL driver allowing KEA images to be used from any GDAL supported +software.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['https://bitbucket.org/chchrsc/kealib/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('HDF5', '1.8.16'), +] + +start_dir = 'trunk' + +sanity_check_paths = { + 'files': ['lib/libkea.%s' % SHLIB_EXT, 'bin/kea-config'], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'data' -- GitLab From 9eb09e00dabc47f82e918cb01e54c7a8eb778785 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:40:46 +1300 Subject: [PATCH 0302/2133] New EasyConfig for flex 2.6.0 with the foss-2015a toolchain --- .../easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb new file mode 100644 index 0000000000..bd783441d3 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' -- GitLab From d80280f52f26f8bb79b1ed4c58ed6bb63f04eb6a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:45:02 +1300 Subject: [PATCH 0303/2133] New EasyConfigs for FreeXL with various toolchains --- .../f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb | 21 +++++++++++++++++ .../f/FreeXL/FreeXL-1.0.1-intel-2015a.eb | 23 +++++++++++++++++++ .../f/FreeXL/FreeXL-1.0.2-foss-2015a.eb | 23 +++++++++++++++++++ 3 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb new file mode 100644 index 0000000000..c7906f58da --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb @@ -0,0 +1,21 @@ +name = 'FreeXL' +version = '1.0.0g' + +homepage = "https://www.gaia-gis.it/fossil/freexl/index" +description = "FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet." + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '2.8.10.2')] + +sanity_check_paths = { + 'files': ["lib/libfreexl.la"], + 'dirs': ["lib"] + } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb new file mode 100644 index 0000000000..727ab2cbec --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb @@ -0,0 +1,23 @@ +name = 'FreeXL' +version = '1.0.1' + +easyblock = 'ConfigureMake' + +homepage = "https://www.gaia-gis.it/fossil/freexl/index" +description = "FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.2.2')] + +sanity_check_paths = { + 'files': ["lib/libfreexl.la"], + 'dirs': ["lib"] + } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb new file mode 100644 index 0000000000..c84e5dcc81 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'FreeXL' +version = '1.0.2' + +easyblock = 'ConfigureMake' + +homepage = "https://www.gaia-gis.it/fossil/freexl/index" +description = "FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet." + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.4.1')] + +sanity_check_paths = { + 'files': ["lib/libfreexl.la"], + 'dirs': ["lib"] + } + +moduleclass = 'lib' -- GitLab From abc2b89926679f2c514fcc9c907ae8b9323fc775 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:49:45 +1300 Subject: [PATCH 0304/2133] New EasyConfig for Python 2.7.11 with the foss-2015a toolchain --- .../p/Python/Python-2.7.11-foss-2015a.eb | 129 ++++++++++++++++++ 1 file changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb new file mode 100644 index 0000000000..aacb5511cd --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -0,0 +1,129 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.10.0'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), # required for pycrypto +# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), +] + +moduleclass = 'lang' -- GitLab From bcc3dbdcac6bfe8f839bb8615369905db14166b9 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 13:58:48 +1300 Subject: [PATCH 0305/2133] New EasyConfigs for FFmpeg with various toolchains; renamed for case consistency --- .../FFmpeg-2.4-intel-2014.06.eb} | 4 +-- .../FFmpeg-2.4-intel-2014b.eb} | 4 +-- .../f/FFmpeg/FFmpeg-2.4-intel-2015a.eb | 28 +++++++++++++++++ .../FFmpeg-2.8-intel-2015b.eb} | 4 +-- .../f/FFmpeg/FFmpeg-2.8.4-foss-2015a.eb | 30 +++++++++++++++++++ .../f/FFmpeg/FFmpeg-2.8.5-foss-2015a.eb | 30 +++++++++++++++++++ 6 files changed, 94 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/f/{ffmpeg/ffmpeg-2.4-intel-2014.06.eb => FFmpeg/FFmpeg-2.4-intel-2014.06.eb} (94%) rename easybuild/easyconfigs/f/{ffmpeg/ffmpeg-2.4-intel-2014b.eb => FFmpeg/FFmpeg-2.4-intel-2014b.eb} (94%) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2015a.eb rename easybuild/easyconfigs/f/{ffmpeg/ffmpeg-2.8-intel-2015b.eb => FFmpeg/FFmpeg-2.8-intel-2015b.eb} (94%) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.4-foss-2015a.eb create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014.06.eb similarity index 94% rename from easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb rename to easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014.06.eb index 4abf658ad6..7c83b15912 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014.06.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'ffmpeg' +name = 'FFmpeg' version = '2.4' homepage = 'https://www.ffmpeg.org/' @@ -8,7 +8,7 @@ description = """A complete, cross-platform solution to record, convert and stre toolchain = {'name': 'intel', 'version': '2014.06'} -sources = [SOURCE_TAR_BZ2] +sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX"' diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014b.eb similarity index 94% rename from easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb rename to easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014b.eb index 4461759fe7..71fa9c97d6 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'ffmpeg' +name = 'FFmpeg' version = '2.4' homepage = 'https://www.ffmpeg.org/' @@ -8,7 +8,7 @@ description = """A complete, cross-platform solution to record, convert and stre toolchain = {'name': 'intel', 'version': '2014b'} -sources = [SOURCE_TAR_BZ2] +sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX"' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2015a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2015a.eb new file mode 100644 index 0000000000..c42dbf3d77 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.4' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX"' + +dependencies = [ + ('NASM', '2.11.05'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8-intel-2015b.eb similarity index 94% rename from easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb rename to easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8-intel-2015b.eb index 9493af88c9..9d99eff993 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8-intel-2015b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'ffmpeg' +name = 'FFmpeg' version = '2.8' homepage = 'https://www.ffmpeg.org/' @@ -8,7 +8,7 @@ description = """A complete, cross-platform solution to record, convert and stre toolchain = {'name': 'intel', 'version': '2015b'} -sources = [SOURCE_TAR_BZ2] +sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.4-foss-2015a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.4-foss-2015a.eb new file mode 100644 index 0000000000..889d11e831 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.4-foss-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.4' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.11.08'), + ('zlib', '1.2.8'), + ('x264', '20160114'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.5-foss-2015a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.5-foss-2015a.eb new file mode 100644 index 0000000000..70c0c62421 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.5-foss-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.5' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.11.08'), + ('zlib', '1.2.8'), + ('x264', '20160114'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From 9fad990c5904e8f1e7bdfa6b21b014cda124ec7e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:06:29 +1300 Subject: [PATCH 0306/2133] New EasyConfig for libxml2-2.9.3 with the foss-2015a toolchain --- .../libxml2-2.9.3-foss-2015a-Python-2.7.11.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb new file mode 100644 index 0000000000..8052162f58 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' -- GitLab From 6fbf081717482250b3700bdbe4496057685c0f41 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:08:52 +1300 Subject: [PATCH 0307/2133] New EasyConfig for SWIG 3.0.8 with the foss-2015a toolchain --- .../SWIG-3.0.8-foss-2015a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2015a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2015a-Python-2.7.11.eb new file mode 100644 index 0000000000..9b8e4b5df8 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2015a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '3.0.8' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.11' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.37'), +] + +moduleclass = 'devel' -- GitLab From 3dcfe55c278c08e44d75c0df4a881729e6faa8d8 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:12:05 +1300 Subject: [PATCH 0308/2133] New EasyConfig for GEOS 3.5.0 with the foss-2015a toolchain --- .../GEOS-3.5.0-foss-2015a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb new file mode 100644 index 0000000000..3053b75ee0 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.5.0' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[0:2]) +versionsuffix = '-Python-%s' % pyver + +dependencies = [('Python', pyver)] + +builddependencies = [('SWIG', '3.0.8', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%s/site-packages/geos' % pyshortver] +} + +moduleclass = 'math' -- GitLab From 8d19ca30efc5ea8e0917f71e2cc867a439028067 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:15:24 +1300 Subject: [PATCH 0309/2133] New EasyConfig for netCDF 4.3.3.1 with the foss-2015a toolchain --- .../n/netCDF/netCDF-4.3.3.1-foss-2015a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015a.eb new file mode 100644 index 0000000000..67ec8a7992 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.3.3.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.46.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.11'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From d20fd461af0643a43a7e80b8cc740aa480f45276 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:18:16 +1300 Subject: [PATCH 0310/2133] New EasyConfig for GDAL 2.0.1 with the foss-2015a toolchain --- .../g/GDAL/GDAL-2.0.1-foss-2015a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb new file mode 100644 index 0000000000..fdbd875ff2 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.1' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('KEALib', '1.4.4'), + ('netCDF', '4.3.3.1'), + ('HDF5', '1.8.16'), + ('expat', '2.1.0'), + ('libxml2', '2.9.3', '-Python-2.7.11'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' -- GitLab From fa11863cf5cb4aa57b73db4336ac0d2cae1b0504 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:20:50 +1300 Subject: [PATCH 0311/2133] New EasyConfigs for libspatialite - various versions and toolchains --- .../libspatialite-4.1.1-goolf-1.5.14.eb | 27 ++++++++++++++++ .../libspatialite-4.3.0-intel-2015a.eb | 32 +++++++++++++++++++ .../libspatialite-4.3.0a-foss-2015a.eb | 32 +++++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..8132d40673 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.1.1' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +patches = ['libspatialite-configure.ac.patch'] + +dependencies = [('FreeXL','1.0.0g'),('GEOS','3.3.5'), ('SQLite', '3.8.4.3'), ('PROJ', '4.8.0')] +configopts = '--disable-geosadvanced' +builddependencies = [('CMake', '2.8.10.2')] + +sanity_check_paths = { + 'files': ["lib/libspatialite.la"], + 'dirs': ["lib","include"] + } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb new file mode 100644 index 0000000000..732c224f99 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.3.0' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('FreeXL','1.0.1'), + ('GEOS','3.3.9'), + ('SQLite', '3.8.9'), + ('PROJ', '4.9.1'), +] + +configopts = '--disable-geosadvanced' + +builddependencies = [('CMake', '3.2.2')] + +sanity_check_paths = { + 'files': ["lib/libspatialite.la"], + 'dirs': ["lib","include"] + } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb new file mode 100644 index 0000000000..0c50d9148b --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.3.0a' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('FreeXL', '1.0.2'), + ('GEOS', '3.5.0', '-Python-2.7.11'), + ('SQLite', '3.10.0'), + ('PROJ', '4.9.1'), +] + +configopts = '--disable-geosadvanced' + +builddependencies = [('CMake', '3.4.1')] + +sanity_check_paths = { + 'files': ["lib/libspatialite.la"], + 'dirs': ["lib","include"] + } + +moduleclass = 'lib' -- GitLab From c54ec0a7e799c9c00520fbd1752886769dfc1129 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:33:14 +1300 Subject: [PATCH 0312/2133] EasyConfig for flex-2.5.35 with the ictce-5.4.0 toolchain --- .../easyconfigs/f/flex/flex-2.5.35-ictce-5.4.0.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.35-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.35-ictce-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.35-ictce-5.4.0.eb new file mode 100644 index 0000000000..653b53ec92 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.35-ictce-5.4.0.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.35' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' -- GitLab From 25937dcd8a790d61c1fd5d194d0bd0c15d1b0264 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:40:34 +1300 Subject: [PATCH 0313/2133] New EasyConfig for Bison 2.5 with the ictce-5.4.0 toolchain --- .../b/Bison/Bison-2.5-ictce-5.4.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb new file mode 100644 index 0000000000..18dbc65289 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.5' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + + +toolchain = {'name': 'ictce', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.16')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 70ddca5975069ab6bff57b38183454b064a9070c Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 15:31:45 +1300 Subject: [PATCH 0314/2133] Added EasyBlock to FreeXL config --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb index c7906f58da..c7a2ae14f5 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb @@ -1,6 +1,8 @@ name = 'FreeXL' version = '1.0.0g' +easyblock = 'ConfigureMake' + homepage = "https://www.gaia-gis.it/fossil/freexl/index" description = "FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet." -- GitLab From 771d76c24113e7b777347eb29d6b4905b51e3e75 Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 2 Feb 2016 14:14:21 +0100 Subject: [PATCH 0315/2133] adding cray 2015.06-XC --- .../b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb | 23 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb | 38 ++++++ .../f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb | 14 +++ .../Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb | 24 ++++ .../libreadline-6.3-CrayGNU-2015.06-XC.eb | 30 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb | 32 +++++ .../m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb | 23 ++++ .../n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb | 22 ++++ .../ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb | 36 ++++++ ...y-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb | 26 ++++ .../Python-2.7.9-CrayGNU-2015.06-XC-bare.eb | 39 ++++++ .../Python/Python-2.7.9-CrayGNU-2015.06-XC.eb | 115 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb | 23 ++++ ...-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb | 19 +++ .../spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb | 22 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb | 39 ++++++ .../WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb | 41 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb | 22 ++++ 20 files changed, 625 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..77bb4a043c --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..5b74aeb4ae --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..2813041da2 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..c1c02c3bcf --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..d9b2e6f439 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..8c50a3c766 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..86d9535460 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..3ef89d660d --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..68ee7aa23b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..9a44adf4a0 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = { 'dynamic': True } + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..39a02a2b9d --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb new file mode 100644 index 0000000000..09f3884a76 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb new file mode 100644 index 0000000000..ae58dbb498 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb @@ -0,0 +1,39 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..d2018b8970 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..621f9235dd --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb new file mode 100644 index 0000000000..b47cc99c57 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..90249a4422 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'dynamic': True, } + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..07d83bd968 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb new file mode 100644 index 0000000000..0b7fd5cfb3 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..e2f5d3e598 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'pic': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 19e35e1b9bab0a773934e803edc04adc2fa21e6d Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 2 Feb 2016 14:16:09 +0100 Subject: [PATCH 0316/2133] Cray 2015.11 XC --- .../b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb | 23 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb | 38 ++++++ .../f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb | 14 +++ .../Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb | 24 ++++ .../libreadline-6.3-CrayGNU-2015.11-XC.eb | 30 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb | 32 +++++ .../m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb | 23 ++++ .../n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb | 22 ++++ .../ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb | 36 ++++++ ...y-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb | 26 ++++ .../Python-2.7.9-CrayGNU-2015.11-XC-bare.eb | 39 ++++++ .../Python/Python-2.7.9-CrayGNU-2015.11-XC.eb | 115 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb | 23 ++++ ...-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb | 19 +++ .../spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb | 22 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb | 39 ++++++ .../WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb | 41 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb | 22 ++++ 20 files changed, 625 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..cfb18be138 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..5666a2e9f5 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..5d449a2077 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..18250df781 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..7fbee438c5 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..ba7eabefb4 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..9f6f591568 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..bfd88b3c4b --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..fd7cafa798 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..f5c36d9c4c --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = { 'dynamic': True } + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..a3d14a3a11 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb new file mode 100644 index 0000000000..91375139ee --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb new file mode 100644 index 0000000000..f91af70f07 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb @@ -0,0 +1,39 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..da85447313 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..d97f4cebb2 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb new file mode 100644 index 0000000000..b69de1aa3b --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..06a6cb2664 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'dynamic': True, } + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..e07994886a --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb new file mode 100644 index 0000000000..d353e6742c --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..7d35b456b3 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From ec0bca72390c31cb16ff117b1f78f085b4be6ec4 Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 2 Feb 2016 14:24:21 +0100 Subject: [PATCH 0317/2133] adding gromacs and jasper --- .../GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb | 38 +++++++++++++++++++ .../JasPer-1.900.1-CrayGNU-2015.11-XC.eb | 21 ++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb new file mode 100644 index 0000000000..0faa18f3de --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..b3d235faba --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' -- GitLab From 7d8aa043176d7a960af65451fcfb2a3b545dcd87 Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 2 Feb 2016 14:32:32 +0100 Subject: [PATCH 0318/2133] added Gromacs and JasPer --- .../GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb | 38 +++++++++++++++++++ .../JasPer-1.900.1-CrayGNU-2015.06-XC.eb | 21 ++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb new file mode 100644 index 0000000000..31d5fed4d1 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb new file mode 100644 index 0000000000..057b6423c3 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' -- GitLab From 712d4a5e1759b6dc388c999882bffdf9779e110a Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 2 Feb 2016 17:27:50 +0100 Subject: [PATCH 0319/2133] added PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb --- ...PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 111 ++++++++++++++++++ 1 file changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..69ae0dc1d2 --- /dev/null +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,111 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'PRINSEQ' +version = '0.20.4' + +homepage = 'http://prinseq.sourceforge.net' +description = """ A bioinformatics tool to PRe-process and show INformation of SEQuence data. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] +sources = ['%(namelower)s-lite-%(version)s.tar.gz'] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::Depends', '0.405', { + 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('ExtUtils::PkgConfig', '1.15', { + 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], + }), + ('Pod::Usage', '1.68', { + 'source_tmpl': 'Pod-Usage-1.68.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + }), + ('File::Temp', '0.2304', { + 'source_tmpl': 'File-Temp-0.2304.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Digest::MD5', '2.54', { + 'source_tmpl': 'Digest-MD5-2.54.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/'], + }), + ('Cairo', '1.106', { + 'source_tmpl': 'Cairo-1.106.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('Statistics::PCA', '0.0.1', { + 'source_tmpl': 'Statistics-PCA-0.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSTH/'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-3.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Math::Cephes::Matrix', '0.5304', { + 'source_tmpl': 'Math-Cephes-0.5304.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + }), + ('Math::MatrixReal', '2.12', { + 'source_tmpl': 'Math-MatrixReal-2.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LETO/'], + }), + ('Text::SimpleTable', '2.03', { + 'source_tmpl': 'Text-SimpleTable-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRAMBERG/'], + }), + ('Contextual::Return', '0.004008', { + 'source_tmpl': 'Contextual-Return-0.004008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], + }), +] + +modextrapaths = { + 'PATH': "", # add installation dir to PATH + 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) +} + +postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + "chmod +x %(installdir)s/*.pl"] # add execution permission + +sanity_check_paths = { + 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 25ee5b39069f77a58dee584edb7deea6cdc1f5df Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 2 Feb 2016 19:43:35 +0100 Subject: [PATCH 0320/2133] added ImageMagick-6.9.3-2-goolf-1.4.10.eb and missing deps --- .../ImageMagick-6.9.3-2-goolf-1.4.10.eb | 29 +++++++++++++++++++ .../l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb | 15 ++++++++++ .../libjpeg-turbo-1.4.1-goolf-1.4.10.eb | 24 +++++++++++++++ 3 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb new file mode 100644 index 0000000000..91d3272c34 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '6.9.3-2' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.imagemagick.org/download/'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('freetype', '2.5.0.1'), + ('Ghostscript', '9.10'), + ('JasPer', '1.900.1'), + ('libjpeg-turbo', '1.4.1'), + ('LibTIFF', '4.0.3'), + ('libX11', '1.6.1'), + ('libXext', '1.3.2'), + ('libXt', '1.1.4'), + ('LittleCMS', '2.7'), +] + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb new file mode 100644 index 0000000000..af18beb748 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.7' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..b5f70e73bc --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.4.10.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.1' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.07'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' -- GitLab From 265a314ee9bc5b53892e6abfebce5c50a638fe07 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 2 Feb 2016 23:36:03 +0100 Subject: [PATCH 0321/2133] added pkg-config dependency --- .../i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb index 91d3272c34..c751d87629 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb @@ -22,6 +22,7 @@ dependencies = [ ('libXext', '1.3.2'), ('libXt', '1.1.4'), ('LittleCMS', '2.7'), + ('pkg-config', '0.27.1'), ] modextravars = {'MAGICK_HOME': '%(installdir)s'} -- GitLab From e1ef6c675000659343591b391917fb1700a6fc15 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 3 Feb 2016 09:28:25 +0100 Subject: [PATCH 0322/2133] moved pkg-config to builddeps --- .../i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb index c751d87629..11edf87c57 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb @@ -11,6 +11,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.imagemagick.org/download/'] +builddependencies = [ + ('pkg-config', '0.27.1'), +] + dependencies = [ ('bzip2', '1.0.6'), ('freetype', '2.5.0.1'), @@ -22,7 +26,6 @@ dependencies = [ ('libXext', '1.3.2'), ('libXt', '1.1.4'), ('LittleCMS', '2.7'), - ('pkg-config', '0.27.1'), ] modextravars = {'MAGICK_HOME': '%(installdir)s'} -- GitLab From baa1751121b1e24467cd176191f6b11f729200a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Feb 2016 15:51:16 +0200 Subject: [PATCH 0323/2133] add easyconfig ASE-3.9.1.4567-intel-2016a-Python-2.7.11.eb --- ...SE-3.9.1.4567-intel-2016a-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.9.1.4567-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.9.1.4567-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.9.1.4567-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..3078c635fc --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.9.1.4567-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.9.1.4567' + +homepage = 'https://wiki.fysik.dtu.dk/ase/' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://wiki.fysik.dtu.dk/ase-files/'] +sources = ['python-%(namelower)s-%(version)s.tar.gz'] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], +} + +moduleclass = 'chem' -- GitLab From 53f6520880cc45a7b2e7445b6e4b08f5567a386e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 4 Feb 2016 09:41:43 +0100 Subject: [PATCH 0324/2133] added latest spades easyconfig --- .../s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..df5ad900a5 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "CMakeMake" + +name = 'SPAdes' +version = '3.6.2' + +homepage = 'http://bioinf.spbau.ru/en/spades' +description = """ Genome assembler for single-cell and isolates data sets """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://spades.bioinf.spbau.ru/release%(version)s/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('CMake', '2.8.12')] + +dependencies = [('zlib', '1.2.8')] + +start_dir = 'src' + +separate_build_dir = True + +sanity_check_commands = [('spades.py', '--test')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bwa-spades", "dipspades", "dipspades.py", + "hammer", "ionhammer", "spades", "spades.py"]], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From 2c80f6c053b517e747b5d256a6768ce7084fcb18 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 4 Feb 2016 09:43:43 +0100 Subject: [PATCH 0325/2133] updated header --- easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb index df5ad900a5..95828fbb10 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics easyblock = "CMakeMake" -- GitLab From 3952aed5dfa6363c7758ca08b3329a9210da3879 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Feb 2016 12:20:35 +0200 Subject: [PATCH 0326/2133] add easyconfig Boost-1.57.0-gimkl-2.11.5-Python-2.7.10.eb --- ...Boost-1.57.0-gimkl-2.11.5-Python-2.7.10.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.57.0-gimkl-2.11.5-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.57.0-gimkl-2.11.5-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-gimkl-2.11.5-Python-2.7.10.eb new file mode 100644 index 0000000000..0efec2bdf2 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-gimkl-2.11.5-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.57.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 456825c036b0f2a829126d009979b985d4d3f8c4 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 4 Feb 2016 18:16:42 +0100 Subject: [PATCH 0327/2133] style fixes --- easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb index 95828fbb10..b09bce53d6 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb @@ -9,7 +9,7 @@ name = 'SPAdes' version = '3.6.2' homepage = 'http://bioinf.spbau.ru/en/spades' -description = """ Genome assembler for single-cell and isolates data sets """ +description = """Genome assembler for single-cell and isolates data sets""" toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -33,4 +33,3 @@ sanity_check_paths = { } moduleclass = 'bio' - -- GitLab From 797147b29f7ba3ec743f81ddf6f7b1eedbb12bb4 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 5 Feb 2016 09:04:22 +0100 Subject: [PATCH 0328/2133] fix some style remarks --- .../p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb index 69ae0dc1d2..0df91cad2a 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -9,7 +9,7 @@ name = 'PRINSEQ' version = '0.20.4' homepage = 'http://prinseq.sourceforge.net' -description = """ A bioinformatics tool to PRe-process and show INformation of SEQuence data. """ +description = """A bioinformatics tool to PRe-process and show INformation of SEQuence data.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -100,8 +100,10 @@ modextrapaths = { 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) } -postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line - "chmod +x %(installdir)s/*.pl"] # add execution permission +postinstallcmds = [ + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + "chmod +x %(installdir)s/*.pl" # add execution permission +] sanity_check_paths = { 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], -- GitLab From 08080db9320bc17bde00b6fb9672477f62706d76 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 5 Feb 2016 10:04:14 +0100 Subject: [PATCH 0329/2133] Add support for PyGTK with intel/2016a toolchain --- .../a/ATK/ATK-2.18.0-intel-2016a.eb | 35 +++++++++++++ .../c/cairo/cairo-1.14.6-intel-2016a.eb | 45 +++++++++++++++++ .../e/expat/expat-2.1.0-intel-2016a.eb | 15 ++++++ .../fontconfig-2.11.94-intel-2016a.eb | 22 ++++++++ .../g/GLib/GLib-2.47.5-intel-2016a.eb | 30 +++++++++++ ...Object-Introspection-1.47.1-intel-2016a.eb | 46 +++++++++++++++++ .../g/GTK+/GTK+-2.24.28-intel-2016a.eb | 26 ++++++++++ .../Gdk-Pixbuf-2.32.3-intel-2016a.eb | 35 +++++++++++++ .../g/gettext/gettext-0.19.6-intel-2016a.eb | 18 +++++++ .../h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb | 35 +++++++++++++ .../l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb | 33 ++++++++++++ .../l/libffi/libffi-3.2.1-intel-2016a.eb | 23 +++++++++ .../libjpeg-turbo-1.4.2-intel-2016a.eb | 24 +++++++++ .../n/NASM/NASM-2.11.08-intel-2016a.eb | 31 ++++++++++++ .../p/Pango/Pango-1.39.0-intel-2016a.eb | 32 ++++++++++++ ...yCairo-1.10.0-intel-2016a-Python-2.7.11.eb | 34 +++++++++++++ ...Object-2.28.6-intel-2016a-Python-2.7.11.eb | 39 +++++++++++++++ .../p/PyGObject/pygobject-enum-types.patch | 50 +++++++++++++++++++ .../PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb | 48 ++++++++++++++++++ .../p/pixman/pixman-0.34.0-intel-2016a.eb | 20 ++++++++ 20 files changed, 641 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PyGObject/pygobject-enum-types.patch create mode 100644 easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb new file mode 100644 index 0000000000..1a5d0e1ef2 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.18.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('GObject-Introspection', '1.47.1') +] + +configopts = " --disable-dependency-tracking --enable-introspection=yes " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb new file mode 100644 index 0000000000..0a62de36aa --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +glibver = '2.47.5' + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), + ('GLib', glibver), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2016a.eb new file mode 100644 index 0000000000..7822366091 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2016a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2016a.eb new file mode 100644 index 0000000000..f008f4125b --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.94' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.6.2'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb new file mode 100644 index 0000000000..beaa30c8cd --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +pysuffix = '-Python-%s' % pyver + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3', pysuffix) +] + +builddependencies = [('Python', pyver)] + +configopts = " --disable-maintainer-mode --disable-silent-rules " +configopts += " --disable-dependency-tracking --disable-libelf --enable-static --enable-shared " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb new file mode 100644 index 0000000000..14604a6073 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.47.1' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +pyver = '2.7.11' + +dependencies = [ + ('Python', pyver), + ('GLib', '2.47.5'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6'), + ('libffi', '3.2.1'), +] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " + +configopts = "--disable-dependency-tracking" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb new file mode 100644 index 0000000000..6a0fe61d40 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.28' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.18.0'), + ('Gdk-Pixbuf', '2.32.3'), + ('Pango', '1.39.0'), + ('GObject-Introspection', '1.47.1'), +] + +configopts = " --disable-dependency-tracking --disable-silent-rules " +configopts += " --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb new file mode 100644 index 0000000000..6c757a9b2b --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.32.3' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('GObject-Introspection', '1.47.1') +] + +configopts = " --disable-dependency-tracking --disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += " --disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb new file mode 100644 index 0000000000..d58aad1970 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.6' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb new file mode 100644 index 0000000000..8826dd1ab6 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6'), + ('freetype', '2.6.2'), + ('GObject-Introspection', '1.47.1') +] + +configopts = " --disable-dependency-tracking --enable-introspection=yes --with-gobject=yes " +configopts += " --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb new file mode 100644 index 0000000000..ed490e66de --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.6' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2016a.eb new file mode 100644 index 0000000000..2096059a85 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a.eb new file mode 100644 index 0000000000..0eed145ebe --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2016a.eb new file mode 100644 index 0000000000..7fa10b2782 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb new file mode 100644 index 0000000000..8006abc5d1 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.39.0' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6'), + ('HarfBuzz', '1.1.3'), + ('GObject-Introspection', '1.47.1'), + ('fontconfig', '2.11.94') +] + +configopts = " --disable-dependency-tracking --disable-silent-rules " +configopts += " --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..13339917a6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'Waf' + +name = 'PyCairo' +version = '1.10.0' + +homepage = 'http://cairographics.org/pycairo/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +# py2cairo is the Python 2 compatible release +sources = ['py2cairo-%(version)s.tar.bz2'] + +pyver_maj_min = '2.7' +pyver = '%s.11' % pyver_maj_min +versionsuffix = '-Python-%s' % (pyver) + +configopts = " --nopyc --nopyo " + +dependencies = [ + ('Python', pyver), + ('cairo', '1.14.6'), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver_maj_min, + 'lib64/python%s/site-packages' % pyver_maj_min]} + +sanity_check_paths = { + 'files': ['include/pycairo/pycairo.h', 'lib/pkgconfig/pycairo.pc'], + 'dirs': ['lib/python%s/site-packages/cairo' % pyver_maj_min], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..7a523a4d67 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'PyGObject' +version = '2.28.6' + +homepage = 'http://www.pygtk.org/' +description = """Python Bindings for GLib/GObject/GIO/GTK+""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +patches = ['pygobject-enum-types.patch'] + +pyver_maj_min = '2.7' +pyver = '%s.11' % pyver_maj_min +versionsuffix = '-Python-%s' % pyver + +glibver = '2.47.5' +dependencies = [ + ('Python', pyver), + ('GLib', glibver), + ('GObject-Introspection', '1.47.1'), + ('PyCairo', '1.10.0', versionsuffix), +] + +configopts = " --disable-dependency-tracking --disable-introspection " + +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver_maj_min, + 'lib64/python%s/site-packages' % pyver_maj_min]} + +sanity_check_paths = { + 'files': ['include/pygtk-%(version_major)s.0/pyglib.h', 'include/pygtk-%(version_major)s.0/pygobject.h', + 'lib/libpyglib-%(version_major)s.0-python.so'], + 'dirs': ['bin', 'lib/python%s/site-packages/' % pyver_maj_min], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/pygobject-enum-types.patch b/easybuild/easyconfigs/p/PyGObject/pygobject-enum-types.patch new file mode 100644 index 0000000000..420f56b036 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/pygobject-enum-types.patch @@ -0,0 +1,50 @@ +From 42d01f060c5d764baa881d13c103d68897163a49 Mon Sep 17 00:00:00 2001 +From: Ryan Lortie +Date: Mon, 12 Mar 2012 16:44:14 -0400 +Subject: gio-types.defs: change some enums to flags + +These flags types were originally incorrectly handled in glib as being +enums. That bug was fixed, but they're still enums here, leading to +warnings about the mismatch. + +Change them to flags. + +https://bugzilla.gnome.org/show_bug.cgi?id=668522 +--- + gio/gio-types.defs | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/gio/gio-types.defs b/gio/gio-types.defs +index 331e0bc..7eee5c8 100644 +--- a/gio/gio-types.defs ++++ b/gio/gio-types.defs +@@ -526,7 +526,7 @@ + ) + ) + +-(define-enum MountMountFlags ++(define-flags MountMountFlags + (in-module "gio") + (c-name "GMountMountFlags") + (gtype-id "G_TYPE_MOUNT_MOUNT_FLAGS") +@@ -545,7 +545,7 @@ + ) + ) + +-(define-enum DriveStartFlags ++(define-flags DriveStartFlags + (in-module "gio") + (c-name "GDriveStartFlags") + (gtype-id "G_TYPE_DRIVE_START_FLAGS") +@@ -770,7 +770,7 @@ + ) + ) + +-(define-enum SocketMsgFlags ++(define-flags SocketMsgFlags + (in-module "gio") + (c-name "GSocketMsgFlags") + (gtype-id "G_TYPE_SOCKET_MSG_FLAGS") +-- +cgit v0.11.2 + diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..d7c932fcb8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'PyGTK' +version = '2.24.0' + +homepage = 'http://www.pygtk.org/' +description = """PyGTK lets you to easily create programs with a graphical user interface + using the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['ftp://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s/'] + +configopts = " --disable-dependency-tracking " + +pyver_maj_min = '2.7' +pyver = '%s.11' % pyver_maj_min +versionsuffix = '-Python-%s' % pyver + +glibver = '2.47.5' +dependencies = [ + ('Python', pyver), + ('GLib', glibver), + ('PyGObject', '2.28.6', versionsuffix), + ('GTK+', '2.24.28'), + ('ATK', '2.18.0'), + ('PyCairo', '1.10.0', versionsuffix), +] + +postinstallcmds = ["sed -i s#'codegendir=${datadir}'#codegendir=$EBROOTPYGOBJECT/share# " + + "%(installdir)s/lib/pkgconfig/pygtk-2.0.pc"] +postinstallcmds += ["sed -i s#'exec_prefix=${prefix}'#exec_prefix=$EBROOTPYGOBJECT# " + + "%(installdir)s/bin/pygtk-codegen-2.0"] + +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver_maj_min, + 'lib64/python%s/site-packages' % pyver_maj_min], + 'PYTHONPATH': ['lib/python%s/site-packages/gtk-2.0' % pyver_maj_min, + 'lib64/python%s/site-packages/gtk-2.0' % pyver_maj_min]} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pygtk-%(version_major)s.0.pc'], + 'dirs': ['lib/pygtk'], +} + +sanity_check_commands = [('python', "-c 'import gtk'")] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016a.eb new file mode 100644 index 0000000000..eb4e677dea --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 951d52673aef7b3e182e7265ee1954bcb92f94c6 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 5 Feb 2016 10:28:45 +0100 Subject: [PATCH 0330/2133] Conform, conform, conform!! --- .../p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb index d7c932fcb8..4ab6601fee 100644 --- a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb @@ -12,8 +12,6 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['ftp://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s/'] -configopts = " --disable-dependency-tracking " - pyver_maj_min = '2.7' pyver = '%s.11' % pyver_maj_min versionsuffix = '-Python-%s' % pyver @@ -28,6 +26,8 @@ dependencies = [ ('PyCairo', '1.10.0', versionsuffix), ] +configopts = " --disable-dependency-tracking " + postinstallcmds = ["sed -i s#'codegendir=${datadir}'#codegendir=$EBROOTPYGOBJECT/share# " + "%(installdir)s/lib/pkgconfig/pygtk-2.0.pc"] postinstallcmds += ["sed -i s#'exec_prefix=${prefix}'#exec_prefix=$EBROOTPYGOBJECT# " + -- GitLab From a270b55ff4522b71706bf6ddcec1e5ff277950bb Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 5 Feb 2016 10:58:12 +0100 Subject: [PATCH 0331/2133] added extra sanity checks --- ...PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 116 ++++++++++++++++++ 1 file changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..2843226d01 --- /dev/null +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,116 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'PRINSEQ' +version = '0.20.4' + +homepage = 'http://prinseq.sourceforge.net' +description = """A bioinformatics tool to PRe-process and show INformation of SEQuence data.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] +sources = ['%(namelower)s-lite-%(version)s.tar.gz'] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::Depends', '0.405', { + 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('ExtUtils::PkgConfig', '1.15', { + 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], + }), + ('Pod::Usage', '1.68', { + 'source_tmpl': 'Pod-Usage-1.68.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + }), + ('File::Temp', '0.2304', { + 'source_tmpl': 'File-Temp-0.2304.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Digest::MD5', '2.54', { + 'source_tmpl': 'Digest-MD5-2.54.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/'], + }), + ('Cairo', '1.106', { + 'source_tmpl': 'Cairo-1.106.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('Statistics::PCA', '0.0.1', { + 'source_tmpl': 'Statistics-PCA-0.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSTH/'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-3.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Math::Cephes::Matrix', '0.5304', { + 'source_tmpl': 'Math-Cephes-0.5304.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + }), + ('Math::MatrixReal', '2.12', { + 'source_tmpl': 'Math-MatrixReal-2.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LETO/'], + }), + ('Text::SimpleTable', '2.03', { + 'source_tmpl': 'Text-SimpleTable-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRAMBERG/'], + }), + ('Contextual::Return', '0.004008', { + 'source_tmpl': 'Contextual-Return-0.004008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], + }), +] + +# this is the script which relies in many extra Perl libraries so we verify here it's working fine +runtest = 'perl %(installdir)s/prinseq-graphs.pl' + +modextrapaths = { + 'PATH': "", # add installation dir to PATH + 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) +} + +postinstallcmds = [ + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + "chmod +x %(installdir)s/*.pl" # add execution permission +] + +sanity_check_paths = { + 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 178c558e2e9c93de6addb1dc4cc389d93ce25ff5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 5 Feb 2016 11:25:25 +0100 Subject: [PATCH 0332/2133] fixed merge conflicts --- .../p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb index 5d81a0e0c1..2843226d01 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -95,12 +95,9 @@ exts_list = [ }), ] -<<<<<<< HEAD # this is the script which relies in many extra Perl libraries so we verify here it's working fine runtest = 'perl %(installdir)s/prinseq-graphs.pl' -======= ->>>>>>> upstream/develop modextrapaths = { 'PATH': "", # add installation dir to PATH 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) -- GitLab From 58a5fd09ae292d1de21e8ffe3350d75e9f1e56bd Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 5 Feb 2016 13:18:45 +0100 Subject: [PATCH 0333/2133] use sanity_check_commands instead of runtest --- .../p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb index 2843226d01..fc0341658f 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -95,8 +95,8 @@ exts_list = [ }), ] -# this is the script which relies in many extra Perl libraries so we verify here it's working fine -runtest = 'perl %(installdir)s/prinseq-graphs.pl' +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = [('perl', '%(installdir)s/prinseq-graphs.pl')] modextrapaths = { 'PATH': "", # add installation dir to PATH -- GitLab From b520afc4de5f3a3ecc7f7a96e77757283b57fd1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 14:18:55 +0200 Subject: [PATCH 0334/2133] add easyconfig CMake-3.4.3-intel-2016a.eb, add easyconfig Doxygen-1.8.11-intel-2016a.eb, add easyconfig cURL-7.47.0-intel-2016a.eb --- .../c/CMake/CMake-3.4.3-intel-2016a.eb | 31 +++++++++++++++++++ .../c/cURL/cURL-7.47.0-intel-2016a.eb | 31 +++++++++++++++++++ .../d/Doxygen/Doxygen-1.8.11-intel-2016a.eb | 19 ++++++++++++ 3 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb new file mode 100644 index 0000000000..31b70f1b8a --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb new file mode 100644 index 0000000000..80ee257e06 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.47.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb new file mode 100644 index 0000000000..2d5dc8597f --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.11' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.3'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' -- GitLab From 00a795ed85bb3c9543ce590de033be7cca6df0c9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 13:35:51 +0100 Subject: [PATCH 0335/2133] Added PCMSolver --- ...PCMSolver-20160205-eigen-include-dir.patch | 14 ++++++ ...lver-20160205-intel-2016a-Python-2.7.11.eb | 45 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-eigen-include-dir.patch create mode 100644 easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-eigen-include-dir.patch b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-eigen-include-dir.patch new file mode 100644 index 0000000000..dcef0d8b3a --- /dev/null +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-eigen-include-dir.patch @@ -0,0 +1,14 @@ +# it doesn't look in the correct directory to find Eigen +diff --git a/cmake/custom/eigen.cmake b/cmake/custom/eigen.cmake +index 8d2f26f..80815e0 100644 +--- a/cmake/custom/eigen.cmake ++++ b/cmake/custom/eigen.cmake +@@ -11,7 +11,7 @@ + # define: '-DEIGEN3_ROOT="{0}"'.format(arguments['--eigen']) + + if(EIGEN3_ROOT) +- set(EIGEN3_INCLUDE_DIR ${EIGEN3_ROOT}/include/eigen3) ++ set(EIGEN3_INCLUDE_DIR ${EIGEN3_ROOT}/include) + find_package(Eigen3 3.1.0) + message(STATUS "Eigen " ${EIGEN3_VERSION} " is located here: " ${EIGEN3_INCLUDE_DIR}) + if(NOT EIGEN3_FOUND) diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0e7d1d1466 --- /dev/null +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'PCMSolver' +version = '20160205' + +homepage = 'https://pcmsolver.readthedocs.org' +description = """An API for the Polarizable Continuum Model.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'c99'} + +sources = ['1d53a584b9a70b.tar.gz'] +source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] + +patches = ['PCMSolver-%(version)s-eigen-include-dir.patch'] + +python = 'Python' +pyver = '2.7.11' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('zlib', '1.2.8'), + ('Boost', '1.59.0', versionsuffix), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Eigen', '3.2.7'), +] + +configopts = '-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN -DCMAKE_CXX_FLAGS="$LIBLAPACK_MT -DEIGEN_USE_MKL_ALL"' + +separate_build_dir = True + +runtest = 'test' + +postinstallcmds = ["chmod +x %(installdir)s/bin/pcmsolver.py"] + +sanity_check_paths = { + 'files': ['bin/pcmsolver.py', 'lib/libpcm.a', 'lib/libpcm.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'chem' -- GitLab From 422db6b8ed6eae35818847193a64867837a810e5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 13:39:54 +0100 Subject: [PATCH 0336/2133] Added git version of PSI4 --- .../PSI-4.0b6-20160201-fix-gitversion.patch | 12 +++++ ...6-20160201-intel-2016a-mt-Python-2.7.11.eb | 45 +++++++++++++++++++ .../p/PSI/PSI-4.0b6-20160201-plugin-fix.patch | 14 ++++++ 3 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-fix-gitversion.patch create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-plugin-fix.patch diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-fix-gitversion.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-fix-gitversion.patch new file mode 100644 index 0000000000..93d3b7eab4 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-fix-gitversion.patch @@ -0,0 +1,12 @@ +# As we have a git version without the git metadata, we tell it which commit we have used +# by wpoely86@gmail.com +diff -ur psi4public-e4070d0024742579a445e084da9dde078310094d.orig/src/bin/psi4/gitversion.py psi4public-e4070d0024742579a445e084da9dde078310094d/src/bin/psi4/gitversion.py +--- psi4public-e4070d0024742579a445e084da9dde078310094d.orig/src/bin/psi4/gitversion.py 2016-02-01 22:43:36.000000000 +0100 ++++ psi4public-e4070d0024742579a445e084da9dde078310094d/src/bin/psi4/gitversion.py 2016-02-04 11:41:37.287312135 +0100 +@@ -104,4 +104,5 @@ + ghash = '' + mmp = '' + +-write_version(branch, mmp, ghash, status) ++#write_version(branch, mmp, ghash, status) ++write_version('master', None, 'e4070d002474257', '') diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb new file mode 100644 index 0000000000..d4fb4f7c93 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb @@ -0,0 +1,45 @@ +name = 'PSI' +version = '4.0b6-20160201' +versionsuffix = '-mt' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/psi4/psi4public/archive/'] +sources = ['e4070d0024742579.tar.gz'] + +patches = [ + 'PSI-%(version)s-fix-gitversion.patch', + 'PSI-%(version)s-plugin-fix.patch', +] + +python = 'Python' +pyver = '2.7.11' +pysuff = '-%s-%s' % (python, pyver) +versionsuffix += pysuff + +dependencies = [ + (python, pyver), + ('Boost', '1.59.0', pysuff), + ('PCMSolver', '20160205', pysuff), + ('CheMPS2', '1.6'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Perl', '5.22.1', '-bare'), # for the test suite +] + +configopts = '-DENABLE_MPI=OFF -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_CHEMPS2=ON -DENABLE_PLUGINS=ON' +configopts += ' -DENABLE_DUMMY_PLUGIN=ON -DCHEMPS2_ROOT=$EBROOTCHEMPS2' +configopts += ' -DENABLE_PCMSOLVER=ON -DPCMSOLVER_ROOT=$EBROOTPCMSOLVER' + +# Execute only the 'quick' tests and run 4 in parallel +runtest = 'ARGS="-V -L quicktests -j 4" test' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-plugin-fix.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-plugin-fix.patch new file mode 100644 index 0000000000..1cd68c1a98 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-plugin-fix.patch @@ -0,0 +1,14 @@ +# Let the plugin makefile system work with our install system: patch the +# directory path to correspond with our install directory +# 01/02/2016 - wpoely86@gmail.com +diff -ur psi4public-e4070d0024742579a445e084da9dde078310094d.orig/CMakeLists.txt psi4public-e4070d0024742579a445e084da9dde078310094d/CMakeLists.txt +--- psi4public-e4070d0024742579a445e084da9dde078310094d.orig/CMakeLists.txt 2016-02-01 22:43:36.000000000 +0100 ++++ psi4public-e4070d0024742579a445e084da9dde078310094d/CMakeLists.txt 2016-02-05 12:40:20.375508374 +0100 +@@ -282,6 +282,7 @@ + foreach(dir ${dirs}) + set(PLUGIN_INCLUDE_DIRECTORIES "-I${dir} ${PLUGIN_INCLUDE_DIRECTORIES}") + endforeach() ++set(PLUGIN_INCLUDE_DIRECTORIES "-I$ENV{PSI_SRC_INSTALL_DIR}/include -I$ENV{PSI_SRC_INSTALL_DIR}/src/lib/ -I$ENV{PSI_OBJ_INSTALL_DIR}/include -I$ENV{PSI_OBJ_INSTALL_DIR}/src/lib/ ${PLUGIN_INCLUDE_DIRECTORIES}") + foreach(def ${defs}) + set(PLUGIN_DEFINES "-D${def} ${PLUGIN_DEFINES}") + endforeach() -- GitLab From b019fe54647e6fffe46a6f4811063f71112de804 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 14:44:53 +0200 Subject: [PATCH 0337/2133] add easyconfig HDF5-1.8.16-intel-2016a.eb --- .../h/HDF5/HDF5-1.8.16-intel-2016a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb new file mode 100644 index 0000000000..dc65dce562 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.16' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From b146200dbd2f7aa7ec3339a4cde3971967c6cd44 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 14:47:42 +0200 Subject: [PATCH 0338/2133] add easyconfig Szip-2.1-intel-2016a.eb --- .../s/Szip/Szip-2.1-intel-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb new file mode 100644 index 0000000000..67b0f10359 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 83cbdcc53f75dba692f751f327f1dc24ab20e7e1 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 13:59:30 +0100 Subject: [PATCH 0339/2133] PCMSolver: patch is mainlined --- .../PCMSolver-20160205-eigen-include-dir.patch | 14 -------------- ...PCMSolver-20160205-intel-2016a-Python-2.7.11.eb | 4 +--- 2 files changed, 1 insertion(+), 17 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-eigen-include-dir.patch diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-eigen-include-dir.patch b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-eigen-include-dir.patch deleted file mode 100644 index dcef0d8b3a..0000000000 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-eigen-include-dir.patch +++ /dev/null @@ -1,14 +0,0 @@ -# it doesn't look in the correct directory to find Eigen -diff --git a/cmake/custom/eigen.cmake b/cmake/custom/eigen.cmake -index 8d2f26f..80815e0 100644 ---- a/cmake/custom/eigen.cmake -+++ b/cmake/custom/eigen.cmake -@@ -11,7 +11,7 @@ - # define: '-DEIGEN3_ROOT="{0}"'.format(arguments['--eigen']) - - if(EIGEN3_ROOT) -- set(EIGEN3_INCLUDE_DIR ${EIGEN3_ROOT}/include/eigen3) -+ set(EIGEN3_INCLUDE_DIR ${EIGEN3_ROOT}/include) - find_package(Eigen3 3.1.0) - message(STATUS "Eigen " ${EIGEN3_VERSION} " is located here: " ${EIGEN3_INCLUDE_DIR}) - if(NOT EIGEN3_FOUND) diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb index 0e7d1d1466..a35d9ea836 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb @@ -9,11 +9,9 @@ description = """An API for the Polarizable Continuum Model.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'cstd': 'c99'} -sources = ['1d53a584b9a70b.tar.gz'] +sources = ['2473699d6c5db36525160e.tar.gz'] source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] -patches = ['PCMSolver-%(version)s-eigen-include-dir.patch'] - python = 'Python' pyver = '2.7.11' versionsuffix = '-%s-%s' % (python, pyver) -- GitLab From 71121908283c712dc7e386a0694ddfa67f70ed48 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 14:00:10 +0100 Subject: [PATCH 0340/2133] Added Eigen 3.2.7 for intel/2016a --- .../easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb new file mode 100644 index 0000000000..5e2d4fc5a2 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.7' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From c16f4d894fb9b8e68f67a31d27bd4d93b6de4852 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 14:00:32 +0100 Subject: [PATCH 0341/2133] Perl bare for intel/2016a --- .../p/Perl/Perl-5.22.1-intel-2016a-bare.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb new file mode 100644 index 0000000000..e7350c64a5 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.22.1' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' -- GitLab From d5a7ac81aaf53300de98be2bef29acd7099d8312 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 14:00:52 +0100 Subject: [PATCH 0342/2133] Add CheMPS2 --- .../c/CheMPS2/CheMPS2-1.6-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb new file mode 100644 index 0000000000..aab739ed19 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.6' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] + +builddependencies = [('CMake', '3.4.1')] + +dependencies = [ + ('GSL', '2.1'), + ('HDF5', '1.8.16') +] + +buildopts = 'VERBOSE=1' + +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' -- GitLab From a8923c12fb51d6397bb2cd2454981c122f736d39 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 14:03:30 +0100 Subject: [PATCH 0343/2133] Added HDF5 for intel/2016a --- .../h/HDF5/HDF5-1.8.16-intel-2016a.eb | 26 +++++++++++++++++++ .../s/Szip/Szip-2.1-intel-2016a.eb | 23 ++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb new file mode 100644 index 0000000000..dc65dce562 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.16' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb new file mode 100644 index 0000000000..67b0f10359 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 8018253d698f211544fb11baa921ae7c0738e5c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 14:11:48 +0100 Subject: [PATCH 0344/2133] include PCRE dep for GLib, remove --disable-dependency-tracking in configopts --- .../a/ATK/ATK-2.18.0-intel-2016a.eb | 2 +- .../g/GLib/GLib-2.47.5-intel-2016a.eb | 7 ++++--- ...Object-Introspection-1.47.1-intel-2016a.eb | 2 -- .../g/GTK+/GTK+-2.24.28-intel-2016a.eb | 3 +-- .../Gdk-Pixbuf-2.32.3-intel-2016a.eb | 4 ++-- .../h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb | 3 +-- .../p/PCRE/PCRE-8.38-intel-2016a.eb | 20 +++++++++++++++++++ .../p/Pango/Pango-1.39.0-intel-2016a.eb | 3 +-- ...Object-2.28.6-intel-2016a-Python-2.7.11.eb | 2 +- .../PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb | 20 +++++++++---------- 10 files changed, 41 insertions(+), 25 deletions(-) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016a.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb index 1a5d0e1ef2..2e24deb654 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb @@ -21,7 +21,7 @@ dependencies = [ ('GObject-Introspection', '1.47.1') ] -configopts = " --disable-dependency-tracking --enable-introspection=yes " +configopts = "--enable-introspection=yes" modextrapaths = { 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb index beaa30c8cd..07094c48e5 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb @@ -19,12 +19,13 @@ pysuffix = '-Python-%s' % pyver dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), - ('libxml2', '2.9.3', pysuffix) + ('libxml2', '2.9.3', pysuffix), + ('PCRE', '8.38'), ] builddependencies = [('Python', pyver)] -configopts = " --disable-maintainer-mode --disable-silent-rules " -configopts += " --disable-dependency-tracking --disable-libelf --enable-static --enable-shared " +configopts = "--disable-maintainer-mode --disable-silent-rules " +configopts += "--disable-libelf --enable-static --enable-shared " moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb index 14604a6073..3b0f223d1e 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -30,8 +30,6 @@ builddependencies = [('Autotools', '20150215')] preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " -configopts = "--disable-dependency-tracking" - modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb index 6a0fe61d40..13dfd28341 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb @@ -20,7 +20,6 @@ dependencies = [ ('GObject-Introspection', '1.47.1'), ] -configopts = " --disable-dependency-tracking --disable-silent-rules " -configopts += " --disable-glibtest --enable-introspection=yes --disable-visibility " +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb index 6c757a9b2b..e5b4a33f0d 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb @@ -25,8 +25,8 @@ dependencies = [ ('GObject-Introspection', '1.47.1') ] -configopts = " --disable-dependency-tracking --disable-maintainer-mode --enable-debug=no --enable-introspection=yes " -configopts += " --disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" modextrapaths = { 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb index 8826dd1ab6..050ccb7858 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb @@ -19,8 +19,7 @@ dependencies = [ ('GObject-Introspection', '1.47.1') ] -configopts = " --disable-dependency-tracking --enable-introspection=yes --with-gobject=yes " -configopts += " --enable-static --enable-shared --with-cairo " +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " modextrapaths = { 'GI_TYPELIB_PATH': 'share', diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016a.eb new file mode 100644 index 0000000000..61beae9c6a --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.38' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf8 --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb index 8006abc5d1..fb5d6493b5 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb @@ -22,8 +22,7 @@ dependencies = [ ('fontconfig', '2.11.94') ] -configopts = " --disable-dependency-tracking --disable-silent-rules " -configopts += " --enable-introspection=yes --enable-static --enable-shared " +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb index 7a523a4d67..17c6ac4dcb 100644 --- a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb @@ -25,7 +25,7 @@ dependencies = [ ('PyCairo', '1.10.0', versionsuffix), ] -configopts = " --disable-dependency-tracking --disable-introspection " +configopts = "--disable-introspection" modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver_maj_min, 'lib64/python%s/site-packages' % pyver_maj_min]} diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb index 4ab6601fee..6eacf5d498 100644 --- a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb @@ -26,17 +26,17 @@ dependencies = [ ('PyCairo', '1.10.0', versionsuffix), ] -configopts = " --disable-dependency-tracking " - -postinstallcmds = ["sed -i s#'codegendir=${datadir}'#codegendir=$EBROOTPYGOBJECT/share# " + - "%(installdir)s/lib/pkgconfig/pygtk-2.0.pc"] -postinstallcmds += ["sed -i s#'exec_prefix=${prefix}'#exec_prefix=$EBROOTPYGOBJECT# " + - "%(installdir)s/bin/pygtk-codegen-2.0"] +postinstallcmds = [ + "sed -i s#'codegendir=${datadir}'#codegendir=$EBROOTPYGOBJECT/share# %(installdir)s/lib/pkgconfig/pygtk-2.0.pc", + "sed -i s#'exec_prefix=${prefix}'#exec_prefix=$EBROOTPYGOBJECT# %(installdir)s/bin/pygtk-codegen-2.0", +] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver_maj_min, - 'lib64/python%s/site-packages' % pyver_maj_min], - 'PYTHONPATH': ['lib/python%s/site-packages/gtk-2.0' % pyver_maj_min, - 'lib64/python%s/site-packages/gtk-2.0' % pyver_maj_min]} +modextrapaths = { + 'PYTHONPATH': ['lib/python%s/site-packages' % pyver_maj_min, + 'lib64/python%s/site-packages' % pyver_maj_min, + 'lib/python%s/site-packages/gtk-2.0' % pyver_maj_min, + 'lib64/python%s/site-packages/gtk-2.0' % pyver_maj_min], +} sanity_check_paths = { 'files': ['lib/pkgconfig/pygtk-%(version_major)s.0.pc'], -- GitLab From e5e8fb96f10b3f441fe3302c37acb15abf3dd77e Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 5 Feb 2016 15:16:42 +0100 Subject: [PATCH 0345/2133] updated ebs to default value for toolchain opts dynamic = True --- easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb | 1 - easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb | 1 - easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb | 2 +- .../easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb | 1 - easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb | 1 - easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb | 2 +- 6 files changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb index 5d449a2077..1a73916b52 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb @@ -8,7 +8,6 @@ description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'dynamic': True} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb index f5c36d9c4c..656ae6d877 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb @@ -9,7 +9,6 @@ description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fa dimensions, of arbitrary input size, and of complex data.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = { 'dynamic': True } source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb index d97f4cebb2..6340c63211 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb @@ -7,7 +7,7 @@ homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'pic': True, } source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb index 06a6cb2664..bdb5c45a5a 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb @@ -7,7 +7,6 @@ homepage = 'http://spglib.sourceforge.net/' description = """Spglib is a C library for finding and handling crystal symmetries.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'dynamic': True, } source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb index e07994886a..3b456bd5d5 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb @@ -21,7 +21,6 @@ description = """Tcsh is an enhanced, but completely compatible version of the B mechanism, job control and a C-like syntax.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'dynamic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [ diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb index 7d35b456b3..0c6915d7cd 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb @@ -9,7 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'pic': True, } sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -- GitLab From 110a98840e1f1d882b83502c94953ef32dfd5d81 Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 5 Feb 2016 15:21:12 +0100 Subject: [PATCH 0346/2133] updated ebs to default value for toolchain opts dynamic = True --- easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb | 1 - easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb | 1 - easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb | 2 +- .../easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb | 1 - easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb | 1 - easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb | 2 +- 6 files changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb index 2813041da2..d4b9c66352 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb @@ -8,7 +8,6 @@ description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'dynamic': True} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb index 9a44adf4a0..4acf581ee5 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb @@ -9,7 +9,6 @@ description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fa dimensions, of arbitrary input size, and of complex data.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = { 'dynamic': True } source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb index 621f9235dd..a075d53839 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb @@ -7,7 +7,7 @@ homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'pic': True, } source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb index 90249a4422..68086c7c98 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb @@ -7,7 +7,6 @@ homepage = 'http://spglib.sourceforge.net/' description = """Spglib is a C library for finding and handling crystal symmetries.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'dynamic': True, } source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb index 07d83bd968..c5db50a961 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb @@ -21,7 +21,6 @@ description = """Tcsh is an enhanced, but completely compatible version of the B mechanism, job control and a C-like syntax.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'dynamic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [ diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb index e2f5d3e598..fbc74998eb 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb @@ -9,7 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'pic': True, } sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -- GitLab From abeb9c17bff1f6a22a51b3fb7ae7608bf06e809e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 16:29:26 +0200 Subject: [PATCH 0347/2133] add easyconfig ADF-2014.02.eb --- easybuild/easyconfigs/a/ADF/ADF-2014.02.eb | 31 ++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/ADF/ADF-2014.02.eb diff --git a/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb b/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb new file mode 100644 index 0000000000..ee9b8f2b52 --- /dev/null +++ b/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'ADF' +version = '2014.02' + +homepage = 'http://www.scm.com/ADF/' +description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and + predict chemical structure and reactivity with density functional theory (DFT).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s%(version)s.pc64_linux.IntelMPI+CUDA.tgz'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +modextravars = { + 'ADFHOME': '%(installdir)s', + 'ADFBIN': '%(installdir)s/bin', + 'ADFRESOURCES': '%(installdir)s/atomicdata', +} + +modloadmsg = "These environment variables need to be defined before using ADF:" +modloadmsg += " * $SCMLICENSE: path to ADF license file" +modloadmsg += " * $SCM_TMPDIR: path to user scratch directory" + +moduleclass = 'chem' -- GitLab From bb762726ebc8558c1d3563530d784a478c805484 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 16:45:32 +0200 Subject: [PATCH 0348/2133] add newlines in modloadmsg --- easybuild/easyconfigs/a/ADF/ADF-2014.02.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb b/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb index ee9b8f2b52..045e5244fd 100644 --- a/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb @@ -24,8 +24,8 @@ modextravars = { 'ADFRESOURCES': '%(installdir)s/atomicdata', } -modloadmsg = "These environment variables need to be defined before using ADF:" -modloadmsg += " * $SCMLICENSE: path to ADF license file" +modloadmsg = "These environment variables need to be defined before using ADF:\n" +modloadmsg += " * $SCMLICENSE: path to ADF license file\n" modloadmsg += " * $SCM_TMPDIR: path to user scratch directory" moduleclass = 'chem' -- GitLab From 4399a52f2c83f3dfc03a2050323febc3da87fb4d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 16:46:40 +0200 Subject: [PATCH 0349/2133] add easyconfig CMake-3.4.3-intel-2016a.eb --- .../c/CMake/CMake-3.4.3-intel-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb new file mode 100644 index 0000000000..31b70f1b8a --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ff782559660c0987251e15d0da52c6aec83284b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 16:47:39 +0200 Subject: [PATCH 0350/2133] add easyconfig HDF5-1.8.16-intel-2016a.eb, add easyconfig Szip-2.1-intel-2016a.eb --- .../h/HDF5/HDF5-1.8.16-intel-2016a.eb | 26 +++++++++++++++++++ .../s/Szip/Szip-2.1-intel-2016a.eb | 23 ++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb new file mode 100644 index 0000000000..dc65dce562 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.16' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb new file mode 100644 index 0000000000..67b0f10359 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 05f1e7f9d3c58a71d4c9619597ca6450fd54199b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 15:53:20 +0100 Subject: [PATCH 0351/2133] remove easyconfigs that are being added through #2447 and #2448 --- .../c/CMake/CMake-3.4.3-intel-2016a.eb | 31 ------------------- .../h/HDF5/HDF5-1.8.16-intel-2016a.eb | 26 ---------------- .../s/Szip/Szip-2.1-intel-2016a.eb | 23 -------------- 3 files changed, 80 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb deleted file mode 100644 index 31b70f1b8a..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.4.3' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = '-- -DCMAKE_USE_OPENSSL=1' - -dependencies = [ - ('ncurses', '6.0'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb deleted file mode 100644 index dc65dce562..0000000000 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'HDF5' -version = '1.8.16' - -homepage = 'http://www.hdfgroup.org/HDF5/' -description = """HDF5 is a unique technology suite that makes possible the management of - extremely large and complex data collections.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} - -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] - -patches = [ - 'HDF5-1.8.15_configure_intel.patch', - 'configure_libtool.patch', -] - -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - -dependencies = [ - ('zlib', '1.2.8'), - ('Szip', '2.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb deleted file mode 100644 index 67b0f10359..0000000000 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1' - -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' -description = "Szip compression software, providing lossless compression of scientific data" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' -- GitLab From c31ab01763787288bd13198a122b8870b9c663d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 16:56:32 +0200 Subject: [PATCH 0352/2133] add easyconfig R-3.2.3-intel-2016a.eb --- .../easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 398 ++++++++++++++++++ 1 file changed, 398 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb new file mode 100644 index 0000000000..2f1c082832 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -0,0 +1,398 @@ +name = 'R' +version = '3.2.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('libpng', '1.6.21'), # for plotting in R + ('libjpeg-turbo', '1.4.2'), # for plottting in R + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.47.0'), # for RCurl + ('libxml2', '2.9.3'), # for XML + ('GDAL', '2.0.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 21st 2016 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.3', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.9', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2.1', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5.1', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-22', ext_options), + ('mime', '0.4', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.1', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.7-0', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-3', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.60.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('checkmate', '1.6.3', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-4', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.1', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.0.2', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.3-0', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringi', '1.0-1', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.8', ext_options), + ('logspline', '2.1.8', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.6-1', ext_options), + ('randomForest', '4.6-12', ext_options), + ('scatterplot3d', '0.3-36', ext_options), + ('SparseM', '1.7', ext_options), + ('tripack', '1.3-7', ext_options), + ('irace', '1.07', ext_options), + ('rJava', '0.9-7', ext_options), + ('lattice', '0.20-33', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-3', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.12.2', ext_options), + ('RcppArmadillo', '0.6.400.2.2', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.3', ext_options), + ('rlecuyer', '0.3-4', ext_options), + ('snow', '0.4-1', ext_options), + ('MASS', '7.3-45', ext_options), + ('tree', '1.0-36', ext_options), + ('pls', '2.5-0', ext_options), + ('class', '7.3-14', ext_options), + ('e1071', '1.6-7', ext_options), + ('nnet', '7.3-11', ext_options), + ('nlme', '3.1-122', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.5.1', ext_options), + ('MatrixModels', '0.4-1', ext_options), + ('quantreg', '5.19', ext_options), + ('mgcv', '1.8-10', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-5', ext_options), + ('sp', '1.2-1', ext_options), + ('zoo', '1.7-12', ext_options), + ('lmtest', '0.9-34', ext_options), + ('vcd', '1.4-1', ext_options), + ('snowfall', '1.84-6.1', ext_options), + ('rpart', '4.1-10', ext_options), + ('survival', '2.38-3', ext_options), + ('mice', '2.25', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-12', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-17', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.3', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.18-1', ext_options), + ('codetools', '0.2-14', ext_options), + ('foreach', '1.4.3', ext_options), + ('doMC', '1.3.4', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-66', ext_options), + ('gam', '1.12', ext_options), + ('gamlss.data', '4.3-2', ext_options), + ('gamlss.dist', '4.3-5', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-0', ext_options), + ('quantmod', '0.4-5', ext_options), + ('mnormt', '1.5-3', ext_options), + ('mvtnorm', '1.0-3', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.1', ext_options), + ('prodlim', '1.5.7', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-4', ext_options), + ('sfsmisc', '1.0-28', ext_options), + ('spatial', '7.3-11', ext_options), + ('VGAM', '1.0-0', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.8-0', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.12', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.2.5', ext_options), + ('R.utils', '2.2.0', ext_options), + ('R.matlab', '3.3.0', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-1', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('reshape2', '1.4.1', ext_options), + ('gtable', '0.1.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.3.0', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '2.0.0', ext_options), + ('gridExtra', '2.0.0', ext_options), + ('Hmisc', '3.17-1', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-47', ext_options), + ('data.table', '1.9.6', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.10', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '2.0.0', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.13', ext_options), + ('ape', '3.4', ext_options), + ('htmltools', '0.3', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.17.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.3', ext_options), + ('R6', '2.1.1', ext_options), + ('jsonlite', '0.9.19', ext_options), + ('rjson', '0.2.15', ext_options), + ('shiny', '0.12.2', ext_options), + ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), + ('spdep', '0.5-92', ext_options), + ('assertthat', '0.1', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.3', ext_options), + ('adegenet', '2.0.0', ext_options), + ('rncl', '0.6.0', ext_options), + ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('praise', '1.0.0', ext_options), + ('testthat', '0.11.0', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.11', ext_options), + ('rmarkdown', '0.9.2', ext_options), + ('curl', '0.9.4', ext_options), + ('httr', '1.0.0', ext_options), + ('reshape', '0.8.5', ext_options), + ('bold', '0.3.0', ext_options), + ('taxize', '0.7.0', ext_options), + ('tidyr', '0.3.1', ext_options), + ('uuid', '0.1-2', ext_options), + ('RNeXML', '2.0.5', ext_options), + ('phylobase', '0.8.0', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.4', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.5.8', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.5-2', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.999-0', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.3-6', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.6', ext_options), + ('glmnet', '2.0-2', ext_options), + ('rgl', '0.95.1441', ext_options), + ('labdsv', '1.7-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.5-0', ext_options), + ('msm', '1.6', ext_options), + ('nor1mix', '1.2-1', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('polspline', '1.1.12', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-1', ext_options), + ('rms', '4.4-1', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6-2', ext_options), + ('TraMineR', '1.8-11', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-5', ext_options), + ('statmod', '1.4.23', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.3-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('optparse', '1.3.2', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '1.0.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.50.1', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-10', ext_options), + ('pbkrtest', '0.4-4', ext_options), + ('car', '2.1-1', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.31.4', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-10', ext_options), + ('BiasedUrn', '1.07', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '1.1', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.9.1', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.1.3', ext_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('VennDiagram', '1.6.16', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-2', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.8-37', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.44-1', ext_options), + ('rgdal', '1.1-3', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.8.8', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-4', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), + ('SuperLearner', '2.0-15', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('caret', '6.0-64', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.6', ext_options), + ('ggvis', '0.4.2', ext_options), + ('mlr', '2.7', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-7', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.10', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.2', ext_options), +] + +moduleclass = 'lang' -- GitLab From 17526505f04477c6fc440195a74d6413ad5b6dfa Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 16:24:12 +0100 Subject: [PATCH 0353/2133] Fix remarks and add more tests --- .../PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb | 6 ++++-- .../easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb index d4fb4f7c93..a713c7f44f 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb @@ -39,7 +39,9 @@ configopts = '-DENABLE_MPI=OFF -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_C configopts += ' -DENABLE_DUMMY_PLUGIN=ON -DCHEMPS2_ROOT=$EBROOTCHEMPS2' configopts += ' -DENABLE_PCMSOLVER=ON -DPCMSOLVER_ROOT=$EBROOTPCMSOLVER' -# Execute only the 'quick' tests and run 4 in parallel -runtest = 'ARGS="-V -L quicktests -j 4" test' +# Execute 4 tests in parallel +runtest = 'ARGS="-V -E \'opt10|pubchem1|pubchem2|pywrap-opt-sowreap|sapt4\' -j 4" test' + + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb index e7350c64a5..43999e6a1a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb @@ -8,7 +8,7 @@ description = """Larry Wall's Practical Extraction and Report Language""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://www.cpan.org/src/5.0'] +source_urls = ['http://www.cpan.org/src/%(version_major)s'] sources = [SOURCELOWER_TAR_GZ] # bare, no extensions -- GitLab From f045c9403ab2a8d555149774a7336bae912785c2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 16:33:26 +0100 Subject: [PATCH 0354/2133] arpack-ng 3.3 for intel/2016a --- .../arpack-ng/arpack-ng-3.3.0-intel-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-intel-2016a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-intel-2016a.eb new file mode 100644 index 0000000000..a242bc1b1e --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.3.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215', '', ('GCC', '4.9.3-2.25'))] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From b59d17655aadf1e3ab56808ca455faa3ace0b698 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 16:33:43 +0100 Subject: [PATCH 0355/2133] Serial version of HDF5 1.8.16 with intel/2016a --- .../h/HDF5/HDF5-1.8.16-intel-2016a-serial.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a-serial.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a-serial.eb new file mode 100644 index 0000000000..dc2e939bfa --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a-serial.eb @@ -0,0 +1,25 @@ +name = 'HDF5' +version = '1.8.16' +versionsuffix = '-serial' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From a8356625b0edb3fb95816588a703e2bd5941d6c0 Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 5 Feb 2016 17:35:08 +0100 Subject: [PATCH 0356/2133] added missing fftw dependency to nfft --- easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb index 4acf581ee5..24a66a56a8 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb @@ -13,6 +13,10 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] +dependencies = [ + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + sanity_check_paths = { 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], -- GitLab From 764ea007f168d57340a7aa9bfa84105d71c0f289 Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 5 Feb 2016 17:36:54 +0100 Subject: [PATCH 0357/2133] added missing fftw dependency to nfft --- easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb index 656ae6d877..10957199be 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb @@ -13,6 +13,10 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] +dependencies = [ + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + sanity_check_paths = { 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], -- GitLab From f63dc4c1bc7b28254ab6ab7c71e1a8c177289877 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 18:03:02 +0100 Subject: [PATCH 0358/2133] Add missing dep for Szip --- .../s/Szip/Szip-2.1-intel-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb new file mode 100644 index 0000000000..0c94946cf2 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From ddce3720ce6605a2893fb246f527aac370cb9427 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 Feb 2016 18:03:48 +0100 Subject: [PATCH 0359/2133] Fix typo --- easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb index 0c94946cf2..67b0f10359 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016a.eb @@ -6,7 +6,7 @@ version = '2.1' homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -- GitLab From 547c166a71fea0be6b62d311684f152fa6634acf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Feb 2016 20:15:35 +0200 Subject: [PATCH 0360/2133] add easyconfig ADF-2014.11.r48287-intel-2016a.eb --- .../a/ADF/ADF-2014.11.r48287-intel-2016a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb diff --git a/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb b/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb new file mode 100644 index 0000000000..03dd1a9301 --- /dev/null +++ b/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb @@ -0,0 +1,16 @@ +name = 'ADF' +version = '2014.11.r48287' + +homepage = 'http://www.scm.com/ADF/' +description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and + predict chemical structure and reactivity with density functional theory (DFT).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s%(version)s.src.tgz'] + +modloadmsg = "These environment variables need to be defined before using ADF:\n" +modloadmsg += " * $SCMLICENSE: path to ADF license file\n" +modloadmsg += " * $SCM_TMPDIR: path to user scratch directory" + +moduleclass = 'chem' -- GitLab From d976704782fe5a842871121e15af43dcb932fa2b Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 5 Feb 2016 19:46:44 +0100 Subject: [PATCH 0361/2133] fix for cray's fftw + cmake detection --- .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb index 0faa18f3de..94600c2c59 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb @@ -31,6 +31,13 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW} && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/../include && " + +dependencies = [ + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + builddependencies = [('CMake', '3.2.2')] runtest = False -- GitLab From 7df75991277ec4893b062d68ec6ca9fe04eea6e7 Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 5 Feb 2016 19:48:37 +0100 Subject: [PATCH 0362/2133] fix for cray's fftw + cmake detection --- .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb index 31d5fed4d1..f4f5d5d089 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb @@ -31,6 +31,13 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW} && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/../include && " + +dependencies = [ + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + builddependencies = [('CMake', '3.2.2')] runtest = False -- GitLab From b858aa12c5eeec33a74209885410e5450fdc08ac Mon Sep 17 00:00:00 2001 From: perettig Date: Sat, 6 Feb 2016 11:41:24 +0100 Subject: [PATCH 0363/2133] fixed fftw minor version to match PE 2015.06 --- .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb | 2 +- easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb index f4f5d5d089..8fe8110183 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb @@ -35,7 +35,7 @@ preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW} && preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/../include && " dependencies = [ - ('fftw/3.3.4.2', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb index 24a66a56a8..f016964748 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb @@ -14,7 +14,7 @@ source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('fftw/3.3.4.2', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), ] sanity_check_paths = { -- GitLab From a0d2192e5651b6dee4811d2491310548d32b6428 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 6 Feb 2016 16:01:22 +0100 Subject: [PATCH 0364/2133] Use newer version of CMake --- .../p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb | 2 +- .../p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb index a35d9ea836..861cd9d963 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.4.1'), + ('CMake', '3.4.3'), ('Eigen', '3.2.7'), ] diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb index a713c7f44f..3f257ab0c1 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb @@ -31,7 +31,7 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.4.1'), + ('CMake', '3.4.3'), ('Perl', '5.22.1', '-bare'), # for the test suite ] -- GitLab From 3f9dce28fb1bdb6884149ea219187a4557193e15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 6 Feb 2016 23:06:36 +0200 Subject: [PATCH 0365/2133] add easyconfig PROJ-4.9.2-intel-2016a.eb --- .../p/PROJ/PROJ-4.9.2-intel-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016a.eb new file mode 100644 index 0000000000..67b8275d1e --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.2' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 09791e5324fc6ef1b1086c687c6d6b03a43fa818 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 Feb 2016 13:41:12 +0100 Subject: [PATCH 0366/2133] fix comment in HOD easyconfigs --- .../hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb | 2 +- .../hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb | 2 +- .../hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb | 2 +- .../hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb index 241e630c35..9272f98ff5 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb @@ -19,7 +19,7 @@ pythonver = '2.7.9' pythonshortver = '.'.join(pythonver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +# a Python version with mpi4py and pbs_python (vsc.utils.fancylogger) is required at runtime dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb index f6063d9ec3..a096633f0b 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb @@ -19,7 +19,7 @@ pythonver = '2.7.9' pythonshortver = '.'.join(pythonver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +# a Python version with mpi4py and pbs_python (vsc.utils.fancylogger) is required at runtime dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb index 9182229d2c..c0a03ce83e 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb @@ -19,7 +19,7 @@ pythonver = '2.7.9' pythonshortver = '.'.join(pythonver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +# a Python version with mpi4py and pbs_python (vsc.utils.fancylogger) is required at runtime dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb index 73433b3081..b6761f7445 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb @@ -19,7 +19,7 @@ pythonver = '2.7.9' pythonshortver = '.'.join(pythonver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +# a Python version with mpi4py and pbs_python (vsc.utils.fancylogger) is required at runtime dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), -- GitLab From 605c7d05db1d676517a472d143795a9747338860 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Feb 2016 15:59:58 +0100 Subject: [PATCH 0367/2133] Correct Perl download URL --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb index 43999e6a1a..2796d0fc7f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a-bare.eb @@ -8,7 +8,7 @@ description = """Larry Wall's Practical Extraction and Report Language""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://www.cpan.org/src/%(version_major)s'] +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] # bare, no extensions -- GitLab From d5905b758140ed024ed2c0ccaf6954525142ab04 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 8 Feb 2016 17:02:25 +0100 Subject: [PATCH 0368/2133] Copy the contrib dirs into place so users can use the scripts. --- .../v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb | 2 ++ .../v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb index 70b05647b0..25dc94bbe0 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb @@ -26,4 +26,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +postinstallcmds = ["cp -a contrib %(installdir)s/"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb index fff6a988ab..1d3524357c 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb @@ -27,4 +27,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +postinstallcmds = ["cp -a contrib %(installdir)s/"] + moduleclass = 'bio' -- GitLab From 0f962338cdfabdd1360e07373d8e350a8bb8c203 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 8 Feb 2016 17:09:49 +0100 Subject: [PATCH 0369/2133] Add velvet contrib for goolf builds too. --- .../v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb | 2 ++ .../v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb | 2 ++ .../v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb index 9c3573c3bc..7bbefcf5e6 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb @@ -23,4 +23,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +postinstallcmds = ["cp -a contrib %(installdir)s/"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb index 3556eea248..6f41fbe5da 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb @@ -22,4 +22,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +postinstallcmds = ["cp -a contrib %(installdir)s/"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb index 56dd2ed094..3fdfb13e56 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb @@ -22,4 +22,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +postinstallcmds = ["cp -a contrib %(installdir)s/"] + moduleclass = 'bio' -- GitLab From e472f51b95ce4d6299d3855ac6b59feecaa950da Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 8 Feb 2016 23:35:55 +0100 Subject: [PATCH 0370/2133] latest IPython and all the dependencies --- ...IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 161 ++++++++++++++++++ ...Q-14.7.0-goolf-1.4.10-Python-2.7.5-zmq3.eb | 33 ++++ .../util-linux-2.26.1-goolf-1.4.10.eb | 33 ++++ .../z/ZeroMQ/ZeroMQ-3.2.5-goolf-1.4.10.eb | 34 ++++ 4 files changed, 261 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-goolf-1.4.10-Python-2.7.5-zmq3.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..87c223eb01 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,161 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'IPython' +version = '4.1.0' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('setuptools', '19.6', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.14.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('jupyter_client', '4.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools_scm', '1.10.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'source_tmpl': 'setuptools_scm-1.10.1.tar.bz2', + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-0.8.1.zip', + }), + ('path.py', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + 'modulename': 'path', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pickleshare', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('pbr', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], + }), + ('notebook', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pyzmq', '15.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], + 'modulename': 'zmq', + }), + #('testpath', '0.3', { + #'source_urls': ['https://github.com/jupyter/testpath/archive/'], #this extension doesn't provide a setup.py and it's required for the sanity checks (iptest, iptest2) + #'source_tmpl': '0.3.tar.gz', + #}), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + #('iptest', ''), # this test fails with 'ImportError: No module named testpath'. testpath cannot be installed with easyconfig + #('iptest2', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-goolf-1.4.10-Python-2.7.5-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-goolf-1.4.10-Python-2.7.5-zmq3.eb new file mode 100644 index 0000000000..f2939de491 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-goolf-1.4.10-Python-2.7.5-zmq3.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.7.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.5' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '3.2.5' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..dec0e334ca --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.26.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = '--disable-chfn-chsh --disable-login --disable-su ' +configopts += '--disable-wall --disable-use-tty-group ' +configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-goolf-1.4.10.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-goolf-1.4.10.eb new file mode 100644 index 0000000000..a6ea95a4c2 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-goolf-1.4.10.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '3.2.5' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.26.1'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 10247c4c210970775fbae08121a7fed7fdcc9786 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Feb 2016 08:59:41 +0100 Subject: [PATCH 0371/2133] minor style fix --- easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb | 4 ++-- .../easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb index c33a4578e1..59d4306b20 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb @@ -25,8 +25,8 @@ dependencies = [(java, javaver)] # add the installation dir to PATH modextrapaths = { - 'PATH': "", - } + 'PATH': '', +} modloadmsg = """ To execute IGV run igv.sh """ diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb index 1753b4227a..7e0037fbd3 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb @@ -25,8 +25,8 @@ dependencies = [(java, javaver)] # add the installation dir to PATH modextrapaths = { - 'PATH': "", - } + 'PATH': '', +} sanity_check_paths = { 'files': ["igvtools.jar", "igvtools"], -- GitLab From a20836ac9b52e76d429b70044be41776ad85143c Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 9 Feb 2016 09:39:03 +0100 Subject: [PATCH 0372/2133] updated to latest release 2.3.68 --- ...{IGV-2.3.60-Java-1.7.0_80.eb => IGV-2.3.68-Java-1.7.0_80.eb} | 2 +- ...2.3.60-Java-1.7.0_80.eb => IGVTools-2.3.68-Java-1.7.0_80.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/i/IGV/{IGV-2.3.60-Java-1.7.0_80.eb => IGV-2.3.68-Java-1.7.0_80.eb} (98%) rename easybuild/easyconfigs/i/IGVTools/{IGVTools-2.3.60-Java-1.7.0_80.eb => IGVTools-2.3.68-Java-1.7.0_80.eb} (98%) diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb similarity index 98% rename from easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb rename to easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb index 59d4306b20..53a0869e8d 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.60-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb @@ -6,7 +6,7 @@ easyblock = 'Tarball' name = 'IGV' -version = '2.3.60' +version = '2.3.68' homepage = 'http://www.broadinstitute.org/software/igv/' description = """ The Integrative Genomics Viewer (IGV) is a high-performance visualization diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb similarity index 98% rename from easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb rename to easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb index 7e0037fbd3..7916d9631b 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.60-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb @@ -6,7 +6,7 @@ easyblock = 'Tarball' name = 'IGVTools' -version = '2.3.60' +version = '2.3.68' homepage = 'http://www.broadinstitute.org/software/igv/' description = """ This package contains command line utilities for preprocessing, -- GitLab From 2e28607cad4e25d10a5ed1318f5dd190a3450546 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 9 Feb 2016 09:40:51 +0100 Subject: [PATCH 0373/2133] updated header --- easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb | 4 ++-- .../easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb index 53a0869e8d..faccbfa2f1 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics easyblock = 'Tarball' diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb index 7916d9631b..bc16033a08 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics easyblock = 'Tarball' -- GitLab From c7c01b3226f6eda03f6f4ac19fd0e020ffdb4d5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Feb 2016 10:59:01 +0100 Subject: [PATCH 0374/2133] copyright update for 2016 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index fecf010363..73bcfd5c01 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2015 Ghent University +# Copyright 2012-2016 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), -- GitLab From 931b9a9f5728494b315e920938340b400af4dedc Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 9 Feb 2016 11:15:34 +0100 Subject: [PATCH 0375/2133] removed PyZMQ from exts_list. Provided as dependency --- .../i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index 87c223eb01..f745db8910 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -130,10 +130,6 @@ exts_list = [ ('ipykernel', '4.2.2', { 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], }), - ('pyzmq', '15.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], - 'modulename': 'zmq', - }), #('testpath', '0.3', { #'source_urls': ['https://github.com/jupyter/testpath/archive/'], #this extension doesn't provide a setup.py and it's required for the sanity checks (iptest, iptest2) #'source_tmpl': '0.3.tar.gz', -- GitLab From 7b738772559dd3d1870644084d5132907356c07d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Feb 2016 14:58:36 +0100 Subject: [PATCH 0376/2133] avoid hardcoded shebang in GLib bin scripts --- easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb index 07094c48e5..fc0f81d335 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb @@ -28,4 +28,6 @@ builddependencies = [('Python', pyver)] configopts = "--disable-maintainer-mode --disable-silent-rules " configopts += "--disable-libelf --enable-static --enable-shared " +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + moduleclass = 'vis' -- GitLab From c5f4d6c9231e1e4871d7a200d8a45e123ac4b543 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Feb 2016 14:59:14 +0100 Subject: [PATCH 0377/2133] avoid hardcoded path to 'python' in GObject-Introspection scripts --- .../GObject-Introspection-1.47.1-intel-2016a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb index 3b0f223d1e..eaa343080d 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -30,6 +30,9 @@ builddependencies = [('Autotools', '20150215')] preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', -- GitLab From 696ae7b147f658b2d75d10bd9632073f7e61205f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Feb 2016 14:59:24 +0100 Subject: [PATCH 0378/2133] fix download URL for PyGTK --- .../p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb index 6eacf5d498..c82f2ddb26 100644 --- a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb @@ -9,8 +9,8 @@ description = """PyGTK lets you to easily create programs with a graphical user toolchain = {'name': 'intel', 'version': '2016a'} +source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['ftp://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s/'] pyver_maj_min = '2.7' pyver = '%s.11' % pyver_maj_min -- GitLab From 24c4650a7f0af2003e727b4081b74d46c28b82f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Feb 2016 17:18:54 +0200 Subject: [PATCH 0379/2133] add easyconfig pip-8.0.2-intel-2016a-Python-2.7.11.eb, add easyconfig testpath-0.3-intel-2016a-Python-2.7.11.eb --- .../pip-8.0.2-intel-2016a-Python-2.7.11.eb | 19 ++++++++++++ .../testpath-0.3-intel-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/pip/pip-8.0.2-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/pip/pip-8.0.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pip/pip-8.0.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..7bc4eae5a1 --- /dev/null +++ b/easybuild/easyconfigs/p/pip/pip-8.0.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,19 @@ +easyblock = 'PythonPackage' + +name = 'pip' +version = '8.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pip.pypa.io' +description = """The PyPA recommended tool for installing Python packages.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..ea6de39dd2 --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'testpath' +version = '0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jupyter/testpath' +description = """Test utilities for code working with files and commands""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/py2.py3/t/testpath/'] +sources = ['testpath-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.11'), +] +builddependencies = [ + ('pip', '8.0.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/testpath'], +} + +moduleclass = 'lib' -- GitLab From c74a8a203fbb60fe2448b7dc3a7fb6340bd6642f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 9 Feb 2016 20:30:39 +0100 Subject: [PATCH 0380/2133] added sqlite dep --- .../i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index f745db8910..6b7bb08515 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -25,6 +25,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), + ('SQLite', '3.8.1'), ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), ] -- GitLab From bdfbf9f48be890a29503bc48c3f1032ec0f9e0e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Feb 2016 20:33:34 +0100 Subject: [PATCH 0381/2133] fix style/sync issues --- easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2016a.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016a.eb | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2016a.eb index 7822366091..b0bbe713ec 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2016a.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb index fc0f81d335..3c6fca0fc4 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] -sources = ['glib-%(version)s.tar.xz'] +sources = [SOURCELOWER_TAR_XZ] pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[:2]) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb index fb5d6493b5..3dc38160e5 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb @@ -10,7 +10,7 @@ context of the GTK+ widget toolkit. Pango forms the core of text and font handli toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] glibver = '2.47.5' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016a.eb index eb4e677dea..79670989c4 100644 --- a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['lib/libpixman-1.so'], + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], 'dirs': [] } -- GitLab From 018035283b2937228c8030fdf58c15bc12c549dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Feb 2016 21:00:02 +0100 Subject: [PATCH 0382/2133] moar style fixes --- .../easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb | 2 +- .../easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb | 10 +++++++--- .../easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb | 2 +- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb | 2 +- .../PyCairo-1.10.0-intel-2016a-Python-2.7.11.eb | 13 +++++++------ .../PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb | 13 +++++++------ ...pes.patch => PyGObject-2.28.6_enum-types.patch} | 0 .../PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb | 14 ++++++++------ 8 files changed, 32 insertions(+), 24 deletions(-) rename easybuild/easyconfigs/p/PyGObject/{pygobject-enum-types.patch => PyGObject-2.28.6_enum-types.patch} (100%) diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb index 2e24deb654..81788119c4 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] glibver = '2.47.5' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb index 3c6fca0fc4..8e34d4cf55 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb @@ -9,7 +9,7 @@ description = """GLib is one of the base libraries of the GTK+ project""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] pyver = '2.7.11' @@ -25,9 +25,13 @@ dependencies = [ builddependencies = [('Python', pyver)] -configopts = "--disable-maintainer-mode --disable-silent-rules " -configopts += "--disable-libelf --enable-static --enable-shared " +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb index 13dfd28341..c29db47cc8 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb @@ -10,7 +10,7 @@ description = """ toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] dependencies = [ diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb index e5b4a33f0d..6348507d8d 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] glibver = '2.47.5' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2016a-Python-2.7.11.eb index 13339917a6..27c3b18391 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2016a-Python-2.7.11.eb @@ -12,9 +12,9 @@ source_urls = ['http://cairographics.org/releases/'] # py2cairo is the Python 2 compatible release sources = ['py2cairo-%(version)s.tar.bz2'] -pyver_maj_min = '2.7' -pyver = '%s.11' % pyver_maj_min -versionsuffix = '-Python-%s' % (pyver) +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-Python-%s' % pyver configopts = " --nopyc --nopyo " @@ -23,12 +23,13 @@ dependencies = [ ('cairo', '1.14.6'), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver_maj_min, - 'lib64/python%s/site-packages' % pyver_maj_min]} +modextrapaths = { + 'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver], +} sanity_check_paths = { 'files': ['include/pycairo/pycairo.h', 'lib/pkgconfig/pycairo.pc'], - 'dirs': ['lib/python%s/site-packages/cairo' % pyver_maj_min], + 'dirs': ['lib/python%s/site-packages/cairo' % pyshortver], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb index 17c6ac4dcb..3291d71bff 100644 --- a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb @@ -11,10 +11,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -patches = ['pygobject-enum-types.patch'] +patches = ['PyGObject-%(version)s_enum-types.patch'] -pyver_maj_min = '2.7' -pyver = '%s.11' % pyver_maj_min +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-Python-%s' % pyver glibver = '2.47.5' @@ -27,13 +27,14 @@ dependencies = [ configopts = "--disable-introspection" -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver_maj_min, - 'lib64/python%s/site-packages' % pyver_maj_min]} +modextrapaths = { + 'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver], +} sanity_check_paths = { 'files': ['include/pygtk-%(version_major)s.0/pyglib.h', 'include/pygtk-%(version_major)s.0/pygobject.h', 'lib/libpyglib-%(version_major)s.0-python.so'], - 'dirs': ['bin', 'lib/python%s/site-packages/' % pyver_maj_min], + 'dirs': ['bin', 'lib/python%s/site-packages/' % pyshortver], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/pygobject-enum-types.patch b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6_enum-types.patch similarity index 100% rename from easybuild/easyconfigs/p/PyGObject/pygobject-enum-types.patch rename to easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6_enum-types.patch diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb index c82f2ddb26..d470f598fa 100644 --- a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb @@ -12,8 +12,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_BZ2] -pyver_maj_min = '2.7' -pyver = '%s.11' % pyver_maj_min +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-Python-%s' % pyver glibver = '2.47.5' @@ -32,10 +32,12 @@ postinstallcmds = [ ] modextrapaths = { - 'PYTHONPATH': ['lib/python%s/site-packages' % pyver_maj_min, - 'lib64/python%s/site-packages' % pyver_maj_min, - 'lib/python%s/site-packages/gtk-2.0' % pyver_maj_min, - 'lib64/python%s/site-packages/gtk-2.0' % pyver_maj_min], + 'PYTHONPATH': [ + 'lib/python%s/site-packages' % pyshortver, + 'lib64/python%s/site-packages' % pyshortver, + 'lib/python%s/site-packages/gtk-%%(version_major)s.0' % pyshortver, + 'lib64/python%s/site-packages/gtk-%%(version_major)s.0' % pyshortver, + ], } sanity_check_paths = { -- GitLab From 7b71fbdc8c2d229b1e9bab1cf27187d8f688cfa9 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 9 Feb 2016 21:19:25 +0100 Subject: [PATCH 0383/2133] updated sqlite dep --- .../i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index 6b7bb08515..af763e233d 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -25,7 +25,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), - ('SQLite', '3.8.1'), + ('SQLite', '3.8.10.2'), ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), ] -- GitLab From 11b19ecd7ebedcddad4f1d6f41e4acfedc667f63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Feb 2016 22:54:36 +0200 Subject: [PATCH 0384/2133] add easyconfig numpy-1.10.4-intel-2016a-Python-2.7.11.eb, add easyconfig scipy-0.17.0-intel-2016a-Python-2.7.11.eb --- .../numpy-1.10.4-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ .../scipy-0.17.0-intel-2016a-Python-2.7.11.eb | 19 +++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.17.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..b76b0c1b2e --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'numpy' +version = '1.10.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.17.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scipy/scipy-0.17.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..abaaff0546 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.17.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.17.0' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.10.4', versionsuffix), +] + +moduleclass = 'math' -- GitLab From b0dcc1752c7be66676ab832332eb46cea6754939 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 9 Feb 2016 22:27:12 +0100 Subject: [PATCH 0385/2133] added STAR-Fusion-0.6.0 and STAR-2.5.1b --- ...R-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb | 55 +++++++++++++++++++ .../s/STAR/STAR-2.5.1b-goolf-1.4.10.eb | 32 +++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..147ee68d6c --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'STAR-Fusion' +version = '0.6.0' + +homepage = 'https://github.com/STAR-Fusion/STAR-Fusion' +description = """STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts + supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner + to map junction reads and spanning reads to a reference annotation set.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/STAR-Fusion/STAR-Fusion/releases/download/v%(version)s/'] +sources = ['%(name)s_v%(version)s.FULL.tar.gz'] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('STAR', '2.5.1b'), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('Set::IntervalTree', '0.10', { + 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/'], + }), + ('DB_File', '1.835', { + 'source_tmpl': 'DB_File-1.835.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], + }), +] + +modextrapaths = { + 'PATH': "", # add installation dir to PATH + 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) +} + +sanity_check_paths = { + 'files': ['STAR-Fusion'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb new file mode 100644 index 0000000000..35b1c5e236 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.5.1b' + +homepage = 'https://code.google.com/p/rna-star/' +description = """ STAR aligns RNA-seq reads to a reference genome using + uncompressed suffix arrays. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] + +# a binary is provided with the source files. We delete it +prebuildopts = 'rm -fr bin/ && ' + +parallel = 1 + +files_to_copy = [(["source/STAR"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] + +sanity_check_paths = { + 'files': ["bin/STAR"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From aba9e244159565b529ab2cf087d5be3c84b18d42 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 10 Feb 2016 00:19:13 +0000 Subject: [PATCH 0386/2133] Add credit to Jordi Blasco --- .../v/VarScan/VarScan-2.4.1-foss-2015b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-foss-2015b.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-foss-2015b.eb new file mode 100644 index 0000000000..e26e49421b --- /dev/null +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-foss-2015b.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman, based on initial work by Jordi Blasco +# The Francis Crick Institute + +easyblock = 'JAR' + +name = 'VarScan' +version = '2.4.1' + +homepage = 'https://github.com/dkoboldt/varscan' +description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%s.v%s.jar' % (name, version)] +source_urls = ['https://github.com/dkoboldt/varscan/releases/download/v%(version)s'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 3fc0b5fb8cde979e1bcad62d1235b1f7bbff53f3 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 09:56:17 +0200 Subject: [PATCH 0387/2133] add easyconfig OpenFOAM-3.0.0-foss-2016a.eb --- .../o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb new file mode 100644 index 0000000000..b41ffda995 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb @@ -0,0 +1,39 @@ +name = 'OpenFOAM' +version = '3.0.0' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-%(version)s_libreadline.patch', + ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0', '-32bitIDX'), + ('ncurses', '5.9'), + ('SCOTCH', '6.0.4'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.4.1'), + ('flex', '2.5.39'), + ('Boost', '1.60.0'), +] + +moduleclass = 'cae' -- GitLab From 5e4154ff9e1788c282a6f7c6881c950c9509d1d7 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 09:57:04 +0200 Subject: [PATCH 0388/2133] add easyconfig Boost-1.60.0-foss-2016a.eb --- .../b/Boost/Boost-1.60.0-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb new file mode 100644 index 0000000000..c50510711d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.60.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From b0d5ee4f516714709722568efd2a967ded6941b2 Mon Sep 17 00:00:00 2001 From: Alan Date: Wed, 10 Feb 2016 09:06:27 +0100 Subject: [PATCH 0389/2133] Update naming of GTK+, PyCairo and Gdk-Pixbuf --- .../GTK+-2.24.28-intel-2015a.eb} | 4 ++-- .../GTK+-2.24.28-intel-2015b.eb} | 4 ++-- .../Gdk-Pixbuf-2.31.4-intel-2015a.eb} | 2 +- .../Gdk-Pixbuf-2.31.4-intel-2015b.eb} | 2 +- easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb | 2 +- .../easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb | 2 +- .../PyCairo-1.10.0-intel-2015b-Python-2.7.10.eb} | 2 +- 8 files changed, 10 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/g/{gtk+/gtk+-2.24.28-intel-2015a.eb => GTK+/GTK+-2.24.28-intel-2015a.eb} (91%) rename easybuild/easyconfigs/g/{gtk+/gtk+-2.24.28-intel-2015b.eb => GTK+/GTK+-2.24.28-intel-2015b.eb} (91%) rename easybuild/easyconfigs/g/{gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb => Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015a.eb} (97%) rename easybuild/easyconfigs/g/{gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b.eb => Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015b.eb} (97%) rename easybuild/easyconfigs/p/{pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10.eb => PyCairo/PyCairo-1.10.0-intel-2015b-Python-2.7.10.eb} (97%) diff --git a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015a.eb similarity index 91% rename from easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb rename to easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015a.eb index 289385029d..2b49aad4ac 100644 --- a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gtk+' +name = 'GTK+' version = '2.24.28' homepage = 'https://developer.gnome.org/gtk+/stable/' @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('ATK', '2.16.0'), - ('gdk-pixbuf', '2.31.4'), + ('Gdk-Pixbuf', '2.31.4'), ('Pango', '1.37.1'), ] diff --git a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015b.eb similarity index 91% rename from easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b.eb rename to easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015b.eb index 9fe946073f..65211f662c 100644 --- a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gtk+' +name = 'GTK+' version = '2.24.28' homepage = 'https://developer.gnome.org/gtk+/stable/' @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('ATK', '2.16.0'), - ('gdk-pixbuf', '2.31.4'), + ('Gdk-Pixbuf', '2.31.4'), ('Pango', '1.37.1'), ] diff --git a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015a.eb similarity index 97% rename from easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb rename to easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015a.eb index 5cb8ff5f1f..3eef94efe9 100644 --- a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gdk-pixbuf' +name = 'Gdk-Pixbuf' version = '2.31.4' homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' diff --git a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015b.eb similarity index 97% rename from easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b.eb rename to easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015b.eb index 018df1e421..628f1553a7 100644 --- a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gdk-pixbuf' +name = 'Gdk-Pixbuf' version = '2.31.4' homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' diff --git a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb index f946da12a2..042f52f5f8 100644 --- a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Atkmm', '2.22.7'), - ('gtk+', '2.24.28'), + ('GTK+', '2.24.28'), ('Pangomm', '2.36.0'), ] diff --git a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb index 60c1e59723..3e73c97004 100644 --- a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb +++ b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Atkmm', '2.22.7'), - ('gtk+', '2.24.28'), + ('GTK+', '2.24.28'), ('Pangomm', '2.36.0'), ] diff --git a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb index 24f8fc1070..a0f2ba3078 100644 --- a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb @@ -15,7 +15,7 @@ patches = ['gtkglext-%(version)s_fix-gtk-compat.patch'] pangover = '1.37.1' dependencies = [ - ('gtk+', '2.24.28'), + ('GTK+', '2.24.28'), ('Pango', pangover), ('pangox-compat', '0.0.2', '-Pango-%s' % pangover), ] diff --git a/easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2015b-Python-2.7.10.eb similarity index 97% rename from easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2015b-Python-2.7.10.eb index f701cf3d28..246a64686d 100644 --- a/easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2015b-Python-2.7.10.eb @@ -1,6 +1,6 @@ easyblock = 'Waf' -name = 'pycairo' +name = 'PyCairo' version = '1.10.0' homepage = 'http://cairographics.org/pycairo/' -- GitLab From 8265d4c2e039eb2ba737c5b6d96832f8d8800f56 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 10 Feb 2016 08:38:52 +0000 Subject: [PATCH 0390/2133] Fix sources and use correct filename --- ...rScan-2.4.1-foss-2015b.eb => VarScan-2.4.1-Java-1.7.0_80.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/v/VarScan/{VarScan-2.4.1-foss-2015b.eb => VarScan-2.4.1-Java-1.7.0_80.eb} (94%) diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-foss-2015b.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb similarity index 94% rename from easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-foss-2015b.eb rename to easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb index e26e49421b..5f66c5f283 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-foss-2015b.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb @@ -12,7 +12,7 @@ description = """Variant calling and somatic mutation/CNV detection for next-gen toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['%s.v%s.jar' % (name, version)] +sources = ['%(name)s.v%(version)s.jar'] source_urls = ['https://github.com/dkoboldt/varscan/releases/download/v%(version)s'] java = 'Java' -- GitLab From f3fd77aeae0887d3ab185eb27016038ad213b6d9 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 10:48:34 +0200 Subject: [PATCH 0391/2133] add easyconfig LLVM-3.7.1-foss-2016a.eb --- .../l/LLVM/LLVM-3.7.1-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb new file mode 100644 index 0000000000..eca1371a7b --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.7.1' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.4.3'), + ('Python', '2.7.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files' : ['bin/llvm-ar'], + 'dirs' : ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' -- GitLab From c8993de7eab3963b83bdfa76ff23529f8f421449 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 10:50:36 +0200 Subject: [PATCH 0392/2133] add easyconfig CMake-3.4.3-foss-2016a.eb --- .../c/CMake/CMake-3.4.3-foss-2016a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb new file mode 100644 index 0000000000..01c585999e --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb @@ -0,0 +1,57 @@ +# Built with EasyBuild version 2.6.0 on 2016-02-01_18-47-09 +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.6.0", + "easybuild-easyblocks_version": "2.6.0", + "timestamp": 1454348829, + "build_time": 304.6, + "install_size": 32428310, + "command_line": ['--buildpath=//opt/cluster/easybuild/build', '--installpath=//opt/cluster/easybuild', '--packagepath=//opt/cluster/easybuild/packages', '--prefix=//opt/cluster/easybuild', '--repositorypath=//opt/cluster/easybuild/ebfiles_repo', '--robot=/opt/cluster/easybuild/software/EasyBuild/2.6.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.6.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=//opt/cluster/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'OpenFOAM-3.0.0-intel-2015b-eb-deps-Python-2.7.10.eb'], + "modules_tool": ('EnvironmentModulesC', '/opt/cluster/Modules/3.2.10/bin/modulecmd', '3.2.10'), + "core_count": 40, + "cpu_model": "Genuine Intel(R) CPU @ 2.30GHz", + "cpu_speed": 2301.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/opt/cluster/easybuild/software/GCCcore/4.9.3/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=//opt/cluster/easybuild/software/GCCcore/4.9.3 --with-local-prefix=//opt/cluster/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "master.hpc.c3e", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.5", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Nov 22 2013, 12:16:22) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "//opt/cluster/easybuild/software/GCCcore/4.9.3/bin/gcc", + "system_python_path": "/usr/bin/python", +}] -- GitLab From 203da5195cf5946ed55cee8ddfbcd7a8c2d6afc2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Feb 2016 10:10:23 +0100 Subject: [PATCH 0393/2133] fix syntax error --- easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb index 8e34d4cf55..5af7f7a410 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb @@ -30,7 +30,7 @@ configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] sanity_check_paths = { - 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%(version_major)s.0.%s' % SHLIB_EXT], + 'files': ['lib/libglib-%%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], 'dirs': ['bin', 'include'], } -- GitLab From 5c327d336b7056f8dd57db438c4ca5cd83242d8f Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 11:25:08 +0200 Subject: [PATCH 0394/2133] modify easyconfig CMake-3.4.3-foss-2016a.eb --- .../c/CMake/CMake-3.4.3-foss-2016a.eb | 24 ------------------- 1 file changed, 24 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb index 01c585999e..069d9f4158 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb @@ -31,27 +31,3 @@ sanity_check_paths = { moduleclass = 'devel' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.6.0", - "easybuild-easyblocks_version": "2.6.0", - "timestamp": 1454348829, - "build_time": 304.6, - "install_size": 32428310, - "command_line": ['--buildpath=//opt/cluster/easybuild/build', '--installpath=//opt/cluster/easybuild', '--packagepath=//opt/cluster/easybuild/packages', '--prefix=//opt/cluster/easybuild', '--repositorypath=//opt/cluster/easybuild/ebfiles_repo', '--robot=/opt/cluster/easybuild/software/EasyBuild/2.6.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.6.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=//opt/cluster/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'OpenFOAM-3.0.0-intel-2015b-eb-deps-Python-2.7.10.eb'], - "modules_tool": ('EnvironmentModulesC', '/opt/cluster/Modules/3.2.10/bin/modulecmd', '3.2.10'), - "core_count": 40, - "cpu_model": "Genuine Intel(R) CPU @ 2.30GHz", - "cpu_speed": 2301.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/opt/cluster/easybuild/software/GCCcore/4.9.3/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=//opt/cluster/easybuild/software/GCCcore/4.9.3 --with-local-prefix=//opt/cluster/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "master.hpc.c3e", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.5", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Nov 22 2013, 12:16:22) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "//opt/cluster/easybuild/software/GCCcore/4.9.3/bin/gcc", - "system_python_path": "/usr/bin/python", -}] -- GitLab From 9916b29f9b8ce0439e82b9009c459862a8b00588 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 11:47:47 +0200 Subject: [PATCH 0395/2133] add easyconfig METIS-5.1.0-foss-2016a.eb --- .../m/METIS/METIS-5.1.0-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb new file mode 100644 index 0000000000..2b65f31212 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, + and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the + multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.4.3')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' -- GitLab From 6cd9c1b94a57d2b855cb753886463f8b9140e01d Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 11:51:04 +0200 Subject: [PATCH 0396/2133] add easyconfig SCOTCH-6.0.4-foss-2016a.eb --- .../s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb new file mode 100644 index 0000000000..431d04e9df --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb @@ -0,0 +1,14 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' -- GitLab From d7d3b01901b056062576f99d660e4b4d3d5eb0e6 Mon Sep 17 00:00:00 2001 From: Alan Date: Wed, 10 Feb 2016 09:06:27 +0100 Subject: [PATCH 0397/2133] Update naming of GTK+, PyCairo and Gdk-Pixbuf --- .../GTK+-2.24.28-intel-2015a.eb} | 4 ++-- .../GTK+-2.24.28-intel-2015b.eb} | 4 ++-- .../Gdk-Pixbuf-2.31.4-intel-2015a.eb} | 2 +- .../Gdk-Pixbuf-2.31.4-intel-2015b.eb} | 2 +- easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb | 2 +- .../easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb | 2 +- .../PyCairo-1.10.0-intel-2015b-Python-2.7.10.eb} | 2 +- 8 files changed, 10 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/g/{gtk+/gtk+-2.24.28-intel-2015a.eb => GTK+/GTK+-2.24.28-intel-2015a.eb} (91%) rename easybuild/easyconfigs/g/{gtk+/gtk+-2.24.28-intel-2015b.eb => GTK+/GTK+-2.24.28-intel-2015b.eb} (91%) rename easybuild/easyconfigs/g/{gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb => Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015a.eb} (97%) rename easybuild/easyconfigs/g/{gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b.eb => Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015b.eb} (97%) rename easybuild/easyconfigs/p/{pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10.eb => PyCairo/PyCairo-1.10.0-intel-2015b-Python-2.7.10.eb} (97%) diff --git a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015a.eb similarity index 91% rename from easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb rename to easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015a.eb index 289385029d..2b49aad4ac 100644 --- a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gtk+' +name = 'GTK+' version = '2.24.28' homepage = 'https://developer.gnome.org/gtk+/stable/' @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('ATK', '2.16.0'), - ('gdk-pixbuf', '2.31.4'), + ('Gdk-Pixbuf', '2.31.4'), ('Pango', '1.37.1'), ] diff --git a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015b.eb similarity index 91% rename from easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b.eb rename to easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015b.eb index 9fe946073f..65211f662c 100644 --- a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2015b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gtk+' +name = 'GTK+' version = '2.24.28' homepage = 'https://developer.gnome.org/gtk+/stable/' @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('ATK', '2.16.0'), - ('gdk-pixbuf', '2.31.4'), + ('Gdk-Pixbuf', '2.31.4'), ('Pango', '1.37.1'), ] diff --git a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015a.eb similarity index 97% rename from easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb rename to easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015a.eb index 5cb8ff5f1f..3eef94efe9 100644 --- a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gdk-pixbuf' +name = 'Gdk-Pixbuf' version = '2.31.4' homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' diff --git a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015b.eb similarity index 97% rename from easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b.eb rename to easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015b.eb index 018df1e421..628f1553a7 100644 --- a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.31.4-intel-2015b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gdk-pixbuf' +name = 'Gdk-Pixbuf' version = '2.31.4' homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' diff --git a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb index f946da12a2..042f52f5f8 100644 --- a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Atkmm', '2.22.7'), - ('gtk+', '2.24.28'), + ('GTK+', '2.24.28'), ('Pangomm', '2.36.0'), ] diff --git a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb index 60c1e59723..3e73c97004 100644 --- a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb +++ b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015b.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Atkmm', '2.22.7'), - ('gtk+', '2.24.28'), + ('GTK+', '2.24.28'), ('Pangomm', '2.36.0'), ] diff --git a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb index 24f8fc1070..a0f2ba3078 100644 --- a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb @@ -15,7 +15,7 @@ patches = ['gtkglext-%(version)s_fix-gtk-compat.patch'] pangover = '1.37.1' dependencies = [ - ('gtk+', '2.24.28'), + ('GTK+', '2.24.28'), ('Pango', pangover), ('pangox-compat', '0.0.2', '-Pango-%s' % pangover), ] diff --git a/easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2015b-Python-2.7.10.eb similarity index 97% rename from easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2015b-Python-2.7.10.eb index f701cf3d28..246a64686d 100644 --- a/easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.10.0-intel-2015b-Python-2.7.10.eb @@ -1,6 +1,6 @@ easyblock = 'Waf' -name = 'pycairo' +name = 'PyCairo' version = '1.10.0' homepage = 'http://cairographics.org/pycairo/' -- GitLab From 889307613c2ad05de511b474c26e17b8fd9140ef Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 12:27:03 +0200 Subject: [PATCH 0398/2133] add easyconfig SCOTCH-6.0.4-foss-2016a.eb --- .../s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb new file mode 100644 index 0000000000..431d04e9df --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb @@ -0,0 +1,14 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' -- GitLab From ba8fc68d902160e45b64a980332a747208de98e0 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 12:41:06 +0200 Subject: [PATCH 0399/2133] add easyconfig METIS-5.1.0-foss-2016a.eb --- .../m/METIS/METIS-5.1.0-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb new file mode 100644 index 0000000000..2b65f31212 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, + and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the + multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.4.3')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' -- GitLab From 1693baf19c228b9eace545b462dd1125f6bf965b Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 12:54:57 +0200 Subject: [PATCH 0400/2133] modify easyconfig CMake-3.4.3-foss-2016a.eb --- easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb index 069d9f4158..83b16aaff5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb @@ -30,4 +30,3 @@ sanity_check_paths = { } moduleclass = 'devel' - -- GitLab From c81401aabbda597934e6c5f5114974c0626e5d70 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 12:56:10 +0200 Subject: [PATCH 0401/2133] modify easyconfig CMake-3.4.3-foss-2016a.eb --- easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb index 83b16aaff5..e6beb92bee 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.6.0 on 2016-02-01_18-47-09 easyblock = 'ConfigureMake' name = 'CMake' -- GitLab From 769020aa88165b8384dc3e9de75b7be4e5e28961 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 15:35:18 +0200 Subject: [PATCH 0402/2133] add easyconfig CMake-3.4.3-foss-2016a.eb --- .../c/CMake/CMake-3.4.3-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb new file mode 100644 index 0000000000..e6beb92bee --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 065c5e9f43e787ace587ccfa59e7739118f2767b Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 15:36:24 +0200 Subject: [PATCH 0403/2133] modify easyconfig OpenFOAM-3.0.0-foss-2016a.eb --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb index b41ffda995..62295adeff 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb @@ -25,13 +25,13 @@ dependencies = [ ('libreadline', '6.3'), # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) ('METIS', '5.1.0', '-32bitIDX'), - ('ncurses', '5.9'), + ('ncurses', '6.0'), ('SCOTCH', '6.0.4'), ] builddependencies = [ ('Bison', '3.0.4'), - ('CMake', '3.4.1'), + ('CMake', '3.4.3'), ('flex', '2.5.39'), ('Boost', '1.60.0'), ] -- GitLab From f3319c7b7ede6ce4699f5c2f1d4765acddb52ebf Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 16:00:12 +0200 Subject: [PATCH 0404/2133] modify easyconfig OpenFOAM-3.0.0-foss-2016a.eb --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb index 62295adeff..7985e4b267 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb @@ -27,13 +27,13 @@ dependencies = [ ('METIS', '5.1.0', '-32bitIDX'), ('ncurses', '6.0'), ('SCOTCH', '6.0.4'), + ('Boost', '1.60.0'), ] builddependencies = [ ('Bison', '3.0.4'), ('CMake', '3.4.3'), ('flex', '2.5.39'), - ('Boost', '1.60.0'), ] moduleclass = 'cae' -- GitLab From ce16703ed6cad6a1db30974f81f6ff44bcbb1961 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 9 Nov 2015 11:31:44 +0100 Subject: [PATCH 0405/2133] libmatheval 1.1.11 with intel/2015b --- .../b/byacc/byacc-20150711-intel-2015b.eb | 22 +++++++++++++ .../g/guile/guile-1.8.8-intel-2015b.eb | 31 +++++++++++++++++ .../l/libffi/libffi-3.0.13-intel-2015b.eb | 25 ++++++++++++++ .../libmatheval-1.1.11-intel-2015b.eb | 33 +++++++++++++++++++ .../libunistring-0.9.3-intel-2015b.eb | 26 +++++++++++++++ .../pkg-config-0.27.1-intel-2015b.eb | 27 +++++++++++++++ 6 files changed, 164 insertions(+) create mode 100644 easybuild/easyconfigs/b/byacc/byacc-20150711-intel-2015b.eb create mode 100644 easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015b.eb diff --git a/easybuild/easyconfigs/b/byacc/byacc-20150711-intel-2015b.eb b/easybuild/easyconfigs/b/byacc/byacc-20150711-intel-2015b.eb new file mode 100644 index 0000000000..1578ff69e4 --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-20150711-intel-2015b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '20150711' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCELOWER_TGZ] +source_urls = ['ftp://invisible-island.net/byacc'] + +checksums = ['2700401030583c4e9169ac7ea7d08de8'] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb new file mode 100644 index 0000000000..766148f244 --- /dev/null +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6', '', ('GNU', '4.9.3-2.25')), + ('GMP', '6.0.0a'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.27.1'), + ('libffi', '3.0.13'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015b.eb b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015b.eb new file mode 100644 index 0000000000..535d967631 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.0.13' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['libffi-%(version)s_include-xmmintrin.patch'] + +sanity_check_paths = { + 'files': ['lib/libffi.%s' % SHLIB_EXT, 'lib/libffi.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb new file mode 100644 index 0000000000..5c07ab422c --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('byacc', '20150711'), + ('guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb new file mode 100644 index 0000000000..0555900e19 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['libunistring_icc_builtin_nan-inf.patch'] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.so'] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015b.eb new file mode 100644 index 0000000000..f271d1a673 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.27.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +# don't use PAX, it might break. +tar_config_opts = True + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 607cc4a860c3f3efc1c7f1fcd35c15b3463ecc4e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 9 Nov 2015 15:48:06 +0100 Subject: [PATCH 0406/2133] Plumed 2.2 with intel/2015b --- .../p/PLUMED/PLUMED-2.2.0-intel-2015b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb new file mode 100644 index 0000000000..62ef96b466 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.2.0' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '1.16'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' -- GitLab From 8ddde6654c3410bd6cc6fea6e52da78c03453c0c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 16 Nov 2015 11:46:24 +0100 Subject: [PATCH 0407/2133] Fix sanity check for libffi --- easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015b.eb b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015b.eb index 535d967631..01fb77588e 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015b.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['libffi-%(version)s_include-xmmintrin.patch'] sanity_check_paths = { - 'files': ['lib/libffi.%s' % SHLIB_EXT, 'lib/libffi.a'], + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], 'dirs': [], } -- GitLab From d878e206912a9131b762d0e8c7cb67585eac4bd9 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 10 Feb 2016 16:59:08 +0200 Subject: [PATCH 0408/2133] add easyconfig METIS-5.1.0-foss-2016a-32bitIDX.eb --- .../METIS/METIS-5.1.0-foss-2016a-32bitIDX.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a-32bitIDX.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a-32bitIDX.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a-32bitIDX.eb new file mode 100644 index 0000000000..b316368934 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a-32bitIDX.eb @@ -0,0 +1,23 @@ +name = 'METIS' +version = '5.1.0' +versionsuffix = '-32bitIDX' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, + and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the + multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.4.3')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' -- GitLab From 5fa69beab4c3bd5e502bdf52e8a4902b84cdea02 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 10 Feb 2016 15:59:16 +0100 Subject: [PATCH 0409/2133] Add PLUMED 2.1.4 and 2.21 for intel & foss 2015b --- .../b/byacc/byacc-20150711-foss-2015b.eb | 22 ++++++++++ .../g/GMP/GMP-6.0.0a-foss-2015b.eb | 27 ++++++++++++ .../easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb | 18 ++++++++ .../g/guile/guile-1.8.8-foss-2015b.eb | 31 ++++++++++++++ .../l/libffi/libffi-3.0.13-foss-2015b.eb | 25 +++++++++++ .../libmatheval-1.1.11-foss-2015b.eb | 33 +++++++++++++++ .../libunistring-0.9.3-foss-2015b.eb | 26 ++++++++++++ .../p/PLUMED/PLUMED-2.1.4-foss-2015b.eb | 42 +++++++++++++++++++ .../p/PLUMED/PLUMED-2.2.1-foss-2015b.eb | 42 +++++++++++++++++++ .../p/PLUMED/PLUMED-2.2.1-intel-2015b.eb | 42 +++++++++++++++++++ 10 files changed, 308 insertions(+) create mode 100644 easybuild/easyconfigs/b/byacc/byacc-20150711-foss-2015b.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb create mode 100644 easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.0.13-foss-2015b.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb diff --git a/easybuild/easyconfigs/b/byacc/byacc-20150711-foss-2015b.eb b/easybuild/easyconfigs/b/byacc/byacc-20150711-foss-2015b.eb new file mode 100644 index 0000000000..6fabc38da7 --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-20150711-foss-2015b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '20150711' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TGZ] +source_urls = ['ftp://invisible-island.net/byacc'] + +checksums = ['2700401030583c4e9169ac7ea7d08de8'] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb new file mode 100644 index 0000000000..ab0d6b9ba8 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.0.0a' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' + diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb new file mode 100644 index 0000000000..ed67148304 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb new file mode 100644 index 0000000000..ad804aa4b1 --- /dev/null +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6', '', ('GNU', '4.9.3-2.25')), + ('GMP', '6.0.0a'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.27.1'), + ('libffi', '3.0.13'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-foss-2015b.eb b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-foss-2015b.eb new file mode 100644 index 0000000000..dac06d1c8d --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.0.13' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['libffi-%(version)s_include-xmmintrin.patch'] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb new file mode 100644 index 0000000000..2fd935d0b5 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('byacc', '20150711'), + ('guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb new file mode 100644 index 0000000000..91f9c37650 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['libunistring_icc_builtin_nan-inf.patch'] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.so'] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb new file mode 100644 index 0000000000..fc4323d74a --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.1.4' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '1.16'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb new file mode 100644 index 0000000000..4747d81041 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.2.1' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.1'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb new file mode 100644 index 0000000000..e509e0c50e --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.2.1' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.1'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' -- GitLab From 68dc1db0481d88f264faa3a09786a1f9c3c96e76 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 10 Feb 2016 16:12:34 +0100 Subject: [PATCH 0410/2133] Forgotten easyconfig for pkg-config --- .../pkg-config-0.27.1-foss-2015b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-foss-2015b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-foss-2015b.eb new file mode 100644 index 0000000000..73c06e7f1b --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-foss-2015b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.27.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +# don't use PAX, it might break. +tar_config_opts = True + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 447a17c99286ce03de02a52d9db7270ed4e991a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Feb 2016 16:21:22 +0100 Subject: [PATCH 0411/2133] fix GLib sanity check --- easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb index 5af7f7a410..3dcfe3ad19 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb @@ -30,7 +30,7 @@ configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] sanity_check_paths = { - 'files': ['lib/libglib-%%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], 'dirs': ['bin', 'include'], } -- GitLab From 7580fb2ca2421bc17618d989dc97a8e150edf095 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Feb 2016 20:05:55 +0100 Subject: [PATCH 0412/2133] rework p4vasp to use intel/2016a and easyconfigs from #2443 --- .../ATK-2.16.0-intel-2015b-GLib-2.29.92.eb | 29 ------------ .../cairo-1.14.2-intel-2015b-GLib-2.29.92.eb | 46 ------------------- .../g/GLib/GLib-2.29.92-intel-2015b.eb | 22 --------- ...ection-0.10.8-intel-2015b-Python-2.7.10.eb | 38 --------------- ...-pixbuf-2.31.4-intel-2015b-GLib-2.29.92.eb | 29 ------------ .../gtk+-2.24.28-intel-2015b-GLib-2.29.92.eb | 23 ---------- ...arfBuzz-0.9.41-intel-2015b-GLib-2.29.92.eb | 28 ----------- .../Pango-1.37.1-intel-2015b-GLib-2.29.92.eb | 24 ---------- ...Object-2.28.6-intel-2015b-Python-2.7.10.eb | 34 -------------- .../PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb | 34 -------------- ...4vasp-0.3.29-intel-2016a-Python-2.7.11.eb} | 4 +- ...-intel-2015b-Python-2.7.10-GLib-2.29.92.eb | 30 ------------ 12 files changed, 2 insertions(+), 339 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015b-GLib-2.29.92.eb delete mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015b-GLib-2.29.92.eb delete mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.29.92-intel-2015b.eb delete mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-0.10.8-intel-2015b-Python-2.7.10.eb delete mode 100644 easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b-GLib-2.29.92.eb delete mode 100644 easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b-GLib-2.29.92.eb delete mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b-GLib-2.29.92.eb delete mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015b-GLib-2.29.92.eb delete mode 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2015b-Python-2.7.10.eb delete mode 100644 easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb rename easybuild/easyconfigs/p/p4vasp/{p4vasp-0.3.29-intel-2015b-Python-2.7.10.eb => p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb} (91%) delete mode 100644 easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10-GLib-2.29.92.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015b-GLib-2.29.92.eb deleted file mode 100644 index afb1976aa4..0000000000 --- a/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015b-GLib-2.29.92.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ATK' -version = '2.16.0' - -homepage = 'https://developer.gnome.org/ATK/stable/' -description = """ - ATK provides the set of accessibility interfaces that are implemented by other - toolkits and applications. Using the ATK interfaces, accessibility tools have - full access to view and control running applications. -""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_XZ] - -glibver = '2.29.92' -versionsuffix = '-GLib-%s' % glibver -dependencies = [ - ('GLib', glibver), -] - -sanity_check_paths = { - 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015b-GLib-2.29.92.eb deleted file mode 100644 index 75af067c33..0000000000 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015b-GLib-2.29.92.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'cairo' -version = '1.14.2' - -homepage = 'http://cairographics.org' -description = """Cairo is a 2D graphics library with support for multiple output devices. - Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, - PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = ['http://cairographics.org/releases/'] -sources = [SOURCE_TAR_XZ] - -glibver = '2.29.92' -versionsuffix = '-GLib-%s' % glibver - -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libpng', '1.6.18'), - ('freetype', '2.6.1'), - ('pixman', '0.32.8'), - ('fontconfig', '2.11.94'), - ('expat', '2.1.0'), - ('GLib', glibver), -] - -# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -configopts = "--enable-symbol-lookup=no --enable-gobject=yes" - -# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" -buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' - -sanity_check_paths = { - 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', - 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', - 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + - ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', - '-script', '-script-interpreter', '-svg', '-version', '-xcb', - '-xlib', '-xlib-xrender']], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.29.92-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.29.92-intel-2015b.eb deleted file mode 100644 index 053d541683..0000000000 --- a/easybuild/easyconfigs/g/GLib/GLib-2.29.92-intel-2015b.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GLib' -version = '2.29.92' - -homepage = 'http://www.gtk.org/' -description = """GLib is one of the base libraries of the GTK+ project""" - -toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] -sources = ['glib-%(version)s.tar.xz'] - -dependencies = [ - ('libffi', '3.2.1'), - ('gettext', '0.19.6'), - ('libxml2', '2.9.2'), -] -builddependencies = [('Python', '2.7.10')] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-0.10.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-0.10.8-intel-2015b-Python-2.7.10.eb deleted file mode 100644 index 669dcee41a..0000000000 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-0.10.8-intel-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GObject-Introspection' -version = '0.10.8' - -homepage = 'https://wiki.gnome.org/GObjectIntrospection/' -description = """GObject introspection is a middleware layer between C libraries - (using GObject) and language bindings. The C library can be scanned at - compile time and generate a metadata file, in addition to the actual - native C library. Then at runtime, language bindings can read this - metadata and automatically provide bindings to call into the C library.""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -pyver = '2.7.10' -versionsuffix = '-Python-%s' % pyver - -dependencies = [ - ('Python', pyver), - ('GLib', '2.29.92'), - ('Bison', '3.0.4'), -] - -sanity_check_paths = { - 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + - ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], - 'dirs': ['include', 'share'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b-GLib-2.29.92.eb deleted file mode 100644 index df97d34492..0000000000 --- a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015b-GLib-2.29.92.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gdk-pixbuf' -version = '2.31.4' - -homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' -description = """ - The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. - It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it - was distributed as part of GTK+ 2 but it was split off into a separate package - in preparation for the change to GTK+ 3. -""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_XZ] - -glibver = '2.29.92' -versionsuffix = '-GLib-%s' % glibver -dependencies = [ - ('GLib', glibver), - ('libjpeg-turbo', '1.4.0'), - ('libpng', '1.6.18'), - ('LibTIFF', '4.0.3'), - -] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b-GLib-2.29.92.eb deleted file mode 100644 index 4fe143fa91..0000000000 --- a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015b-GLib-2.29.92.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gtk+' -version = '2.24.28' -versionsuffix = '-GLib-2.29.92' - -homepage = 'https://developer.gnome.org/gtk+/stable/' -description = """ - The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. -""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('ATK', '2.16.0', versionsuffix), - ('gdk-pixbuf', '2.31.4', versionsuffix), - ('Pango', '1.37.1', versionsuffix), -] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b-GLib-2.29.92.eb deleted file mode 100644 index 890b5853fb..0000000000 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015b-GLib-2.29.92.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'HarfBuzz' -version = '0.9.41' - -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' -description = """HarfBuzz is an OpenType text shaping engine.""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] -sources = [SOURCELOWER_TAR_BZ2] - -patches = ['HarfBuzz-%(version)s_no_symbolic.patch'] - -glibver = '2.29.92' -versionsuffix = '-GLib-%s' % glibver -dependencies = [ - ('GLib', glibver), - ('cairo', '1.14.2', versionsuffix), -] - -sanity_check_paths = { - 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015b-GLib-2.29.92.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015b-GLib-2.29.92.eb deleted file mode 100644 index bf4f60f01b..0000000000 --- a/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015b-GLib-2.29.92.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Pango' -version = '1.37.1' - -homepage = 'http://www.pango.org/' -description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. -Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the -context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_XZ] - -glibver = '2.29.92' -versionsuffix = '-GLib-%s' % glibver -dependencies = [ - ('GLib', glibver), - ('cairo', '1.14.2', versionsuffix), - ('HarfBuzz', '0.9.41', versionsuffix), -] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2015b-Python-2.7.10.eb deleted file mode 100644 index 3c627c6217..0000000000 --- a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PyGObject' -version = '2.28.6' - -homepage = 'http://www.pygtk.org/' -description = """Python Bindings for GLib/GObject/GIO/GTK+""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] - -pyver_maj_min = '2.7' -pyver = '%s.10' % pyver_maj_min -versionsuffix = '-Python-%s' % pyver - -glibver = '2.29.92' -dependencies = [ - ('Python', pyver), - ('GLib', glibver), - ('GObject-Introspection', '0.10.8', versionsuffix), - ('pycairo', '1.10.0', versionsuffix + '-GLib-%s' % glibver), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['include/pygtk-%(version_major)s.0/pyglib.h', 'include/pygtk-%(version_major)s.0/pygobject.h', - 'lib/libpyglib-%(version_major)s.0-python.so'], - 'dirs': ['bin', 'lib/python%s/site-packages/' % pyver_maj_min], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb deleted file mode 100644 index f7d18d2696..0000000000 --- a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PyGTK' -version = '2.24.0' - -homepage = 'http://www.pygtk.org/' -description = """PyGTK lets you to easily create programs with a graphical user interface - using the Python programming language.""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -pyver_maj_min = '2.7' -pyver = '%s.10' % pyver_maj_min -versionsuffix = '-Python-%s' % pyver - -glibver = '2.29.92' -dependencies = [ - ('Python', pyver), - ('GLib', glibver), - ('PyGObject', '2.28.6', versionsuffix), - ('gtk+', '2.24.28', '-GLib-%s' % glibver), -] - -sanity_check_paths = { - 'files': ['lib/pkgconfig/pygtk-%(version_major)s.0.pc'], - 'dirs': ['lib/pygtk'], -} - -sanity_check_commands = [('python', "-c 'import gtk'")] - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb similarity index 91% rename from easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb index 7fcc6c3b0b..7903d62ba9 100644 --- a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb @@ -2,12 +2,12 @@ easyblock = 'ConfigureMake' name = 'p4vasp' version = '0.3.29' -versionsuffix = '-Python-2.7.10' +versionsuffix = '-Python-2.7.11' homepage = 'http://www.p4vasp.at/' description = """Visualization suite for VASP""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2016a'} # download via http://www.p4vasp.at/index.php/downloads sources = [SOURCE_TGZ] diff --git a/easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10-GLib-2.29.92.eb b/easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10-GLib-2.29.92.eb deleted file mode 100644 index 23337bffcc..0000000000 --- a/easybuild/easyconfigs/p/pycairo/pycairo-1.10.0-intel-2015b-Python-2.7.10-GLib-2.29.92.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'Waf' - -name = 'pycairo' -version = '1.10.0' - -homepage = 'http://cairographics.org/pycairo/' -description = """Python bindings for the cairo library""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = ['http://cairographics.org/releases/'] -# py2cairo is the Python 2 compatible release -sources = ['py2cairo-%(version)s.tar.bz2'] - -pyver_maj_min = '2.7' -pyver = '%s.10' % pyver_maj_min -glibver = '2.29.92' -versionsuffix = '-Python-%s-GLib-%s' % (pyver, glibver) - -dependencies = [ - ('Python', pyver), - ('cairo', '1.14.2', '-GLib-%s' % glibver), -] - -sanity_check_paths = { - 'files': ['include/pycairo/pycairo.h', 'lib/pkgconfig/pycairo.pc'], - 'dirs': ['lib/python%s/site-packages/cairo' % pyver_maj_min], -} - -moduleclass = 'vis' -- GitLab From 1fdcf663ecdec9aab0d0ede65421a5d39dbc7409 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 10:53:30 +0100 Subject: [PATCH 0413/2133] style fixes --- easybuild/easyconfigs/l/libffi/libffi-3.0.13-foss-2015b.eb | 2 -- .../l/libunistring/libunistring-0.9.3-foss-2015b.eb | 4 +--- .../l/libunistring/libunistring-0.9.3-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb | 4 ++-- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb | 4 ++-- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb | 4 ++-- 7 files changed, 10 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-foss-2015b.eb b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-foss-2015b.eb index dac06d1c8d..e22ff76c36 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-foss-2015b.eb @@ -15,8 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -patches = ['libffi-%(version)s_include-xmmintrin.patch'] - sanity_check_paths = { 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb index 91f9c37650..3c6b226b5a 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb @@ -12,12 +12,10 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -patches = ['libunistring_icc_builtin_nan-inf.patch'] - parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.so'] + + 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', 'stdio', 'str', 'types', 'wbrk', 'width']], 'dirs' : ['include/unistring'], diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb index 0555900e19..19e0b26c92 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb @@ -17,7 +17,7 @@ patches = ['libunistring_icc_builtin_nan-inf.patch'] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.so'] + + 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', 'stdio', 'str', 'types', 'wbrk', 'width']], 'dirs' : ['include/unistring'], diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb index fc4323d74a..9cac08c076 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb @@ -30,12 +30,12 @@ configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' sanity_check_paths = { - 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], 'dirs': ['lib/plumed'] } modextrapaths = { - 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, 'PLUMED_ROOT': 'lib/plumed', } diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb index 62ef96b466..c6b4f4fabd 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb @@ -30,12 +30,12 @@ configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' sanity_check_paths = { - 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], 'dirs': ['lib/plumed'] } modextrapaths = { - 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, 'PLUMED_ROOT': 'lib/plumed', } diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb index 4747d81041..f3480b9f42 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb @@ -30,12 +30,12 @@ configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' sanity_check_paths = { - 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], 'dirs': ['lib/plumed'] } modextrapaths = { - 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, 'PLUMED_ROOT': 'lib/plumed', } diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb index e509e0c50e..a8664f7399 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb @@ -30,12 +30,12 @@ configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' sanity_check_paths = { - 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], 'dirs': ['lib/plumed'] } modextrapaths = { - 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, 'PLUMED_ROOT': 'lib/plumed', } -- GitLab From 8225389086673400fbdbe49d0db8a6025f6550e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 12:13:22 +0200 Subject: [PATCH 0414/2133] modify easyconfig ADF-2014.11.r48287-intel-2016a.eb --- .../easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb b/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb index 03dd1a9301..384f92299e 100644 --- a/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb @@ -7,7 +7,10 @@ description = """ADF is an accurate, parallelized, powerful computational chemis toolchain = {'name': 'intel', 'version': '2016a'} -sources = ['%(namelower)s%(version)s.src.tgz'] +sources = [ + '%(namelower)s%(version)s.src.tgz', + 'fix2014.pc64_linux.intelmpi.r48660.2.555.bin.tgz', +] modloadmsg = "These environment variables need to be defined before using ADF:\n" modloadmsg += " * $SCMLICENSE: path to ADF license file\n" -- GitLab From a1330edd407fd80249f875c86ed657010a6076ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 12:14:26 +0200 Subject: [PATCH 0415/2133] modify easyconfig ADF-2014.11.r48287-intel-2016a.eb --- easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb b/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb index 384f92299e..c209140e55 100644 --- a/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb @@ -9,6 +9,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [ '%(namelower)s%(version)s.src.tgz', + # no exact match on revision ID available, but not strictly needed 'fix2014.pc64_linux.intelmpi.r48660.2.555.bin.tgz', ] -- GitLab From b9363e5cd142c4808a229a9c755954392254f6b6 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 11 Feb 2016 12:11:06 +0100 Subject: [PATCH 0416/2133] switch to use %(perlver)s and %(perlshortver)s templates --- .../STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb index 147ee68d6c..609d04133f 100644 --- a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb @@ -7,6 +7,7 @@ easyblock = 'Tarball' name = 'STAR-Fusion' version = '0.6.0' +versionsuffix = '-%(perlver)s-%(perlshortver)s' homepage = 'https://github.com/STAR-Fusion/STAR-Fusion' description = """STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts @@ -18,12 +19,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/STAR-Fusion/STAR-Fusion/releases/download/v%(version)s/'] sources = ['%(name)s_v%(version)s.FULL.tar.gz'] -perl = 'Perl' -perlver = '5.16.3' -versionsuffix = '-%s-%s' % (perl, perlver) - dependencies = [ - (perl, perlver), + ('Perl', '5.16.3'), ('STAR', '2.5.1b'), ] @@ -44,7 +41,7 @@ exts_list = [ modextrapaths = { 'PATH': "", # add installation dir to PATH - 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' } sanity_check_paths = { -- GitLab From d12272fcb025dc9e5a893b5adb3c4c41cfb0fa54 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 11 Feb 2016 12:46:24 +0100 Subject: [PATCH 0417/2133] fixed typo --- .../s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb index 609d04133f..58fcb58c2d 100644 --- a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb @@ -7,7 +7,7 @@ easyblock = 'Tarball' name = 'STAR-Fusion' version = '0.6.0' -versionsuffix = '-%(perlver)s-%(perlshortver)s' +versionsuffix = '-Perl-%(perlver)s' homepage = 'https://github.com/STAR-Fusion/STAR-Fusion' description = """STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts -- GitLab From 9d522334b94f0477f80ab39ab92d99ce38ce97aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 15:15:26 +0200 Subject: [PATCH 0418/2133] modify easyconfig matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb --- ...plotlib-1.5.1-intel-2016a-Python-2.7.11.eb | 33 +++++++++++++------ 1 file changed, 23 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb index 192e60d3a1..c62d74a1eb 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb @@ -1,7 +1,8 @@ -easyblock = 'PythonPackage' +easyblock = 'Bundle' name = 'matplotlib' version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of @@ -10,23 +11,35 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = '-Python-%s' % pyver +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c "import %(ext_name)s"', '') dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ('freetype', '2.6.2'), ('libpng', '1.6.21'), ] +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + moduleclass = 'vis' -- GitLab From 5163430e4eb145704a2faefa71dbd9aa217bd93e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 16:23:11 +0100 Subject: [PATCH 0419/2133] switch to Python 2.7.11, intel/2016a and HDF5 1.8.16 --- .../f/freetype/freetype-2.6.2-intel-2015b.eb | 22 ----------- ...0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb | 33 +++++++++++++++++ .../l/libpng/libpng-1.6.21-intel-2015b.eb | 26 ------------- ...plotlib-1.5.1-intel-2015b-Python-2.7.10.eb | 32 ---------------- ...ntel-2016a-Python-2.7.11-timed-pingpong.eb | 37 +++++++++++++++++++ ...ngpong-0.7.0-intel-2016a-Python-2.7.11.eb} | 13 +++---- 6 files changed, 75 insertions(+), 88 deletions(-) delete mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb delete mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb delete mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb rename easybuild/easyconfigs/m/mympingpong/{mympingpong-0.7.0-intel-2015b-Python-2.7.10.eb => mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb} (66%) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb deleted file mode 100644 index 0811253154..0000000000 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'freetype' -version = '2.6.2' - -homepage = 'http://freetype.org' -description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and - portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display - servers, font conversion tools, text image generation tools, and many other products as well.""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = [GNU_SAVANNAH_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [('libpng', '1.6.21')] - -sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, - 'lib/pkgconfig/freetype2.pc'], - 'dirs': ['include/freetype2'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb new file mode 100644 index 0000000000..f28ee11756 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.16' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.11'), + ('HDF5', hdf5ver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb deleted file mode 100644 index b76c98f402..0000000000 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpng' -version = '1.6.21' - -homepage = 'http://www.libpng.org/pub/png/libpng.html' -description = "libpng is the official PNG reference library" - -toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('zlib', '1.2.8')] - -configopts = "--with-pic" - -majminver = ''.join(version.split('.')[:2]) -sanity_check_paths = { - 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', - 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' %(majminver, SHLIB_EXT)], - 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.10.eb deleted file mode 100644 index e3cf47e553..0000000000 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'matplotlib' -version = '1.5.1' - -homepage = 'http://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -pyver = '2.7.10' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = '-Python-%s' % pyver - -dependencies = [ - ('Python', pyver), - ('freetype', '2.6.2'), - ('libpng', '1.6.21'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb new file mode 100644 index 0000000000..e9f3d00f6f --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '1.3.1' +label = 'timed-pingpong' +versionsuffix = '-Python-%%(pyver)s-%s' % label + +homepage = 'https://bitbucket.org/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + BITBUCKET_DOWNLOADS, + GOOGLECODE_SOURCE, +] +sources = [SOURCE_TAR_GZ] + +patches = ['mpi4py-%%(version)s_%s.patch' % label] + +dependencies = [('Python', '2.7.11')] + +# force rebuilding everything, including patched files +buildopts = '--force' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'], +} + +# check that timed pingpong routines that are added via the patch are available +sanity_check_commands = [ + ('python', '-c "from mpi4py.MPI import Comm; import sys; sys.exit((1, 0)[\'PingpongRS\' in dir(Comm)])"'), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb similarity index 66% rename from easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb index dc119b0460..95fb7c2e93 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb @@ -2,35 +2,32 @@ easyblock = 'PythonPackage' name = 'mympingpong' version = '0.7.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/hpcugent/mympingpong' description = """A mpi4py based random pair pingpong network stress test.""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -pyver = '2.7.10' -versionsuffix = '-Python-%s' % pyver - vsc_base_ver = '2.4.16' dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ('vsc-base', vsc_base_ver, versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-%s' % vsc_base_ver), ('matplotlib', '1.5.1', versionsuffix), - ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.15-patch1'), + ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.16'), ('mpi4py', '1.3.1', versionsuffix + '-timed-pingpong'), ] options = {'modulename': 'vsc.mympingpong'} -pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': ['bin/mympingpong', 'bin/mympingponganalysis'], - 'dirs': ['lib/python%(pyver)s/site-packages/mympingpong-%%(version)s-py%(pyver)s.egg' % {'pyver': pyshortver}], + 'dirs': ['lib/python%(pyver)s/site-packages'], } moduleclass = 'perf' -- GitLab From bd3bc0173d4bb6dfa7d843636736138a0b62f814 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 16:29:27 +0100 Subject: [PATCH 0420/2133] switch to Python 2.7.11, intel/2016a --- ... => vsc-base-2.4.16-intel-2016a-Python-2.7.11.eb} | 10 ++++------ ... vsc-install-0.9.12-intel-2016a-Python-2.7.11.eb} | 10 ++++------ ...4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.16.eb} | 12 +++++------- 3 files changed, 13 insertions(+), 19 deletions(-) rename easybuild/easyconfigs/v/vsc-base/{vsc-base-2.4.16-intel-2015b-Python-2.7.10.eb => vsc-base-2.4.16-intel-2016a-Python-2.7.11.eb} (69%) rename easybuild/easyconfigs/v/vsc-install/{vsc-install-0.9.12-intel-2015b-Python-2.7.10.eb => vsc-install-0.9.12-intel-2016a-Python-2.7.11.eb} (65%) rename easybuild/easyconfigs/v/vsc-mympirun/{vsc-mympirun-3.4.2-intel-2015b-Python-2.7.10-vsc-base-2.4.16.eb => vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.16.eb} (60%) diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2016a-Python-2.7.11.eb similarity index 69% rename from easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2016a-Python-2.7.11.eb index e9057b41f7..01545f551e 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2016a-Python-2.7.11.eb @@ -2,29 +2,27 @@ easyblock = 'PythonPackage' name = 'vsc-base' version = '2.4.16' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/vsc-base' description = """Base library for Python tools developed by UGent's HPC group, including generaloption (option parser) and fancylogger (logging functionality).""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] -pyver = '2.7.10' -versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ('vsc-install', '0.9.12', versionsuffix), ] options = {'modulename': 'vsc.utils.fancylogger'} -shortpyver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages' % shortpyver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2016a-Python-2.7.11.eb similarity index 65% rename from easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2016a-Python-2.7.11.eb index 27d473bb9f..a369a98d26 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2016a-Python-2.7.11.eb @@ -2,28 +2,26 @@ easyblock = 'PythonPackage' name = 'vsc-install' version = '0.9.12' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/vsc-install' description = """vsc-install provides shared setuptools functions and classes for Python libraries developed by UGent's HPC group""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] -pyver = '2.7.10' -versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ] options = {'modulename': 'vsc.install'} -shortpyver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages' % shortpyver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.10-vsc-base-2.4.16.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.16.eb similarity index 60% rename from easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.10-vsc-base-2.4.16.eb rename to easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.16.eb index 9f4a65aee3..6bcb2553b9 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.10-vsc-base-2.4.16.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.16.eb @@ -6,18 +6,17 @@ version = '3.4.2' homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] -pyver = '2.7.10' vsc_base_ver = '2.4.16' -versionsuffix = '-Python-%s-vsc-base-%s' % (pyver, vsc_base_ver) +versionsuffix = '-Python-%%(pyver)s-vsc-base-%s' % vsc_base_ver dependencies = [ - ('Python', pyver), - ('vsc-base', vsc_base_ver, '-Python-%s' % pyver), + ('Python', '2.7.11'), + ('vsc-base', vsc_base_ver, '-Python-%(pyver)s'), ] # we ship something in bin/fake @@ -25,10 +24,9 @@ modextrapaths = {'PATH': 'bin/fake'} options = {'modulename': 'vsc.mympirun'} -shortpyver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': ['bin/mympirun'], - 'dirs': ['lib/python%(pyver)s/site-packages/vsc_mympirun-%%(version)s-py%(pyver)s.egg' % {'pyver': shortpyver}], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'tools' -- GitLab From a10f753e479dfc20c6823c34f160c271b5f473cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 17:03:26 +0100 Subject: [PATCH 0421/2133] bump to vsc-base 2.4.17 and vsc-install 0.9.18 --- ...2.7.11.eb => vsc-base-2.4.17-intel-2016a-Python-2.7.11.eb} | 4 ++-- ....11.eb => vsc-install-0.9.18-intel-2016a-Python-2.7.11.eb} | 2 +- ...mpirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.17.eb} | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/v/vsc-base/{vsc-base-2.4.16-intel-2016a-Python-2.7.11.eb => vsc-base-2.4.17-intel-2016a-Python-2.7.11.eb} (90%) rename easybuild/easyconfigs/v/vsc-install/{vsc-install-0.9.12-intel-2016a-Python-2.7.11.eb => vsc-install-0.9.18-intel-2016a-Python-2.7.11.eb} (96%) rename easybuild/easyconfigs/v/vsc-mympirun/{vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.16.eb => vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.17.eb} (97%) diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2016a-Python-2.7.11.eb similarity index 90% rename from easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2016a-Python-2.7.11.eb index 01545f551e..bf597beacd 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.16-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2016a-Python-2.7.11.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'vsc-base' -version = '2.4.16' +version = '2.4.17' versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/vsc-base' @@ -15,7 +15,7 @@ source_urls = [PYPI_SOURCE] dependencies = [ ('Python', '2.7.11'), - ('vsc-install', '0.9.12', versionsuffix), + ('vsc-install', '0.9.18', versionsuffix), ] options = {'modulename': 'vsc.utils.fancylogger'} diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2016a-Python-2.7.11.eb similarity index 96% rename from easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2016a-Python-2.7.11.eb index a369a98d26..a3123a79e4 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.12-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2016a-Python-2.7.11.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'vsc-install' -version = '0.9.12' +version = '0.9.18' versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/vsc-install' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.16.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.17.eb similarity index 97% rename from easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.16.eb rename to easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.17.eb index 6bcb2553b9..9ff223125f 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.16.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.17.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] -vsc_base_ver = '2.4.16' +vsc_base_ver = '2.4.17' versionsuffix = '-Python-%%(pyver)s-vsc-base-%s' % vsc_base_ver dependencies = [ -- GitLab From d6638cfc0366296529a5220ad58d41885ec3f646 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 17:25:57 +0100 Subject: [PATCH 0422/2133] add lxml dep for mympingpong --- .../m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb index 95fb7c2e93..66db77c98e 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb @@ -21,6 +21,7 @@ dependencies = [ ('matplotlib', '1.5.1', versionsuffix), ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.16'), ('mpi4py', '1.3.1', versionsuffix + '-timed-pingpong'), + ('lxml', '3.5.0', versionsuffix), ] options = {'modulename': 'vsc.mympingpong'} -- GitLab From 7711db422a26d03a9a9932b755fe186ea4640c7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 17:51:33 +0100 Subject: [PATCH 0423/2133] fix sanity check for mympingpong --- .../mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb index 66db77c98e..572fe6edeb 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb @@ -28,7 +28,7 @@ options = {'modulename': 'vsc.mympingpong'} sanity_check_paths = { 'files': ['bin/mympingpong', 'bin/mympingponganalysis'], - 'dirs': ['lib/python%(pyver)s/site-packages'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'perf' -- GitLab From c88613656ca870fdf029d9b36b89e948a2cf7419 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 18:55:46 +0100 Subject: [PATCH 0424/2133] add bitstring extension to Python 2.7.11 easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 4 ++++ 3 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 4bce06c8fe..b7680c2e37 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -124,6 +124,10 @@ exts_list = [ 'modulename': 'enum', 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), + ('bitstring', '3.1.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index c697adc7c7..c0a4533e39 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -124,6 +124,10 @@ exts_list = [ 'modulename': 'enum', 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), + ('bitstring', '3.1.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index b615ded539..03577e9e83 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -124,6 +124,10 @@ exts_list = [ 'modulename': 'enum', 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), + ('bitstring', '3.1.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), ] moduleclass = 'lang' -- GitLab From 7a77071db4ae5f4647d2a2fbce0e68614cd39e3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 18:58:45 +0100 Subject: [PATCH 0425/2133] don't hardcode CC/CXX in OpenMPI easyconfigs --- .../o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 1 - .../OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index ca0afea9dc..df5eafaf60 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -15,7 +15,6 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support -configopts += ' CC=icc FC=ifort CXX=icpc ' configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading dependencies = [('hwloc', '1.10.0')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 10e25e882a..a142e4f128 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -15,7 +15,6 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support -configopts += ' CC=icc FC=ifort CXX=icpc ' configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading dependencies = [('hwloc', '1.11.1')] -- GitLab From c921dcaf31521ffcc579dfd3413713341a9d1ebd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Feb 2016 23:07:20 +0100 Subject: [PATCH 0426/2133] add sanity check commands for OpenMPI built with icc/ifort --- .../o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 6 ++++++ .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 6 ++++++ .../OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 6 ++++++ .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 6 ++++++ .../OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb | 7 ++++++- .../o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb | 6 ++++++ .../OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb | 6 ++++++ .../OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 6 ++++++ .../OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 6 ++++++ 9 files changed, 54 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index d88a606fa0..340ca867a1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -30,4 +30,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 4fc8978e4d..ef20ec58de 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -30,4 +30,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 0bb4349893..ec62deb537 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -28,4 +28,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index e9f2f244ec..e5dcb5929f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -30,4 +30,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index c6c6f0c9ab..c0e27137e3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -28,5 +28,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } -moduleclass = 'mpi' +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index f5e9417cad..19949c397c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -29,4 +29,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index 780c3c78ba..d39ca71b30 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -30,4 +30,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index df5eafaf60..86eed73b49 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -30,4 +30,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index a142e4f128..34da0e5297 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -30,4 +30,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + moduleclass = 'mpi' -- GitLab From 0b207b5b1a25ab195c1fe7898bd400eaf4d18243 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2016 08:51:05 +0100 Subject: [PATCH 0427/2133] bump vsc-base version to 2.4.17 --- .../mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb index 572fe6edeb..b5da145493 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2016a-Python-2.7.11.eb @@ -12,8 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -vsc_base_ver = '2.4.16' - +vsc_base_ver = '2.4.17' dependencies = [ ('Python', '2.7.11'), ('vsc-base', vsc_base_ver, versionsuffix), -- GitLab From 41dcc36c227b11447b35386eddeb24b2925001dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2016 09:04:57 +0100 Subject: [PATCH 0428/2133] add license_file spec --- easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb b/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb index c209140e55..21843552e8 100644 --- a/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2014.11.r48287-intel-2016a.eb @@ -13,6 +13,8 @@ sources = [ 'fix2014.pc64_linux.intelmpi.r48660.2.555.bin.tgz', ] +license_file = HOME + "/licenses/ADF/license.txt" + modloadmsg = "These environment variables need to be defined before using ADF:\n" modloadmsg += " * $SCMLICENSE: path to ADF license file\n" modloadmsg += " * $SCM_TMPDIR: path to user scratch directory" -- GitLab From 4d6e0521eb802c644fb19469f12fb7ff09e32259 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2016 09:32:21 +0100 Subject: [PATCH 0429/2133] remove Google Code source URL for mpi4py --- .../m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 5 +---- .../m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb | 5 +---- .../m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb | 5 +---- .../m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb | 5 +---- .../m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb | 5 +---- .../m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb | 5 +---- .../m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb | 5 +---- .../mpi4py-1.3.1-intel-2015b-Python-2.7.10-timed-pingpong.eb | 5 +---- .../m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10.eb | 5 +---- .../mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb | 5 +---- .../m/mpi4py/mpi4py-2.0.0-intel-2015b-Python-2.7.10.eb | 5 +---- 11 files changed, 11 insertions(+), 44 deletions(-) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index de5230e1fa..b4a81e41a3 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -9,10 +9,7 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb index c04cd339fd..e5d94c2ee2 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -9,10 +9,7 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb index bc0d20fdcb..4e871b0231 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb @@ -10,10 +10,7 @@ language, allowing any Python program to exploit multiple processors.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb index ad06de5d4f..40a44908c4 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb @@ -9,10 +9,7 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb index c69d7c6073..71702ea79c 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb @@ -9,10 +9,7 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb index 94b5a9f2f8..14d09f706a 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb @@ -9,10 +9,7 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb index 07635c8d39..96628ba336 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb @@ -9,10 +9,7 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10-timed-pingpong.eb index 85752ecebf..e8592db2a2 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10-timed-pingpong.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10-timed-pingpong.eb @@ -9,10 +9,7 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] label = 'timed-pingpong' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10.eb index b6e7008371..9ee5130156 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10.eb @@ -9,10 +9,7 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] py_maj_min = '2.7' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb index e9f3d00f6f..654b6f59ec 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb @@ -11,10 +11,7 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] patches = ['mpi4py-%%(version)s_%s.patch' % label] diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2015b-Python-2.7.10.eb index 336877544b..0bec59079b 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2015b-Python-2.7.10.eb @@ -9,10 +9,7 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = [ - BITBUCKET_DOWNLOADS, - GOOGLECODE_SOURCE, -] +source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] py_maj_min = '2.7' -- GitLab From afdb2fcbcdb96a1bfe7263985e8946047de56863 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2016 12:21:36 +0200 Subject: [PATCH 0430/2133] add easyconfig mympingpong-0.7.0-intel-2015b-Python-2.7.11.eb, add easyconfig freetype-2.6.2-intel-2015b.eb, add easyconfig h5py-2.5.0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb, add easyconfig libpng-1.6.21-intel-2015b.eb, add easyconfig libxslt-1.1.28-intel-2015b-Python-2.7.11.eb, add easyconfig lxml-3.5.0-intel-2015b-Python-2.7.11.eb, add easyconfig matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb, add easyconfig mpi4py-1.3.1-intel-2015b-Python-2.7.11-timed-pingpong.eb, modify easyconfig mympingpong-0.7.0-intel-2015b-Python-2.7.11.eb, add easyconfig vsc-base-2.4.17-intel-2015b-Python-2.7.11.eb, add easyconfig vsc-install-0.9.18-intel-2015b-Python-2.7.11.eb, add easyconfig vsc-mympirun-3.4.2-intel-2015b-Python-2.7.11-vsc-base-2.4.17.eb --- .../f/freetype/freetype-2.6.2-intel-2015b.eb | 22 +++++++++ ...0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb | 33 ++++++++++++++ .../l/libpng/libpng-1.6.21-intel-2015b.eb | 26 +++++++++++ ...ibxslt-1.1.28-intel-2015b-Python-2.7.11.eb | 25 +++++++++++ .../lxml-3.5.0-intel-2015b-Python-2.7.11.eb | 30 +++++++++++++ ...plotlib-1.5.1-intel-2015b-Python-2.7.11.eb | 45 +++++++++++++++++++ ...ntel-2015b-Python-2.7.11-timed-pingpong.eb | 34 ++++++++++++++ ...ingpong-0.7.0-intel-2015b-Python-2.7.11.eb | 33 ++++++++++++++ ...c-base-2.4.17-intel-2015b-Python-2.7.11.eb | 28 ++++++++++++ ...nstall-0.9.18-intel-2015b-Python-2.7.11.eb | 27 +++++++++++ ...tel-2015b-Python-2.7.11-vsc-base-2.4.17.eb | 32 +++++++++++++ 11 files changed, 335 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015b-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2015b-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.11-timed-pingpong.eb create mode 100644 easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2015b-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2015b-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.11-vsc-base-2.4.17.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb new file mode 100644 index 0000000000..0811253154 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb new file mode 100644 index 0000000000..62610f6762 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.16' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.11'), + ('HDF5', hdf5ver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb new file mode 100644 index 0000000000..b76c98f402 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' %(majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015b-Python-2.7.11.eb new file mode 100644 index 0000000000..8b44117332 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015b-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3', versionsuffix), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2015b-Python-2.7.11.eb new file mode 100644 index 0000000000..c1b483c4c3 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-3.5.0-intel-2015b-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '3.5.0' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('libxml2', '2.9.3', versionsuffix), + ('libxslt', '1.1.28', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb new file mode 100644 index 0000000000..1364208cee --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c "import %(ext_name)s"', '') + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.11-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.11-timed-pingpong.eb new file mode 100644 index 0000000000..8f22d6b607 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.11-timed-pingpong.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '1.3.1' +label = 'timed-pingpong' +versionsuffix = '-Python-%%(pyver)s-%s' % label + +homepage = 'https://bitbucket.org/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [BITBUCKET_DOWNLOADS] +sources = [SOURCE_TAR_GZ] + +patches = ['mpi4py-%%(version)s_%s.patch' % label] + +dependencies = [('Python', '2.7.11')] + +# force rebuilding everything, including patched files +buildopts = '--force' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'], +} + +# check that timed pingpong routines that are added via the patch are available +sanity_check_commands = [ + ('python', '-c "from mpi4py.MPI import Comm; import sys; sys.exit((1, 0)[\'PingpongRS\' in dir(Comm)])"'), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.11.eb new file mode 100644 index 0000000000..e243ebde53 --- /dev/null +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.0-intel-2015b-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'mympingpong' +version = '0.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hpcugent/mympingpong' +description = """A mpi4py based random pair pingpong network stress test.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +vsc_base_ver = '2.4.17' +dependencies = [ + ('Python', '2.7.11'), + ('vsc-base', vsc_base_ver, versionsuffix), + ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-%s' % vsc_base_ver), + ('matplotlib', '1.5.1', versionsuffix), + ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.16'), + ('mpi4py', '1.3.1', versionsuffix + '-timed-pingpong'), + ('lxml', '3.5.0', versionsuffix), +] + +options = {'modulename': 'vsc.mympingpong'} + +sanity_check_paths = { + 'files': ['bin/mympingpong', 'bin/mympingponganalysis'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2015b-Python-2.7.11.eb new file mode 100644 index 0000000000..29c125cb6e --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.17-intel-2015b-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'vsc-base' +version = '2.4.17' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/vsc-base' +description = """Base library for Python tools developed by UGent's HPC group, including generaloption (option parser) +and fancylogger (logging functionality).""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Python', '2.7.11'), + ('vsc-install', '0.9.18', versionsuffix), +] + +options = {'modulename': 'vsc.utils.fancylogger'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2015b-Python-2.7.11.eb new file mode 100644 index 0000000000..d0d69c63a6 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.9.18-intel-2015b-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'vsc-install' +version = '0.9.18' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/vsc-install' +description = """vsc-install provides shared setuptools functions and classes for Python libraries + developed by UGent's HPC group""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Python', '2.7.11'), +] + +options = {'modulename': 'vsc.install'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.11-vsc-base-2.4.17.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.11-vsc-base-2.4.17.eb new file mode 100644 index 0000000000..100ec4fa94 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-intel-2015b-Python-2.7.11-vsc-base-2.4.17.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'vsc-mympirun' +version = '3.4.2' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] + +vsc_base_ver = '2.4.17' +versionsuffix = '-Python-%%(pyver)s-vsc-base-%s' % vsc_base_ver + +dependencies = [ + ('Python', '2.7.11'), + ('vsc-base', vsc_base_ver, '-Python-%(pyver)s'), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +options = {'modulename': 'vsc.mympirun'} + +sanity_check_paths = { + 'files': ['bin/mympirun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From 5501e44a4c1fe76e3523064e9ed168e637c90e8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2016 11:45:10 +0100 Subject: [PATCH 0431/2133] h5py requires pkgconfig Python module --- .../h5py-2.5.0-intel-2015a-Python-2.7.9.eb | 1 + ...Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 1 + ...-2015b-Python-2.7.10-HDF5-1.8.15-patch1.eb | 1 + ...0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb | 1 + .../pkg-config/pkg-config-0.29-intel-2015a.eb | 27 +++++++++++++++++++ .../pkg-config/pkg-config-0.29-intel-2015b.eb | 6 ++--- .../pkg-config/pkg-config-0.29-intel-2016a.eb | 27 +++++++++++++++++++ ...kgconfig-1.1.0-intel-2015a-Python-2.7.9.eb | 26 ++++++++++++++++++ ...gconfig-1.1.0-intel-2015b-Python-2.7.10.eb | 26 ++++++++++++++++++ ...gconfig-1.1.0-intel-2016a-Python-2.7.11.eb | 26 ++++++++++++++++++ 10 files changed, 139 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb index 41181b753b..4bd7c5cc0e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb @@ -25,6 +25,7 @@ prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' dependencies = [ (python, pyver), ('HDF5', '1.8.14'), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb index 8cfa9b21c9..f070e8c226 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -22,6 +22,7 @@ versionsuffix = '-Python-%s-HDF5-%s-serial' % (pyver, hdf5ver) dependencies = [ ('Python', pyver), ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1.eb index d9106c2244..bb6d007d2c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1.eb @@ -25,6 +25,7 @@ prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' dependencies = [ ('Python', pyver), ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb index f28ee11756..40b2a15fa2 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16.eb @@ -23,6 +23,7 @@ prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' dependencies = [ ('Python', '2.7.11'), ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015a.eb new file mode 100644 index 0000000000..55e66932e2 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015b.eb index 7a14bc5799..245547ce08 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015b.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015b.eb @@ -9,14 +9,14 @@ description = """pkg-config is a helper tool used when compiling applications an gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).""" -# don't use PAX, it might break. -tar_config_opts = True - toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +# don't use PAX, it might break. +tar_config_opts = True + configopts = " --with-internal-glib" sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2016a.eb new file mode 100644 index 0000000000..cc9d6a1ec7 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..e534f029a1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.9'), + ('pkg-config', '0.29'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..5280c70319 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.10'), + ('pkg-config', '0.29'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..6fb647d4b8 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('pkg-config', '0.29'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From 42daeb7b11a9dd7ae17e65edbe1c8f484e612fc3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2016 12:46:37 +0200 Subject: [PATCH 0432/2133] modify easyconfig h5py-2.5.0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb, add easyconfig pkgconfig-1.1.0-intel-2015b-Python-2.7.11.eb --- ...0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb | 1 + ...gconfig-1.1.0-intel-2015b-Python-2.7.11.eb | 26 +++++++++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015b-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb index 62610f6762..eb3653329e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.11-HDF5-1.8.16.eb @@ -23,6 +23,7 @@ prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' dependencies = [ ('Python', '2.7.11'), ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015b-Python-2.7.11.eb new file mode 100644 index 0000000000..591418bb38 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2015b-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('pkg-config', '0.29'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From 28e16800c2f64d02b6846ee2aaac88f1719bf719 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 12 Feb 2016 16:11:23 +0100 Subject: [PATCH 0433/2133] added git-lfs easyconfig --- .../easyconfigs/g/git-lfs/git-lfs-1.1.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100755 easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb new file mode 100755 index 0000000000..2baa195a5a --- /dev/null +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "Tarball" + +name = 'git-lfs' +version = '1.1.1' + +homepage = 'https://git-lfs.github.com/' +description = """Git Large File Storage (LFS) replaces large files such as audio samples, videos, + datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server + like GitHub.com or GitHub Enterprise.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/github/git-lfs/releases/download/v%(version)s/'] +sources = ['%(name)s-linux-amd64-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ["git-lfs"], + 'dirs': [""] +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', + } + +# delete to provide installation script +postinstallcmds = ["rm -fr %(installdir)s/install.sh"] + +moduleclass = 'tools' -- GitLab From 76aa48ad0922eb21b3bc5ef4ee7ef197768963b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2016 22:35:06 +0100 Subject: [PATCH 0434/2133] use mpif90 in sanity check command for OpenMPI 1.6.x --- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 340ca867a1..8e4b15732d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -33,7 +33,7 @@ sanity_check_paths = { sanity_check_commands = [ ('mpicc --version | grep icc', ''), ('mpicxx --version | grep icpc', ''), - ('mpifort --version | grep ifort', ''), + ('mpif90 --version | grep ifort', ''), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index ef20ec58de..069c5ad3b9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -33,7 +33,7 @@ sanity_check_paths = { sanity_check_commands = [ ('mpicc --version | grep icc', ''), ('mpicxx --version | grep icpc', ''), - ('mpifort --version | grep ifort', ''), + ('mpif90 --version | grep ifort', ''), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index ec62deb537..702e7940ba 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -31,7 +31,7 @@ sanity_check_paths = { sanity_check_commands = [ ('mpicc --version | grep icc', ''), ('mpicxx --version | grep icpc', ''), - ('mpifort --version | grep ifort', ''), + ('mpif90 --version | grep ifort', ''), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index e5dcb5929f..bba9f06666 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -33,7 +33,7 @@ sanity_check_paths = { sanity_check_commands = [ ('mpicc --version | grep icc', ''), ('mpicxx --version | grep icpc', ''), - ('mpifort --version | grep ifort', ''), + ('mpif90 --version | grep ifort', ''), ] moduleclass = 'mpi' -- GitLab From 67e8369d71fbc6489383b3ca8a43adf1fe2ed2d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Feb 2016 11:18:45 +0100 Subject: [PATCH 0435/2133] fix source URL for ImageMagick, add sanity checks + minor version bumps --- ...eb => ImageMagick-6.9.3-3-goolf-1.4.10.eb} | 11 +++++-- .../l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb | 6 ++++ ...eb => libjpeg-turbo-1.4.2-goolf-1.4.10.eb} | 10 ++++-- .../n/NASM/NASM-2.11.08-goolf-1.4.10.eb | 31 +++++++++++++++++++ 4 files changed, 53 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/i/ImageMagick/{ImageMagick-6.9.3-2-goolf-1.4.10.eb => ImageMagick-6.9.3-3-goolf-1.4.10.eb} (68%) rename easybuild/easyconfigs/l/libjpeg-turbo/{libjpeg-turbo-1.4.1-goolf-1.4.10.eb => libjpeg-turbo-1.4.2-goolf-1.4.10.eb} (63%) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.08-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb similarity index 68% rename from easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb rename to easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb index c751d87629..adc09ca30a 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'ImageMagick' -version = '6.9.3-2' +version = '6.9.3-3' homepage = 'http://www.imagemagick.org/' description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" @@ -9,14 +9,14 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.imagemagick.org/download/'] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] dependencies = [ ('bzip2', '1.0.6'), ('freetype', '2.5.0.1'), ('Ghostscript', '9.10'), ('JasPer', '1.900.1'), - ('libjpeg-turbo', '1.4.1'), + ('libjpeg-turbo', '1.4.2'), ('LibTIFF', '4.0.3'), ('libX11', '1.6.1'), ('libXext', '1.3.2'), @@ -25,6 +25,11 @@ dependencies = [ ('pkg-config', '0.27.1'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + modextravars = {'MAGICK_HOME': '%(installdir)s'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb index af18beb748..13281d87fa 100644 --- a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb @@ -12,4 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] sources = ['lcms2-%(version)s.tar.gz'] +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-goolf-1.4.10.eb similarity index 63% rename from easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-goolf-1.4.10.eb index b5f70e73bc..548eb81065 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-goolf-1.4.10.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libjpeg-turbo' -version = '1.4.1' +version = '1.4.2' homepage = 'http://sourceforge.net/libjpeg-turbo/' description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG @@ -15,10 +15,16 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('NASM', '2.07'), + ('NASM', '2.11.08'), ] configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'man', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-goolf-1.4.10.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-goolf-1.4.10.eb new file mode 100644 index 0000000000..617fb03523 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From b0fe338bf3afc9c779ce96cb47f16200b983cf68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Feb 2016 11:22:46 +0100 Subject: [PATCH 0436/2133] add custom sanity check for libjpeg-turbo --- .../l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.3.0-intel-2014b.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-5.5.0.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.2.5.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.3.5.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014b.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015a.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.5.14.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2015b.eb | 6 ++++++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a.eb | 6 ++++++ 21 files changed, 126 insertions(+) diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb index 7289b72f8d..2fd1231c7a 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-intel-2014b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-intel-2014b.eb index 97496de156..d23e5354dd 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-intel-2014b.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb index d2b54d01ff..4a756d191d 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-5.5.0.eb index f611dfc78d..53e32391dc 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-5.5.0.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.2.5.eb index ecec75e230..1f077dd9e4 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.2.5.eb @@ -22,4 +22,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.3.5.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.3.5.eb index f987aae4d5..bdd416258a 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.3.5.eb @@ -22,4 +22,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb index c76e470179..9186528df6 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014b.eb index 70fac12c9e..8e30c1bc84 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014b.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb index d6bc643d57..ad986ffea8 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015a.eb index 57eea7cba0..5e83491d3f 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015a.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.5.14.eb index 6af6464ee6..85a9c802fa 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.5.14.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb index 4197b7c635..e148186d4c 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb index 24b1cf1a07..f76124a8a3 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb index 765e1c4ea1..e15ae065d4 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb index 2bb0e8f9bc..eab64da24e 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb index eb2697c94d..eb2ff2229c 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb index af63e0180b..fb752c1fdd 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb index 3f922516d9..76f9c8ecfe 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb index 49b99b98b3..312b7f35a9 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2015b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2015b.eb index 11356694c2..a9bd6e3500 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2015b.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a.eb index 0eed145ebe..c23fea50a0 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a.eb @@ -21,4 +21,10 @@ dependencies = [ configopts = "--with-jpeg8" runtest = "test" +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + moduleclass = 'lib' -- GitLab From 06bca8ee8114827dcb4cbfd4c828727af8fcb603 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Feb 2016 17:55:16 +0100 Subject: [PATCH 0437/2133] add pic/precise toolchain opts + Autotools build dep --- easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2015a.eb index 7ddae5e22f..e5c8c08ed9 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-foss-2015a.eb @@ -8,10 +8,15 @@ description = """GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. """ toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'precise': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] +builddependencies = [ + ('Autotools', '20150215'), +] + # enable C++ interface configopts = '--enable-cxx' -- GitLab From 19bfbc65cc254cf2b8108f9c3b7917c2cef81aeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Feb 2016 18:03:18 +0100 Subject: [PATCH 0438/2133] extend sanity check for SQLite --- easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb index be167b2761..c435d47a74 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb @@ -20,7 +20,6 @@ description = 'SQLite: SQL Database Engine in a C Library' toolchain = {'name': 'foss', 'version': '2015a'} -# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz source_urls = ['http://www.sqlite.org/2016/'] version_minor_etc = version.split('.')[1:] version_minor_etc += '0' * (3 - len(version_minor_etc)) @@ -33,8 +32,9 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], } moduleclass = 'devel' -- GitLab From 73259c1e3bf5de237f9a055c52b3c1181c68e567 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Feb 2016 19:30:01 +0100 Subject: [PATCH 0439/2133] rename ffmpeg to FFmpeg --- .../a/animation/animation-2.4-intel-2015b-R-3.2.1.eb | 2 +- .../FFmpeg-2.4-intel-2014.06.eb} | 2 +- .../FFmpeg-2.4-intel-2014b.eb} | 2 +- .../FFmpeg-2.8-intel-2015b.eb} | 2 +- easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb | 2 +- easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/f/{ffmpeg/ffmpeg-2.4-intel-2014.06.eb => FFmpeg/FFmpeg-2.4-intel-2014.06.eb} (98%) rename easybuild/easyconfigs/f/{ffmpeg/ffmpeg-2.4-intel-2014b.eb => FFmpeg/FFmpeg-2.4-intel-2014b.eb} (98%) rename easybuild/easyconfigs/f/{ffmpeg/ffmpeg-2.8-intel-2015b.eb => FFmpeg/FFmpeg-2.8-intel-2015b.eb} (98%) diff --git a/easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb b/easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb index 9260cfb552..871016656b 100644 --- a/easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb +++ b/easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb @@ -20,7 +20,7 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), - ('ffmpeg', '2.8'), + ('FFmpeg', '2.8'), ('GraphicsMagick', '1.3.21'), ] diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014.06.eb similarity index 98% rename from easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb rename to easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014.06.eb index 4abf658ad6..efbfa05e7c 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014.06.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'ffmpeg' +name = 'FFmpeg' version = '2.4' homepage = 'https://www.ffmpeg.org/' diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014b.eb similarity index 98% rename from easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb rename to easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014b.eb index 4461759fe7..4c00df33b8 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2014b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'ffmpeg' +name = 'FFmpeg' version = '2.4' homepage = 'https://www.ffmpeg.org/' diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8-intel-2015b.eb similarity index 98% rename from easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb rename to easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8-intel-2015b.eb index 9493af88c9..6847042d88 100644 --- a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8-intel-2015b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'ffmpeg' +name = 'FFmpeg' version = '2.8' homepage = 'https://www.ffmpeg.org/' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb index cda5e655b4..f0a1d2bf7f 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_79' dependencies = [ (python, pythonver), ('zlib', '1.2.8'), - ('ffmpeg', '2.4'), + ('FFmpeg', '2.4'), ('libjpeg-turbo', '1.3.1'), ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb index 2db6adbc74..7d27269ff9 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb @@ -32,7 +32,7 @@ javaver = '1.7.0_60' dependencies = [ (python, pythonver), ('zlib', '1.2.8'), - ('ffmpeg', '2.4'), + ('FFmpeg', '2.4'), ('libjpeg-turbo', '1.3.1'), ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), -- GitLab From 1f5a8f39134b57028141b695d13899842eadea4a Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 11 Feb 2016 23:43:21 +0100 Subject: [PATCH 0440/2133] Build MetaVelvet. --- .../v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb | 2 +- .../v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb | 2 +- .../v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb | 2 +- .../v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb | 2 +- .../v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb index 7bbefcf5e6..7c27a7683f 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb @@ -23,6 +23,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] -postinstallcmds = ["cp -a contrib %(installdir)s/"] +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb index 6f41fbe5da..8457ee4903 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb @@ -22,6 +22,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] -postinstallcmds = ["cp -a contrib %(installdir)s/"] +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb index 3fdfb13e56..ad56fb1790 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb @@ -22,6 +22,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] -postinstallcmds = ["cp -a contrib %(installdir)s/"] +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb index 25dc94bbe0..52c0ab85db 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb @@ -26,6 +26,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] -postinstallcmds = ["cp -a contrib %(installdir)s/"] +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb index 1d3524357c..c23584dddd 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb @@ -27,6 +27,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] -postinstallcmds = ["cp -a contrib %(installdir)s/"] +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] moduleclass = 'bio' -- GitLab From 3782600d2774d0eea0cc8cf4b7a04ad054e55359 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Feb 2016 14:40:57 +0200 Subject: [PATCH 0441/2133] add easyconfig vsc-mympirun-scoop-3.4.0-intel-2015b-Python-2.7.10.eb --- ...n-scoop-3.4.0-intel-2015b-Python-2.7.10.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.0-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.0-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..a787efcddf --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.0-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,32 @@ +easyblock = 'VSCPythonPackage' + +name = 'vsc-mympirun-scoop' +version = '3.4.0' + +homepage = 'http://hpcugent.github.com/vsc-mympirun/' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/hpcugent/vsc-mympirun-scoop/archive/'] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [ + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), + ('vsc-mympirun', '3.4.2', '', True), + (python, pyver), + ('SCOOP', '0.6.2', versionsuffix), +] + +options = {'modulename': 'vsc.mympirun.scoop'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/vsc/mympirun/scoop'], +} + +moduleclass = 'tools' -- GitLab From 0c02ae6c6ac6c8161cc88012f1ea2914f794a113 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Feb 2016 16:32:36 +0100 Subject: [PATCH 0442/2133] bump vsc-mympirun-scoop version to 3.4.1 --- ...eb => vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/v/vsc-mympirun-scoop/{vsc-mympirun-scoop-3.4.0-intel-2015b-Python-2.7.10.eb => vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb} (97%) diff --git a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb similarity index 97% rename from easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.0-intel-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb index a787efcddf..24d1ff604f 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb @@ -1,7 +1,7 @@ easyblock = 'VSCPythonPackage' name = 'vsc-mympirun-scoop' -version = '3.4.0' +version = '3.4.1' homepage = 'http://hpcugent.github.com/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" -- GitLab From d58c113f81f36682a2aa2ada039447ac047a6755 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Feb 2016 18:32:04 +0200 Subject: [PATCH 0443/2133] add easyconfig WEKA-3.7.0-Java-1.7.0_80.eb --- .../w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb new file mode 100644 index 0000000000..396230d2a7 --- /dev/null +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'WEKA' +version = '3.7.0' + +homepage = 'http://www.cs.waikato.ac.nz/ml/weka/index.html' +description = """ Weka is a collection of machine learning algorithms for data mining tasks. + The algorithms can either be applied directly to a dataset or called from your own Java code. + Weka contains tools for data pre-processing, classification, regression, clustering, + association rules, and visualization. It is also well-suited for developing new machine + learning schemes.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://prdownloads.sourceforge.net/weka/'] +sources = ['%s-%s.zip' % (name.lower(), version.replace('.', '-'))] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["weka.jar"], + 'dirs': [] +} + +modextravars = { + 'WEKAINSTALL': '$root', +} + +modloadmsg = " execute WEKA: java -jar \\$EBROOTWEKA/weka.jar " + +moduleclass = 'bio' -- GitLab From 9cac1c3eea7e2f0f4daadf18d0c66d29ea1d7003 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 16 Feb 2016 10:05:27 +1300 Subject: [PATCH 0444/2133] New EasyConfig for flex 2.6.0 with the GCC 4.9.2 compiler --- .../easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb new file mode 100644 index 0000000000..3664582fdd --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' -- GitLab From 2cd9d919559ddde538055004d5b55f12385b6b96 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 16 Feb 2016 10:26:42 +1300 Subject: [PATCH 0445/2133] Add build dependency on CMake --- easybuild/easyconfigs/k/KEALib/KEALib-1.4.4-foss-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/k/KEALib/KEALib-1.4.4-foss-2015a.eb b/easybuild/easyconfigs/k/KEALib/KEALib-1.4.4-foss-2015a.eb index 81322d46f5..6d613af708 100644 --- a/easybuild/easyconfigs/k/KEALib/KEALib-1.4.4-foss-2015a.eb +++ b/easybuild/easyconfigs/k/KEALib/KEALib-1.4.4-foss-2015a.eb @@ -22,6 +22,10 @@ dependencies = [ ('HDF5', '1.8.16'), ] +builddependencies = [ + ('CMake', '3.4.1'), +] + start_dir = 'trunk' sanity_check_paths = { -- GitLab From cdf12d46eff5743af67cf80615ac0800ce10c11a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 16 Feb 2016 12:08:41 +1300 Subject: [PATCH 0446/2133] Add RSH_COMMAND variable to module files for ORCA --- easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb | 6 +++++- easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb | 6 +++++- easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb | 6 +++++- easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb | 6 +++++- 4 files changed, 20 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index 1082a356d5..1f68602fad 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -29,5 +29,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb index 1d969f2204..976f97b5d5 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb @@ -30,5 +30,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb index 39d6350aed..e21c8f3ed4 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -30,5 +30,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb index adeb3b2fac..547be86ff0 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb @@ -30,5 +30,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } -- GitLab From ed27bd5494fa431eb55631d35f7360e390ffb7c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 07:58:26 +0100 Subject: [PATCH 0447/2133] add bitstring extension --- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index aacb5511cd..7f06897c75 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -124,6 +124,10 @@ exts_list = [ 'modulename': 'enum', 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), + ('bitstring', '3.1.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), ] moduleclass = 'lang' -- GitLab From f303c19d1a8cdd6082ec5c55a26708fda423ae05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 08:00:07 +0100 Subject: [PATCH 0448/2133] use flex easyblock --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb index 3664582fdd..3626cfd239 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'flex' version = '2.6.0' -- GitLab From 7742120f5c1d28c3d8023bdf2fcab0098feead88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 08:02:21 +0100 Subject: [PATCH 0449/2133] use available flex easyblock --- .../easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb | 2 -- easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb | 2 -- .../easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb | 2 -- easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb | 2 -- .../easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb | 2 -- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb | 2 -- easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb | 2 -- 7 files changed, 14 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb index 55d2930dcc..98e5ff5527 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'flex' version = '2.5.39' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb index 9b7e0571f2..1c15e90f19 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'flex' version = '2.5.39' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb index 1d773d362f..667f205b69 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'flex' version = '2.5.39' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb index 4b71406750..034599b7bc 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'flex' version = '2.5.39' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb index b6406b3fee..75d18ede78 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'flex' version = '2.5.39' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb index ecfc6d2f7e..bd9f2b71e7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'flex' version = '2.5.39' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb index 7c5e4528e0..3b653b0adc 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'flex' version = '2.5.39' -- GitLab From 64913b847cf50adf55d3a5bf5e40573b9d6f46c4 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 16 Feb 2016 08:12:38 +0100 Subject: [PATCH 0450/2133] {lang}[intel/2016a] Python 3.5.1 (REVIEW) --- .../p/Python/Python-3.5.1-intel-2016a.eb | 112 ++++++++++++++++++ 1 file changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb new file mode 100644 index 0000000000..af27ca14ec --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -0,0 +1,112 @@ +name = 'Python' +version = '3.5.1' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.4' +scipyversion = '0.17.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), +# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# order is important! +# package versions updated Feb 25th 2016 +exts_list = [ + ('setuptools', '20.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('pbr', '0.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('decorator', '4.0.9', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' -- GitLab From ffdae35405f281975d41ae497963829ce5732bde Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 16 Feb 2016 09:25:56 +0100 Subject: [PATCH 0451/2133] pbr version corrected --- easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index af27ca14ec..0a2f41e168 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -58,7 +58,7 @@ exts_list = [ 'paycheck-1.0.2_setup-open-README-utf8.patch', ], }), - ('pbr', '0.11.1', { + ('pbr', '1.8.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], }), ('lockfile', '0.12.2', { -- GitLab From 4aa5fb7c8bc4d82d20166a91bf3639846d8827f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 10:17:36 +0100 Subject: [PATCH 0452/2133] use Trinity easyblock, add ant+zlib deps --- .../a/ant/ant-1.9.6-Java-1.7.0_80.eb | 23 ++++++++++++ .../j/JUnit/JUnit-4.12-Java-1.7.0_80.eb | 22 ++++++++++++ .../t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 36 ++++--------------- 3 files changed, 52 insertions(+), 29 deletions(-) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb create mode 100644 easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb new file mode 100644 index 0000000000..d93ecdb14e --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb @@ -0,0 +1,23 @@ +name = 'ant' +version = '1.9.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.7.0_80')] + +builddependencies = [('JUnit', '4.12', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.7.0_80.eb new file mode 100644 index 0000000000..c0074dc071 --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.7.0_80.eb @@ -0,0 +1,22 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb index d17305cb3c..ab623eb5f9 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -3,45 +3,23 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'ConfigureMake' - name = 'Trinity' version = '2.0.4' homepage = 'http://trinityrnaseq.github.io/' -description = """ Trinity assembles transcript sequences from Illumina RNA-Seq data. """ +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] sources = ['v%(version)s.tar.gz'] -unpack_options = '--strip-components=1' - -java = 'Java' -javaver = '1.7.0_80' - dependencies = [ - (java, javaver, '', True) - ] - -skipsteps = ['configure', 'install'] - -parallel = 1 - -buildininstalldir = True - -buildopts = ' && make plugins' - -sanity_check_paths = { - 'files': ["Chrysalis/Chrysalis", "Inchworm/bin/inchworm", - "trinity-plugins/rsem/rsem-run-em", "trinity-plugins/jellyfish/bin/jellyfish"], - 'dirs': [""], -} - -# add install dir to PATH -modextrapaths = { - 'PATH': '' -} + ('Java', '1.7.0_80', '', True), + ('ant', '1.9.6', '-Java-%(javaver)s', True), + ('zlib', '1.2.8'), +] moduleclass = 'bio' -- GitLab From 8bc99d2b0fc48268dbadfb5b2af4cd18f1a4b73d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 12:39:09 +0100 Subject: [PATCH 0453/2133] add patch file to fix linking against EB-provided zlib --- .../t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 3 +++ .../Trinity-2.0.4_plugins-Makefile.patch | 24 +++++++++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.0.4_plugins-Makefile.patch diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb index ab623eb5f9..1f448f04b9 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -16,9 +16,12 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['Trinity-%(version)s_plugins-Makefile.patch'] + dependencies = [ ('Java', '1.7.0_80', '', True), ('ant', '1.9.6', '-Java-%(javaver)s', True), + ('ncurses', '5.9'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4_plugins-Makefile.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4_plugins-Makefile.patch new file mode 100644 index 0000000000..0fa19b8876 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4_plugins-Makefile.patch @@ -0,0 +1,24 @@ +fix linking against EB-provided zlib +author: Kenneth Hoste (Ghent University) +--- trinityrnaseq-2.0.4/trinity-plugins/Makefile.orig 2015-02-14 20:34:09.000000000 +0100 ++++ trinityrnaseq-2.0.4/trinity-plugins/Makefile 2016-02-16 11:21:03.430691000 +0100 +@@ -13,6 +13,9 @@ + endif + + ++CC?=gcc ++CXX?=g++ ++ + ####################### + ### Required by Trinity + ####################### +@@ -52,7 +55,8 @@ + + rsem: + tar -zxvf ${RSEM_CODE}.tar.gz +- cd ${RSEM_CODE} && $(MAKE) LIBCURSES="${RSEM_LIBCURSES}" ++ sed -i -e 's@-lz@-L${EBROOTZLIB}/lib -lz@g' ${RSEM_CODE}/Makefile ++ cd ${RSEM_CODE} && $(MAKE) LIBCURSES="${RSEM_LIBCURSES}" LIBPATH="-L${EBROOTNCURSES}/lib -L${EBROOTZLIB}/lib" + ln -sf ${RSEM_CODE} rsem + + transdecoder_target: -- GitLab From 2907988b99797148d14c91bf6c334a54bbbe2814 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 12:52:04 +0100 Subject: [PATCH 0454/2133] more style fixes in ATLAS easyconfigs --- .../ATLAS-3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0.eb | 6 +++--- ...TLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb | 11 ++++++----- .../a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED.eb | 6 +++--- 3 files changed, 12 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0.eb b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0.eb index ec567b4cbe..60ab20b787 100644 --- a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0.eb +++ b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0.eb @@ -10,8 +10,8 @@ description = """ATLAS (Automatically Tuned Linear Algebra Software) is the appl toolchain = {'name': 'gompi', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -sources = ['%s%s.tar.bz2' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/math-atlas/files/Stable/%s' % version, 'download')] +sources = ['%(namelower)s%(version)s.tar.bz2'] +source_urls = [('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s', 'download')] lapack = 'LAPACK' lapackver = '3.4.0' @@ -19,7 +19,7 @@ lapackver = '3.4.0' builddependencies = [(lapack, lapackver)] versionsuffix = '-%s-%s' % (lapack, lapackver) -patches = ['ATLAS-3.8.4_illegal-instruction-fix.patch'] +patches = ['ATLAS-%(version)s_illegal-instruction-fix.patch'] # build full LAPACK library with supplied netlib LAPACK full_lapack = True diff --git a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb index a05c00d082..b85e7b5063 100644 --- a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb +++ b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED-with-shared-libs.eb @@ -11,12 +11,13 @@ description = """ATLAS (Automatically Tuned Linear Algebra Software) is the appl toolchain = {'name': 'gompi', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -sources = ['%s%s.tar.bz2' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/math-atlas/files/Stable/%s' % version, 'download')] +sources = ['%(namelower)s%(version)s.tar.bz2'] +source_urls = [('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s', 'download')] -patches = ['ATLAS-3.8.4_illegal-instruction-fix.patch', - 'ATLAS-3.8.4_make-install-shared.patch' - ] +patches = [ + 'ATLAS-%(version)s_illegal-instruction-fix.patch', + 'ATLAS-%(version)s_make-install-shared.patch', +] # fix for http://math-atlas.sourceforge.net/errata.html#sharedProbe configopts = "-Ss f77lib '-L${EBROOTGCC}/lib64 -lgfortran'" diff --git a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED.eb index 5fa842f1c8..d541339cb7 100644 --- a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.8.4-gompi-1.1.0-no-OFED.eb @@ -10,10 +10,10 @@ description = """ATLAS (Automatically Tuned Linear Algebra Software) is the appl toolchain = {'name': 'gompi', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -sources = ['%s%s.tar.bz2' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/math-atlas/files/Stable/%s' % version, 'download')] +sources = ['%(namelower)s%(version)s.tar.bz2'] +source_urls = [('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s', 'download')] -patches = ['ATLAS-3.8.4_illegal-instruction-fix.patch'] +patches = ['ATLAS-%(version)s_illegal-instruction-fix.patch'] # fix for http://math-atlas.sourceforge.net/errata.html#sharedProbe configopts = "-Ss f77lib '-L$(EBTROOTGCC)/lib64 -lgfortran'" -- GitLab From 049a84b592ab80117fa8f8d1e8c5290b9469a19b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 13:03:31 +0100 Subject: [PATCH 0455/2133] also use Trinity easyblock in v2.0.6 easyconfig --- .../t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb | 34 +++++-------------- 1 file changed, 9 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb index 69e40a1027..30e64b353f 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb @@ -3,42 +3,26 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'ConfigureMake' - name = 'Trinity' version = '2.0.6' homepage = 'http://trinityrnaseq.github.io/' -description = """ Trinity assembles transcript sequences from Illumina RNA-Seq data. """ +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] sources = ['v%(version)s.tar.gz'] -java = 'Java' -javaver = '1.7.0_21' +patches = ['Trinity-2.0.4_plugins-Makefile.patch'] dependencies = [ - (java, javaver, '', True) - ] - -skipsteps = ['configure', 'install'] - -parallel = 1 - -buildininstalldir = True - -buildopts = ' && make plugins' - -sanity_check_paths = { - 'files': ["Chrysalis/Chrysalis", "Inchworm/bin/inchworm", "trinity-plugins/rsem/rsem-run-em"], - 'dirs': [""], -} - -# add install dir to PATH -modextrapaths = { - 'PATH': '' -} + ('Java', '1.7.0_80', '', True), + ('ant', '1.9.6', '-Java-%(javaver)s', True), + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] moduleclass = 'bio' -- GitLab From 1a68c82e7357bab9a1433cac4015b7727b2e5dea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 13:08:15 +0100 Subject: [PATCH 0456/2133] more style fixes in BOINC easyconfigs --- .../easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb | 2 +- easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-GCC-4.8.2-client.eb | 2 +- .../easyconfigs/b/BOINC/BOINC-7.2.42-ictce-5.5.0-client.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb b/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb index 5d421fbcca..38d7535bfa 100644 --- a/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb +++ b/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb @@ -29,7 +29,7 @@ files_to_copy = [(['client/boin*[cd]'], 'bin')] # make sure the binary are available after installation sanity_check_paths = { - 'files': ["bin/boinc", "bin/boinccmd"], + 'files': ['bin/boinc', 'bin/boinccmd'], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-GCC-4.8.2-client.eb b/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-GCC-4.8.2-client.eb index 20337ea09b..be4ba09c0d 100644 --- a/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-GCC-4.8.2-client.eb +++ b/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-GCC-4.8.2-client.eb @@ -35,7 +35,7 @@ files_to_copy = [(['client/boinc', 'client/boinccmd'], 'bin')] # make sure the binary are available after installation sanity_check_paths = { - 'files': ["bin/boinc", ], + 'files': ['bin/boinc'], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-ictce-5.5.0-client.eb b/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-ictce-5.5.0-client.eb index 1915ed43fc..66f39d890d 100644 --- a/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-ictce-5.5.0-client.eb +++ b/easybuild/easyconfigs/b/BOINC/BOINC-7.2.42-ictce-5.5.0-client.eb @@ -35,7 +35,7 @@ files_to_copy = [(['client/boinc', 'client/boinccmd'], 'bin')] # make sure the binary are available after installation sanity_check_paths = { - 'files': ["bin/boinc", ], + 'files': ['bin/boinc'], 'dirs': [], } -- GitLab From ce152880cdb9bdb74c2fcc13921600734774f9f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 13:09:14 +0100 Subject: [PATCH 0457/2133] more style fixes in BioPython easyconfigs --- .../b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb | 3 +-- .../b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb index 45922449e6..a3dca17749 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb @@ -36,8 +36,7 @@ dependencies = [ sanity_check_paths = { 'files': [], 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, - 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version, - pyshortver), + 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version, pyshortver), 'lib/python%s/site-packages/BioSQL' % pyshortver] } diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb index cdbf5d2851..5efa64f0e0 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb @@ -36,8 +36,7 @@ dependencies = [ sanity_check_paths = { 'files': [], 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, - 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version, - pyshortver), + 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version, pyshortver), 'lib/python%s/site-packages/BioSQL' % pyshortver] } -- GitLab From 2ec7736f54ac1e201089653748e14f2694709a9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 13:09:38 +0100 Subject: [PATCH 0458/2133] more style fixes in Bismark easyconfigs --- easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb index 9fe13b94a1..ee96cc0a43 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -18,7 +18,7 @@ determine cytosine methylation states""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["http://www.bioinformatics.babraham.ac.uk/projects/bismark/"] -sources = ['%s_v%s.tar.gz' % (name.lower(), version)] +sources = ['%(namelower)s_v%(version)s.tar.gz'] dependencies = [('Bowtie2', '2.0.2')] -- GitLab From 91dc79ffd24e129aaabe5dedae544f39b5b1695b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 13:13:09 +0100 Subject: [PATCH 0459/2133] more style fixes in Bowtie2 easyconfigs --- .../b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb | 4 ++-- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb | 4 ++-- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb | 2 +- 9 files changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb index 89e89457fa..99061a9473 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb @@ -21,8 +21,8 @@ description = """Bowtie 2 is an ultrafast and memory-efficient tool toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s-%s-source.zip' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] # N.B. the download option above -> required for sourceforge moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb index e98e0de64e..13ddeb08e1 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb @@ -21,8 +21,8 @@ for aligning sequencing reads to long reference sequences.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s-%s-source.zip' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] # N.B. the download option above -> required for sourceforge moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb index ffd1114704..15a2db61d2 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb @@ -21,8 +21,8 @@ description = """Bowtie 2 is an ultrafast and memory-efficient tool toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s-%s-source.zip' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] # N.B. the download option above -> required for sourceforge moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb index f08ff35329..7f8fbd5ca6 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb @@ -22,8 +22,8 @@ description = """Bowtie 2 is an ultrafast and memory-efficient tool toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s-%s-source.zip' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] # N.B. the download option above -> required for sourceforge moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index dc88165bd7..361932b89c 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -17,12 +17,12 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s-source.zip' % (name.lower(), version)] +sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), - "doc", "example", "scripts", ] + "doc", "example", "scripts"] sanity_check_paths = { 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index f0363a6b44..02e855be5b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -17,7 +17,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s-source.zip' % (name.lower(), version)] +sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] files_to_copy = [ diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index 9de79dd21c..2877853840 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -17,7 +17,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s-source.zip' % (name.lower(), version)] +sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] files_to_copy = [ diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index 19af7a159b..58e8cf38d8 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -17,7 +17,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s-source.zip' % (name.lower(), version)] +sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] files_to_copy = [ diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb index cc0a728014..da15149173 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb @@ -17,7 +17,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s-source.zip' % (name.lower(), version)] +sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] files_to_copy = [ -- GitLab From 38a8cd70a6c9bd29ab4ea494dea62e119d74b0ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:16:32 +0100 Subject: [PATCH 0460/2133] more style fixes in CONTRAfold, Cube, cutadapt easyconfigs --- .../easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb | 2 +- .../easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb | 4 ++-- easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb | 3 ++- easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb | 3 ++- easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb | 3 ++- easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb | 3 ++- easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb | 3 ++- .../c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb | 2 +- .../c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb | 2 +- .../c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb | 2 +- .../c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb | 2 +- .../c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb | 2 +- .../c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb | 2 +- 14 files changed, 20 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb index 77c3defd88..7f2755eaba 100644 --- a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb @@ -14,7 +14,7 @@ description = ''' CONditional TRAining for RNA Secondary Structure Prediction ' toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] -sources = ['%s_v%s.tar.gz' % (name.lower(), version.replace('.', '_'))] +sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] patches = ['contrafold-gcc47.patch'] diff --git a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb index 856776f4e7..94eaf15f8d 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb @@ -38,8 +38,8 @@ configopts = "--with-qmake=$EBROOTQT/bin/qmake" sanity_check_paths = { 'files': ["bin/cube3%s" % x for x in ["", "-qt", "_clean", "_cmp", "_cut", "_diff", "_mean", "_merge", "_part", "_remap", "_score", "_stat", "_topoassist"]] + - ["bin/cube-config", "bin/tau2cube3", "include/cube3/Cube.h", "include/cube3/cube_error.h", - "include/stats/P2Statistic.h", "lib/libcube3.a", "lib/libcubew3.a", "lib/libstats.a"], + ["bin/cube-config", "bin/tau2cube3", "include/cube3/Cube.h", "include/cube3/cube_error.h", + "include/stats/P2Statistic.h", "lib/libcube3.a", "lib/libcubew3.a", "lib/libstats.a"], 'dirs': ["include/cubew3"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index 5cb3746c74..df627c9d7b 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -48,7 +48,8 @@ dependencies = [('Qt', '4.8.4')] configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), + ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb index 67d71a581b..ad5e3d68d5 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -34,7 +34,8 @@ dependencies = [('Qt', '4.8.4')] configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), + ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb index fb1b773cd4..5763a26ed1 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -40,7 +40,8 @@ dependencies = [('Qt', '4.8.6')] configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), + ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb index 27232c720c..ced2f5b555 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb @@ -40,7 +40,8 @@ dependencies = [('Qt', '4.8.4')] configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), + ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb index c04c268ec1..c274b99b8c 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb @@ -34,7 +34,8 @@ checksums = [ dependencies = [('Qt', '4.8.6')] sanity_check_paths = { - 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), + ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb index 6104aff87d..d487d344f6 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -31,7 +31,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt', 'lib/python2.7/site-packages/cutadapt/calign.%s' % SHLIB_EXT, ], + 'files': ['bin/cutadapt', 'lib/python2.7/site-packages/cutadapt/calign.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb index 47e9fde842..aceb217de4 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb @@ -31,7 +31,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt', 'lib/python2.7/site-packages/cutadapt/calign.%s' % SHLIB_EXT, ], + 'files': ['bin/cutadapt', 'lib/python2.7/site-packages/cutadapt/calign.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb index bb39813021..9d2802684e 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb @@ -29,7 +29,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt', ], + 'files': ['bin/cutadapt'], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb index b50da0fe87..edcade8044 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb @@ -29,7 +29,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt', ], + 'files': ['bin/cutadapt'], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb index a12667f4b2..6d660f5bc5 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb @@ -29,7 +29,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt', ], + 'files': ['bin/cutadapt'], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb index 6968ed00cd..7e135e5021 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb @@ -29,7 +29,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt', ], + 'files': ['bin/cutadapt'], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb index 9fe18ae0c4..ccfea59372 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb @@ -29,7 +29,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt', ], + 'files': ['bin/cutadapt'], 'dirs': [], } -- GitLab From d7194068b74cd1fed52b0be5abf062550386abf1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:22:10 +0100 Subject: [PATCH 0461/2133] more style fixes in ECore, QLogicMPI, wiki2beamer easyconfigs --- .../e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb | 2 +- .../q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb | 8 ++++---- .../wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 5 ++--- .../wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb | 5 ++--- .../wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb | 5 ++--- 5 files changed, 11 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb index fafcf623a0..56e86c8e44 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb @@ -21,7 +21,7 @@ sanity_check_paths = { 'files': ['arch/linux-rh5-x86_64/bin/%s' % x for x in ['absperm', 'FormationFactor', 'nmr', 'orterun', 'packer', 'randomwalkffmpi', 'unpacker']] + - ['absperm.sh', 'formationfactor.sh', 'nmr.sh', 'rw_formationfactor.sh'], + ['absperm.sh', 'formationfactor.sh', 'nmr.sh', 'rw_formationfactor.sh'], 'dirs': [], } diff --git a/easybuild/easyconfigs/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb b/easybuild/easyconfigs/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb index 20ed128824..657fc8204a 100644 --- a/easybuild/easyconfigs/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb +++ b/easybuild/easyconfigs/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb @@ -15,11 +15,11 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # download the rpm directly or get it from the .bin file and extract it with ./nameoffile.bin -x and type yes sources = [ - 'mpi-benchmark-%s.x86_64.rpm' % version, - 'mpi-libs-%s.x86_64.rpm' % version, - 'mpi-frontend-%s.i386.rpm' % version, + 'mpi-benchmark-%(version)s.x86_64.rpm', + 'mpi-libs-%(version)s.x86_64.rpm', + 'mpi-frontend-%(version)s.i386.rpm', 'qlogic-mpi-register-0.1.0-926.1005_rhel5_qlc.noarch.rpm', - 'mpi-devel-%s.noarch.rpm' % version + 'mpi-devel-%(version)s.noarch.rpm', ] makesymlinks = ['usr/lib', 'usr/lib64', 'usr/include', 'usr/bin'] diff --git a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb index dabd647780..e43780a277 100644 --- a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -22,9 +22,8 @@ description = """wiki2beamer converts a simple wiki-like syntax to complex LaTeX toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -# eg. http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5/wiki2beamer-0.9.5.zip/download -sources = ['wiki2beamer-0.9.5.zip'] -source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5', 'download'] +sources = ['wiki2beamer-%(version)s.zip'] +source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-%(version)s', 'download'] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb index 330c38528f..71553532b1 100644 --- a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb @@ -22,9 +22,8 @@ description = """wiki2beamer converts a simple wiki-like syntax to complex LaTeX toolchain = {'name': 'goolf', 'version': '1.4.10'} -# eg. http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5/wiki2beamer-0.9.5.zip/download -sources = ['wiki2beamer-0.9.5.zip'] -source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5', 'download'] +sources = ['wiki2beamer-%(version)s.zip'] +source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-%(version)s', 'download'] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb index d475ee038e..b2e2623f1f 100644 --- a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb @@ -22,9 +22,8 @@ description = """wiki2beamer converts a simple wiki-like syntax to complex LaTeX toolchain = {'name': 'ictce', 'version': '5.3.0'} -# eg. http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5/wiki2beamer-0.9.5.zip/download -sources = ['wiki2beamer-0.9.5.zip'] -source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5', 'download'] +sources = ['wiki2beamer-%(version)s.zip'] +source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-%(version)s', 'download'] python = 'Python' pyver = '2.7.3' -- GitLab From 74fb1ccb0b9a8db16345c98a01d606fc4fd859e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:26:47 +0100 Subject: [PATCH 0462/2133] style fix in FFmpeg easyconfigs --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2015a.eb | 2 +- easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.4-foss-2015a.eb | 2 +- easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.5-foss-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2015a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2015a.eb index c42dbf3d77..2a1ef9245e 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.4-intel-2015a.eb @@ -19,7 +19,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.4-foss-2015a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.4-foss-2015a.eb index 889d11e831..ecba492e06 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.4-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.4-foss-2015a.eb @@ -21,7 +21,7 @@ configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enab configopts += '--enable-libx264' sanity_check_paths = { - 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.5-foss-2015a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.5-foss-2015a.eb index 70c0c62421..3b5612efce 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.5-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.5-foss-2015a.eb @@ -21,7 +21,7 @@ configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enab configopts += '--enable-libx264' sanity_check_paths = { - 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], 'dirs': ['include'] -- GitLab From a79da37bd550ac5e0f6b8bf1dbe67da8fc515ba7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:29:32 +0100 Subject: [PATCH 0463/2133] style fix in FASTX-Toolkit easyconfigs --- .../FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb | 10 +++++----- .../FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb | 10 +++++----- .../FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb | 10 +++++----- .../FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb | 10 +++++----- 4 files changed, 20 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb index cc92c2f5a3..4bda1588f1 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb @@ -34,11 +34,11 @@ sanity_check_paths = { 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', - 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', - 'to_fasta', 'quality_filter', 'quality_trimmer', - 'masker']], + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', + 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', + 'to_fasta', 'quality_filter', 'quality_trimmer', + 'masker']], 'dirs': ['.'] } diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb index 98cc1b1ac3..3b0992eef6 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb @@ -34,11 +34,11 @@ sanity_check_paths = { 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', - 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', - 'to_fasta', 'quality_filter', 'quality_trimmer', - 'masker']], + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', + 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', + 'to_fasta', 'quality_filter', 'quality_trimmer', + 'masker']], 'dirs': ['.'] } diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb index 01f7d5e8e2..b9a9acd1bf 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb @@ -36,11 +36,11 @@ sanity_check_paths = { 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', - 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', - 'to_fasta', 'quality_filter', 'quality_trimmer', - 'masker']], + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', + 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', + 'to_fasta', 'quality_filter', 'quality_trimmer', + 'masker']], 'dirs': ['.'] } diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb index 0af3bc5808..1f15e35214 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb @@ -37,11 +37,11 @@ sanity_check_paths = { 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', - 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', - 'to_fasta', 'quality_filter', 'quality_trimmer', - 'masker']], + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', + 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', + 'to_fasta', 'quality_filter', 'quality_trimmer', + 'masker']], 'dirs': ['.'] } -- GitLab From f7ba552d3fbcd361d1538d0deac4c90c76f926bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:35:42 +0100 Subject: [PATCH 0464/2133] fix indent in FFTW easyconfigs --- .../easyconfigs/f/FFTW/FFTW-3.3.1-gompi-1.1.0-no-OFED.eb | 4 ++-- .../easyconfigs/f/FFTW/FFTW-3.3.2-gmvapich2-1.7.9a2.eb | 4 ++-- easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb | 4 ++-- .../easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12.eb | 4 ++-- .../easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12rc1.eb | 8 ++++---- easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb | 8 ++++---- .../easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb | 4 ++-- easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb | 4 ++-- .../easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12-no-OFED.eb | 4 ++-- easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12.eb | 4 ++-- easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.10.eb | 4 ++-- easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb | 4 ++-- .../easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb | 4 ++-- .../easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb | 4 ++-- easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb | 4 ++-- easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb | 4 ++-- 16 files changed, 36 insertions(+), 36 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.1-gompi-1.1.0-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.1-gompi-1.1.0-no-OFED.eb index ebce2cd9e3..0870e0a4fd 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.1-gompi-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.1-gompi-1.1.0-no-OFED.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.2-gmvapich2-1.7.9a2.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.2-gmvapich2-1.7.9a2.eb index 47f16bc4a3..39962ff9f0 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.2-gmvapich2-1.7.9a2.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.2-gmvapich2-1.7.9a2.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb index 228133848f..50af5b9be2 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12.eb index 7348b00826..a179659dbf 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12rc1.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12rc1.eb index d5647435f6..a5ea76020c 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12rc1.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmvapich2-1.7.12rc1.eb @@ -25,10 +25,10 @@ configopts = [ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb index 8f61ad3268..cf777562ee 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb @@ -25,10 +25,10 @@ configopts = [ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb index 0d10db3dc0..1c3d9dac4d 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb index 0d03ca311a..bc9593354f 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12-no-OFED.eb index 6d9e48f885..ef28bb596b 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12-no-OFED.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12.eb index 7e3372ad72..a66c54abe4 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.5.12.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.10.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.10.eb index 361d76b7d2..43a89950f1 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.10.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.10.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb index 83140eb85e..52dc0f0662 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb index 93a27c610b..1c30e50534 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb index 9cf62510e7..38fbcdb5bc 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb index 52ec320554..0e6bf98a48 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb index 13413d4abc..34e8f524fb 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb @@ -26,8 +26,8 @@ sanity_check_paths = { 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], 'dirs': ['lib/pkgconfig'], } -- GitLab From b01104101d3bf05f1b49f0a28d47310c6de63476 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:36:29 +0100 Subject: [PATCH 0465/2133] style fix in FIAT easyconfigs --- .../easyconfigs/f/FIAT/FIAT-1.1-ictce-5.2.0-Python-2.7.3.eb | 3 ++- .../easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../easyconfigs/f/FIAT/FIAT-1.1-intel-2014b-Python-2.7.8.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.2.0-Python-2.7.3.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.2.0-Python-2.7.3.eb index acfceb386c..7333fc753b 100644 --- a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.2.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.2.0-Python-2.7.3.eb @@ -11,7 +11,8 @@ arbitrary order instances of Jacobi-type quadrature rules on the same element sh toolchain = {'name': 'ictce', 'version': '5.2.0'} source_urls = [ - 'https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/'] + 'https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/', +] sources = [SOURCELOWER_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb index 25b886e5b9..b09c96da46 100644 --- a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb @@ -11,7 +11,8 @@ arbitrary order instances of Jacobi-type quadrature rules on the same element sh toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [ - 'https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/'] + 'https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/', +] sources = [SOURCELOWER_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-intel-2014b-Python-2.7.8.eb index cc9dc901e8..8515a18e69 100644 --- a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-intel-2014b-Python-2.7.8.eb @@ -11,7 +11,8 @@ arbitrary order instances of Jacobi-type quadrature rules on the same element sh toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [ - 'https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/'] + 'https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/', +] sources = [SOURCELOWER_TAR_GZ] python = "Python" -- GitLab From 11e4d8832a48907aee1a94a84f4bfc37d41125d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:45:14 +0100 Subject: [PATCH 0466/2133] style fixes in GCCcore easyconfig --- easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index 2e4f04adbb..268b052687 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -13,8 +13,7 @@ mpfr_version = '3.1.2' gcc_name = 'GCC' source_urls = [ - 'http://ftpmirror.gnu.org/%s/%s-%s' % (gcc_name.lower(), gcc_name.lower(), - version), # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official -- GitLab From f6c5d7b5a24f3aa4f0134411d67e5314e23425c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:47:06 +0100 Subject: [PATCH 0467/2133] style fixes in GHC easyconfigs --- easybuild/easyconfigs/g/GHC/GHC-6.12.3.eb | 4 ++-- easybuild/easyconfigs/g/GHC/GHC-7.4.2-goalf-1.1.0-no-OFED.eb | 4 ++-- easybuild/easyconfigs/g/GHC/GHC-7.4.2-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/g/GHC/GHC-7.6.2-goalf-1.1.0-no-OFED.eb | 4 ++-- easybuild/easyconfigs/g/GHC/GHC-7.6.2-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/g/GHC/GHC-7.8.3-goalf-1.1.0-no-OFED.eb | 4 ++-- easybuild/easyconfigs/g/GHC/GHC-7.8.3-goolf-1.4.10.eb | 4 ++-- 7 files changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/g/GHC/GHC-6.12.3.eb b/easybuild/easyconfigs/g/GHC/GHC-6.12.3.eb index 0b40688cd7..125cb4abdd 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-6.12.3.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-6.12.3.eb @@ -6,7 +6,7 @@ description = """The Glorious/Glasgow Haskell Compiler""" toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['%s-%s-x86_64-unknown-linux-n.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +sources = ['%(namelower)s-%(version)s-x86_64-unknown-linux-n.tar.bz2'] +source_urls = ['http://www.haskell.org/ghc/dist/%(version)s/'] moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GHC/GHC-7.4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GHC/GHC-7.4.2-goalf-1.1.0-no-OFED.eb index fbac11c814..08afbb7d98 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-7.4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-7.4.2-goalf-1.1.0-no-OFED.eb @@ -7,8 +7,8 @@ description = """The Glorious/Glasgow Haskell Compiler""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -sources = ['%s-%s-src.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] +source_urls = ['http://www.haskell.org/ghc/dist/%(version)s/'] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/g/GHC/GHC-7.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GHC/GHC-7.4.2-goolf-1.4.10.eb index 76088a4fcb..2f7b37d7ff 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-7.4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-7.4.2-goolf-1.4.10.eb @@ -6,8 +6,8 @@ description = """The Glorious/Glasgow Haskell Compiler""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} -sources = ['%s-%s-src.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] +source_urls = ['http://www.haskell.org/ghc/dist/%(version)s/'] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goalf-1.1.0-no-OFED.eb index ab5b8f6d40..898e8c42ae 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goalf-1.1.0-no-OFED.eb @@ -6,8 +6,8 @@ description = """GHC is the Glasgow Haskell Compiler.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -sources = ['%s-%s-src.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] +source_urls = ['http://www.haskell.org/ghc/dist/%(version)s/'] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goolf-1.4.10.eb index a2a6d5433e..60a039090d 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-7.6.2-goolf-1.4.10.eb @@ -5,8 +5,8 @@ homepage = 'http://www.haskell.org/ghc' description = """GHC is the Glasgow Haskell Compiler.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s-src.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] +source_urls = ['http://www.haskell.org/ghc/dist/%(version)s/'] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goalf-1.1.0-no-OFED.eb index 52ae11225d..2a900a5028 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goalf-1.1.0-no-OFED.eb @@ -5,8 +5,8 @@ homepage = 'http://www.haskell.org/ghc' description = """GHC is the Glasgow Haskell Compiler.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -sources = ['%s-%s-src.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] +source_urls = ['http://www.haskell.org/ghc/dist/%(version)s/'] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goolf-1.4.10.eb index b6feb9a68c..1a594faa37 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-7.8.3-goolf-1.4.10.eb @@ -5,8 +5,8 @@ homepage = 'http://www.haskell.org/ghc' description = """GHC is the Glasgow Haskell Compiler.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s-src.tar.bz2' % (name.lower(), version)] -source_urls = ['http://www.haskell.org/ghc/dist/%s/' % version] +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] +source_urls = ['http://www.haskell.org/ghc/dist/%(version)s/'] dependencies = [ ('GMP', '5.0.5'), -- GitLab From 795652300909c7987146e33179ed0f3f9b241610 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:48:28 +0100 Subject: [PATCH 0468/2133] style fixes in GLib easyconfig --- easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb index c44d4a669f..e534334b71 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -5,7 +5,8 @@ version = '2.41.2' homepage = 'http://www.gtk.org/' description = """GLib is one of the base libraries of the GTK+ project""" -toolchain = {'name': 'intel', 'version': '2014b'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) + +toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] -- GitLab From 4b2794986fa4ad396adca83b7656b3e0d0c01e6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:49:55 +0100 Subject: [PATCH 0469/2133] style fixes in glproto easyconfig --- .../g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb | 3 +-- easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb | 3 +-- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb | 3 +-- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb | 3 +-- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb | 3 +-- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb | 3 +-- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb | 3 +-- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb | 3 +-- 8 files changed, 8 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb index a111fa37d7..f9c5e14a8e 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb @@ -13,8 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb index 824d2e05e3..06b846c04c 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb @@ -12,8 +12,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb index fbc9e27321..42dc60dd5e 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb @@ -13,8 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb index 69cf5deb96..8b99a901c9 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb @@ -13,8 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb index 99f5e68e02..6ccc91bb75 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb @@ -14,8 +14,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb index 828a170d20..2566876879 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb @@ -13,8 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb index e647894422..4eb87a66ef 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb @@ -13,8 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb index 251ef35798..a1f9a0b9d2 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb @@ -13,8 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', - 'glxtokens', 'internal/glcore']], + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], 'dirs': [], } -- GitLab From c1b65c22fe456329dabbdbff222b7d36bc2a2a2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:50:39 +0100 Subject: [PATCH 0470/2133] style fixes in gnutls easyconfigs --- .../easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb index 989ba1dc22..6090cb398e 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb @@ -22,7 +22,7 @@ configopts = "--with-guile-site-dir=$EBROOTGUILE" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'danetool', 'gnutls-cli', 'gnutls-cli-debug', 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + - ['lib/libgnutls%s' % x for x in ['.a', 'xx.a', '-xssl.a', '-openssl.a']], + ['lib/libgnutls%s' % x for x in ['.a', 'xx.a', '-xssl.a', '-openssl.a']], 'dirs': ['include/gnutls'], } diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb index 24da5d4615..f7c7021f17 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb @@ -21,7 +21,7 @@ configopts = "--with-guile-site-dir=$EBROOTGUILE" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'danetool', 'gnutls-cli', 'gnutls-cli-debug', 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + - ['lib/libgnutls%s' % x for x in ['.a', 'xx.a', '-xssl.a', '-openssl.a']], + ['lib/libgnutls%s' % x for x in ['.a', 'xx.a', '-xssl.a', '-openssl.a']], 'dirs': ['include/gnutls'], } diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb index 28416d4ec1..d883037773 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb @@ -32,8 +32,8 @@ configopts = "--with-guile-site-dir=$EBROOTGUILE --enable-openssl-compatibility sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'crywrap', 'gnutls-cli', 'gnutls-cli-debug', 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + - ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]] + - ['lib/guile/%s/guile-gnutls-v-2.so' % guileshortver], + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]] + + ['lib/guile/%s/guile-gnutls-v-2.so' % guileshortver], 'dirs': ['include/gnutls'], } -- GitLab From d1f8711aa4067a44954d65c1353edea3adde79b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 14:52:10 +0100 Subject: [PATCH 0471/2133] style fixes in guile easyconfigs --- easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb | 3 ++- easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb | 3 ++- .../easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb | 3 ++- easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb | 3 ++- easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb | 3 ++- easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb | 3 ++- 8 files changed, 16 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb index 561706f56f..65946ec224 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb @@ -24,7 +24,8 @@ dependencies = [ configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb index ad804aa4b1..8e2c6a3db0 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb @@ -24,7 +24,8 @@ dependencies = [ configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb index bfbad1d7a3..35f61dcc34 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb @@ -24,7 +24,8 @@ dependencies = [ configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb index 04db861e00..1ff3a6fc78 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb @@ -23,7 +23,8 @@ dependencies = [ configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb index 0d3cfc351b..88054289c0 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb @@ -24,7 +24,8 @@ dependencies = [ configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb index 18eb7970f8..0ed91b3039 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb @@ -24,7 +24,8 @@ dependencies = [ configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb index d66e7cf118..d10a3259ca 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb @@ -24,7 +24,8 @@ dependencies = [ configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], 'dirs': [] } diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb index 766148f244..ecd844f29d 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb @@ -24,7 +24,8 @@ dependencies = [ configopts = " --enable-error-on-warning=no" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], 'dirs': [] } -- GitLab From 4985135790c013dc68da43c93fe6448d89f09b76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 16:27:13 +0200 Subject: [PATCH 0472/2133] add easyconfig FFmpeg-2.8.6-intel-2016a.eb, add easyconfig Yasm-1.3.0-intel-2016a.eb, add easyconfig x264-20160114-intel-2016a.eb --- .../f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb | 30 ++++++++++++++++++ .../x/x264/x264-20160114-intel-2016a.eb | 24 ++++++++++++++ .../y/Yasm/Yasm-1.3.0-intel-2016a.eb | 31 +++++++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20160114-intel-2016a.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb new file mode 100644 index 0000000000..feaec72ba5 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.6' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.11.08'), + ('zlib', '1.2.8'), + ('x264', '20160114'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x264/x264-20160114-intel-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160114-intel-2016a.eb new file mode 100644 index 0000000000..9937ee8cc3 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160114-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160114' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://ftp.videolan.org/pub/videolan/x264/snapshots/'] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb new file mode 100644 index 0000000000..b5dae68924 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 6175a91c0e8ecafc5cdd7becc881ca1c35f47248 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 16 Feb 2016 16:05:59 +0100 Subject: [PATCH 0473/2133] Add support for BioPerl in Velvet so VelvetOptimizer can use it. --- ...BioPerl-1.6.923-intel-2015b-Perl-5.20.3.eb | 26 +++++++++++++++++++ .../Velvet-1.2.10-intel-2015b-mt-kmer_100.eb | 8 ++++++ .../Velvet-1.2.10-intel-2015b-mt-kmer_31.eb | 8 ++++++ 3 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-intel-2015b-Perl-5.20.3.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-intel-2015b-Perl-5.20.3.eb new file mode 100644 index 0000000000..13d2badd18 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-intel-2015b-Perl-5.20.3.eb @@ -0,0 +1,26 @@ +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.6.923' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.tar.gz' % version.replace('.', '-')] + +perl = 'Perl' +perlver = '5.20.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('DB_File', '1.831', versionsuffix), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb index 52c0ab85db..03213c3c49 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb @@ -24,6 +24,14 @@ toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} sources = ['%(namelower)s_%(version)s.tgz'] source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] +perl = 'Perl' +perlver = '5.20.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + ('BioPerl', '1.6.923', versionsuffix), +] + buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb index c23584dddd..5c33817b8c 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb @@ -24,6 +24,14 @@ toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} sources = ['%(namelower)s_%(version)s.tgz'] source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] +perl = 'Perl' +perlver = '5.20.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + ('BioPerl', '1.6.923', versionsuffix), +] + # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] -- GitLab From 01fe0b406351d74228ca08c8d2775562634e3a97 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 19:31:50 +0200 Subject: [PATCH 0474/2133] modify easyconfig FFmpeg-2.8.6-intel-2016a.eb --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb index feaec72ba5..40be8fe314 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb @@ -21,7 +21,7 @@ configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enab configopts += '--enable-libx264' sanity_check_paths = { - 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], 'dirs': ['include'] -- GitLab From d3900a63b39890408135f6ecb109e1f650039ecb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 22:28:34 +0100 Subject: [PATCH 0475/2133] more style fixes in Infernal --- .../i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb index 7c8fc6de1a..807ce3ee01 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb @@ -27,7 +27,7 @@ source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', - 'fetch', 'press', 'scan', 'search', 'stat']], + 'fetch', 'press', 'scan', 'search', 'stat']], 'dirs': [] } diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb index c22660d902..9c4049ce58 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb @@ -27,7 +27,7 @@ source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', - 'fetch', 'press', 'scan', 'search', 'stat']], + 'fetch', 'press', 'scan', 'search', 'stat']], 'dirs': [] } diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb index 38ffbd9b19..3fb03037b9 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb @@ -27,7 +27,7 @@ source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', - 'fetch', 'press', 'scan', 'search', 'stat']], + 'fetch', 'press', 'scan', 'search', 'stat']], 'dirs': [] } diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb index 8e85417cc3..ee33a329e8 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb @@ -27,7 +27,7 @@ source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', - 'fetch', 'press', 'scan', 'search', 'stat']], + 'fetch', 'press', 'scan', 'search', 'stat']], 'dirs': [] } -- GitLab From 2f05752d75f5095f5e81705cba584632cd933a7e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 22:34:07 +0100 Subject: [PATCH 0476/2133] style fixes in libXmu easyconfigs --- .../easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb | 7 ++----- .../easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.5.14.eb | 7 ++----- .../easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb | 2 +- .../l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb | 2 +- 5 files changed, 7 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb index 5db2a158ca..2aab0fa578 100644 --- a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb @@ -18,11 +18,8 @@ dependencies = [ ('libXt', '1.1.4'), ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in [ - '%(name)s.a', '%(name)s.so', - ] - ], - 'dirs': [] + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%%(name)s.%s' % SHLIB_EXT]], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.5.14.eb index d781bd04fe..f13c6ad715 100644 --- a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.5.14.eb @@ -18,11 +18,8 @@ dependencies = [ ('libXt', '1.1.4'), ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in [ - '%(name)s.a', '%(name)s.so', - ] - ], - 'dirs': [] + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%%(name)s.%s' % SHLIB_EXT]], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb index 5ab7c61a44..3bb4dae201 100644 --- a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb @@ -18,7 +18,7 @@ dependencies = [ ('libXpm', '3.5.11'), ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%%(name)s.%s' % SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb index df5f4eeafa..2f2b809d17 100644 --- a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('libXpm', '3.5.11'), ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%%(name)s.%s' % SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb index 083f86b1a3..de13f643a2 100644 --- a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb @@ -19,7 +19,7 @@ dependencies = [ ('libXpm', '3.5.11'), ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%%(name)s.%s' % SHLIB_EXT]], 'dirs': [], } -- GitLab From d1585908aa790a8f9aca3727354602e50427eeac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 22:41:39 +0100 Subject: [PATCH 0477/2133] style fixes in libreadline easyconfigs --- .../l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb | 4 ++-- .../l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb | 4 ++-- .../l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb | 4 ++-- .../l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb | 4 ++-- .../l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb | 4 ++-- .../l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb | 4 ++-- .../l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb | 4 ++-- .../l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb | 4 ++-- .../l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb | 4 ++-- .../l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb | 4 ++-- .../l/libreadline/libreadline-6.2-goolf-1.4.10.eb | 4 ++-- .../l/libreadline/libreadline-6.2-goolf-1.5.14.eb | 4 ++-- .../l/libreadline/libreadline-6.2-ictce-4.0.10.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb | 4 ++-- .../l/libreadline/libreadline-6.2-ictce-4.1.13.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb | 4 ++-- .../l/libreadline/libreadline-6.2-iomkl-4.6.13.eb | 4 ++-- .../l/libreadline/libreadline-6.2-iqacml-3.7.3.eb | 4 ++-- .../l/libreadline/libreadline-6.2-iqacml-4.4.13.eb | 4 ++-- .../l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb | 4 ++-- .../l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb | 4 ++-- .../l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb | 4 ++-- .../l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb | 4 ++-- .../l/libreadline/libreadline-6.3-foss-2015.05.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb | 4 ++-- .../l/libreadline/libreadline-6.3-gimkl-2.11.5.eb | 4 ++-- .../l/libreadline/libreadline-6.3-gompi-1.5.16.eb | 4 ++-- .../l/libreadline/libreadline-6.3-goolf-1.4.10.eb | 4 ++-- .../l/libreadline/libreadline-6.3-goolf-1.5.14.eb | 4 ++-- .../l/libreadline/libreadline-6.3-goolf-1.7.20.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb | 5 ++--- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb | 5 ++--- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb | 4 ++-- .../l/libreadline/libreadline-6.3-intel-2014.06.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb | 4 ++-- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb | 4 ++-- 46 files changed, 92 insertions(+), 94 deletions(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb index 4dd7cf1754..17ca0fce10 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb index 9d00ffb356..8d2ea29b4c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb index 0643af2756..aea7099ee4 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb index 588120ecab..7216c9ca1c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb index 7da7fb3704..a36ac06d74 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb index 7c3f729114..4425696364 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb index 1a77989db2..8892dfc907 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb index b6b43d3824..7778abffff 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb index 80b3a5a0d2..157a15b6bb 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb index 854b550334..6a9bcf9cdd 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb index 2efb23ba2e..c5324cbad1 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb index d88ab955d5..b07b7634b9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb index 962152ab77..853816b19b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb index b8808453c0..26cadb84b9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb index 8f1f90ef44..055d457da0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb index 982a87c7a5..6f9a153abf 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb index eef6f459fc..a4bce470a5 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb index 74795ae7ed..15a227218e 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb index ab71b53ec7..9236fd84d0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb index cd50046e7d..7435fb5029 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb index 5642e6cf66..a669b4f5be 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb index 076e004cc9..a120dd4307 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb index e3b44ca6d3..65fe6a0a4e 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb index 614b7bd324..fd2b32116b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb index 89fb87f2b4..33718181a7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb index 8b23cf9ec2..252a86c527 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb @@ -21,8 +21,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb index 900f704348..afd0f9f313 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb index b7b9cde8c0..05d8476935 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb index c11aec2551..362df4f9bd 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 7ee9565173..763ccd9488 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb index 648d05fb6e..d3b76459b6 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb index 0b20f1e897..66ecad79ff 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb index b43dd2d7e6..037141ab77 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb index 24911170bc..fb2145ca85 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb index bbba152986..8845b7c009 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb index b30c90c988..793dcaf0af 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb index c30f50b9af..e594babc96 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb index f3b5e8f280..ec5413615c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb index 9556601362..35af50be83 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb @@ -24,9 +24,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in - ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', - 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb index a59ced555e..2db2e85326 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb @@ -24,9 +24,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in - ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', - 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb index 6db8fe535c..c9c675d484 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb index f1faaddd9c..46eef59b19 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb index b50756b18b..583b41298f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb index b04629e2d3..3e67c20449 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb index 5a7988af7c..2c8752c400 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb index b871f9f93f..de76493eec 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb @@ -22,8 +22,8 @@ preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } -- GitLab From bd7b9fd525a9f2a8491cd3f7b1cbcb1e4c841f0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Feb 2016 22:42:42 +0100 Subject: [PATCH 0478/2133] style fixes in libunistring easyconfigs --- .../l/libunistring/libunistring-0.9.3-GNU-4.9.3-2.25.eb | 4 ++-- .../l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb | 4 ++-- .../l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb | 4 ++-- .../l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb | 4 ++-- .../l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb | 4 ++-- .../l/libunistring/libunistring-0.9.3-intel-2015a.eb | 4 ++-- 6 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GNU-4.9.3-2.25.eb index 82f0603122..be0b09dcd1 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GNU-4.9.3-2.25.eb @@ -16,8 +16,8 @@ parallel = 1 sanity_check_paths = { 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], 'dirs': ['include/unistring'], } diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb index 59ff430657..299596c2dc 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb @@ -16,8 +16,8 @@ parallel = 1 sanity_check_paths = { 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], 'dirs': ['include/unistring'], } diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb index 35adecc8cc..15da458c2e 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb @@ -15,8 +15,8 @@ parallel = 1 sanity_check_paths = { 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], 'dirs': ['include/unistring'], } diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb index 038fce3de2..0302ef0229 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb @@ -18,8 +18,8 @@ parallel = 1 sanity_check_paths = { 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], 'dirs': ['include/unistring'], } diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb index 7f7fae3c87..1a64772a1e 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb @@ -18,8 +18,8 @@ parallel = 1 sanity_check_paths = { 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], 'dirs': ['include/unistring'], } diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb index 41074c5f41..4bce236806 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb @@ -18,8 +18,8 @@ parallel = 1 sanity_check_paths = { 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], 'dirs': ['include/unistring'], } -- GitLab From 29eaaf802b48c7c51b9e6fe78538c75fb6d2e70a Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 17 Feb 2016 10:22:48 +0100 Subject: [PATCH 0479/2133] Add DB_File dep. --- .../DB_File-1.831-intel-2015b-Perl-5.20.3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb new file mode 100644 index 0000000000..051ab1254e --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.831' + +homepage = 'http://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('DB', '2.7.7')] + +perl = 'Perl' +perlver = '5.20.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), +] + +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DB_File.pm' % (perlmajver, perlver)], + 'dirs': [], +} + +moduleclass = 'data' + -- GitLab From 4616904582be192cdb264ed5cd9dabdd24d377a4 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 17 Feb 2016 10:52:37 +0100 Subject: [PATCH 0480/2133] Fix versionsuffix. --- .../v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb | 3 +-- .../v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb index 03213c3c49..70e8d09dda 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb @@ -26,10 +26,9 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] perl = 'Perl' perlver = '5.20.3' -versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ - ('BioPerl', '1.6.923', versionsuffix), + ('BioPerl', '1.6.923', '-%s-%s' % (perl, perlver)), ] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb index 5c33817b8c..950d5d555a 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb @@ -26,10 +26,9 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] perl = 'Perl' perlver = '5.20.3' -versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ - ('BioPerl', '1.6.923', versionsuffix), + ('BioPerl', '1.6.923', '-%s-%s' % (perl, perlver)), ] # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous -- GitLab From 15e5a58569408a5e07b0ed65503c5213ccff5785 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 17 Feb 2016 11:38:42 +0100 Subject: [PATCH 0481/2133] Use Perl suffix and factor out 'kmer' --- ... => Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb} | 5 +++-- ...b => Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb} | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/v/Velvet/{Velvet-1.2.10-intel-2015b-mt-kmer_100.eb => Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb} (90%) rename easybuild/easyconfigs/v/Velvet/{Velvet-1.2.10-intel-2015b-mt-kmer_31.eb => Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb} (91%) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb similarity index 90% rename from easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb rename to easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb index 70e8d09dda..1c6d79be47 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb @@ -13,7 +13,6 @@ name = 'Velvet' version = '1.2.10' -versionsuffix = '-mt-kmer_100' homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' description = """Sequence assembler for very short reads""" @@ -26,12 +25,14 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] perl = 'Perl' perlver = '5.20.3' +kmer = '100' +versionsuffix = '-mt-kmer_%s-%s-%s' % (kmer, perl, perlver) dependencies = [ ('BioPerl', '1.6.923', '-%s-%s' % (perl, perlver)), ] -buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % kmer postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb similarity index 91% rename from easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb rename to easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb index 950d5d555a..3f031878a4 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb @@ -13,7 +13,6 @@ name = 'Velvet' version = '1.2.10' -versionsuffix = '-mt-kmer_31' homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' description = """Sequence assembler for very short reads""" @@ -26,13 +25,15 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] perl = 'Perl' perlver = '5.20.3' +kmer = '31' +versionsuffix = '-mt-kmer_%s-%s-%s' % (kmer, perl, perlver) dependencies = [ ('BioPerl', '1.6.923', '-%s-%s' % (perl, perlver)), ] # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous -buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % kmer postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] -- GitLab From bb11692efbd8e5828a4f150f0eb34e61ee0e3495 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 17 Feb 2016 11:58:01 +0100 Subject: [PATCH 0482/2133] Messing w/ the %s vs %%(perl)s style interpolation. --- .../Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb | 4 ++-- .../Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb index 1c6d79be47..8102a2d352 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb @@ -26,10 +26,10 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] perl = 'Perl' perlver = '5.20.3' kmer = '100' -versionsuffix = '-mt-kmer_%s-%s-%s' % (kmer, perl, perlver) +versionsuffix = '-mt-kmer_%s-%%(perl)s-%%(perlver)s' % kmer dependencies = [ - ('BioPerl', '1.6.923', '-%s-%s' % (perl, perlver)), + ('BioPerl', '1.6.923', '-%(perl)s-%(perlver)s'), ] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % kmer diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb index 3f031878a4..15491a3ef4 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb @@ -26,10 +26,10 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] perl = 'Perl' perlver = '5.20.3' kmer = '31' -versionsuffix = '-mt-kmer_%s-%s-%s' % (kmer, perl, perlver) +versionsuffix = '-mt-kmer_%s-%%(perl)s-%%(perlver)s' % kmer dependencies = [ - ('BioPerl', '1.6.923', '-%s-%s' % (perl, perlver)), + ('BioPerl', '1.6.923', '-%(perl)s-%(perlver)s'), ] # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous -- GitLab From 012d718821e15861595c5e5fddbed80a02a7ad3f Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Wed, 17 Feb 2016 12:06:24 +0100 Subject: [PATCH 0483/2133] Use of source name template --- easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb index 742b46640d..5b2154b146 100644 --- a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb +++ b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb @@ -19,7 +19,7 @@ description = """rpmrebuild is a tool to build an RPM file from a package that h toolchain = {'version': 'dummy', 'name': 'dummy'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%s-%s.tar.gz' % (name.lower(), version)] +sources = [SOURCELOWER_TAR_GZ] modextrapaths = {'PATH': ['']} modextravars = {'RPMREBUILD_ROOT_DIR': '%(installdir)s'} -- GitLab From d07783ab0ce8fff472e9ce4a981e88a17a3f9cc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 14:04:47 +0100 Subject: [PATCH 0484/2133] additional style fixes in MCR easyconfigs --- easybuild/easyconfigs/m/MCR/MCR-R2014a.eb | 3 ++- easybuild/easyconfigs/m/MCR/MCR-R2015a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb index 939aae0af8..1c593f7430 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb @@ -9,7 +9,8 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/'] + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] dependencies = [('Java', '1.8.0_31')] diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb index 29d916a9f4..f459048eeb 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb @@ -9,7 +9,8 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/'] + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] dependencies = [('Java', '1.8.0_31')] -- GitLab From ef94057e3d56e9bd6be1ddd85e7f84230fa3824d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 14:06:03 +0100 Subject: [PATCH 0485/2133] additional style fixes in MultiNest easyconfigs --- .../easyconfigs/m/MultiNest/MultiNest-3.10-intel-2015b.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2015b.eb b/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2015b.eb index 37117a4be0..13350aae1f 100644 --- a/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2015b.eb +++ b/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2015b.eb @@ -18,8 +18,9 @@ builddependencies = [('CMake', '3.4.0')] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ackley', 'eggboxC', 'eggboxC++', 'gaussian', 'gauss_shell', 'himmelblau', 'obj_detect', 'rosenbrock']] + - ['lib/lib%s' % x for x in ['multinest.a', 'multinest_mpi.a', 'multinest_mpi.%s' % SHLIB_EXT, 'multinest.%s' % SHLIB_EXT]] + - ['include/multinest.h'], + ['lib/lib%s' % x for x in ['multinest.a', 'multinest_mpi.a', 'multinest_mpi.%s' % SHLIB_EXT, + 'multinest.%s' % SHLIB_EXT]] + + ['include/multinest.h'], 'dirs': ['modules'], } -- GitLab From 7508ab4a860edb0e4e9720befbd94a0d926bffa1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 14:14:02 +0100 Subject: [PATCH 0486/2133] additional style fixes in NCO easyconfigs --- easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb | 7 ++++--- easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb | 2 +- .../n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb | 2 +- .../n/NCO/NCO-4.5.1-intel-2015a-Python-2.7.10.eb | 4 +++- 4 files changed, 9 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb index 010a358d92..7fd080e24f 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb @@ -20,9 +20,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['ncap2', 'ncatted', 'ncbo', 'ncdiff', 'ncea', 'ncecat', 'nces', 'ncflint', - 'ncks', 'ncpdq', 'ncra', 'ncrcat', 'ncrename']], - 'dirs': [], + 'files': ['bin/nc%s' % x for x in ['ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', 'flint', + 'ks', 'pdq', 'ra', 'rcat', 'rename']] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb index 98cce01c87..91425320d2 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb @@ -22,7 +22,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/nc%s' % x for x in ['ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename']] + - ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb index b0e417a669..b849d1d7cc 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.7-intel-2015b-Python-2.7.10.eb @@ -38,7 +38,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/nc%s' % x for x in ('ap', 'ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + - ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.5.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/NCO/NCO-4.5.1-intel-2015a-Python-2.7.10.eb index a6ab3c607d..88f85c4110 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.5.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.5.1-intel-2015a-Python-2.7.10.eb @@ -34,7 +34,9 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/nc%s' % x for x in ('ap', 'ap2', 'atted', 'bo', 'ecat', 'flint', 'ks', 'pdq', 'ra', 'rename', 'wa')], + 'files': ['bin/nc%s' % x for x in ('ap', 'ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], 'dirs': ['include'], } -- GitLab From 0aae47387ccc460d950af4679a6f5fab44cec6b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 14:17:41 +0100 Subject: [PATCH 0487/2133] additional style fixes in ncurses easyconfigs --- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 6 +++--- .../n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.4.0.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb | 6 +++--- 55 files changed, 165 insertions(+), 165 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 701d4f5b32..634fda5b4d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 5039753d61..4f21474dcf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 19a447fb27..a71c6aab72 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index fba7788bef..f2a6bbb76a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 0af76e5309..5ef3e822ad 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index f539996103..96cc600747 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 266e0372ef..a1409a10e6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb index 6aaa93881b..6b7bb1c347 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb index 376ac3284c..01680ab5b7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb index b4e88ed329..6f00fdbd51 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index 597f627fd5..37a2fff35a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index 18b80dd5b4..96e1f45472 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 5e59d7a015..5dd295c39e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 0e4f38f6b4..3071876ad2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index e71416ed21..c5e4c7e93d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb index 7d22fac6d5..a769a56170 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index f71a1ebf66..5125329966 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb index 7496dc385d..82fd4d66d0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index 6fba11778b..7278bb4ccf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index f3025721f3..37d7e04809 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index a3e060e522..cff4af273d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index e5277365c6..b529181479 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index dcacd6eb8f..aaa5b2bd78 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -32,9 +32,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index 4438ab7164..f8ee92d094 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -30,9 +30,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 5bf835f0f9..9936cdbc6c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index b8cefe2085..b5428d27b0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index bd62e235e7..21128a21c5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb index c1ef51469e..e272a823d6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index a193ec004c..fa8d19afbb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index 95a00cbe48..cdf8cdb5ce 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb index 676d1b38e4..9a1708ba34 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index fd2250632c..36b5053e62 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 1862eb1eb3..292cec33e2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 5dc04b26ca..0b4bbba9ad 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 4ebf61d594..b5099d8795 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 8e3894ae7f..94e44f7817 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 1871a9bd84..b1c1a88d75 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 67488363dc..fed58a89dd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 278feeefd1..bf996a362f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.4.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.4.0.eb index 63a4e678bd..3c9a948aef 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.4.0.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index acf30f2ceb..671b5796ac 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index d70ebf22fe..61118f9005 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index 19ed9c2c9e..278cc8d64a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -29,9 +29,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index eba66cce94..38c7d07988 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb index 252f009474..d67fc45cbf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 176634e08b..9fa751952c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 3d58c86438..24097805bc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index f18c6b0cd2..115d1bd981 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index 56c27e1dd1..e4351873f4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 2360219b0e..529b47259f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 16f90cd0e9..dd70b0800a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb index 2ec6dcb703..eab9da36db 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb @@ -27,9 +27,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb index 4f00fe676a..4012f0e69b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb @@ -25,9 +25,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb index 83fce4b28a..6029357e96 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb @@ -25,9 +25,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb index e9bc3f20c2..852b0df6bb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb @@ -25,9 +25,9 @@ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], 'dirs': ['include', 'include/ncursesw'], } -- GitLab From 59a047ec1c48c40e1424d554b18746f02d519acd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 14:18:29 +0100 Subject: [PATCH 0488/2133] additional style fixes in nettle easyconfigs --- .../easyconfigs/n/nettle/nettle-2.6-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/nettle/nettle-2.6-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/nettle/nettle-2.6-goalf-1.1.0-no-OFED.eb index 19f109d73f..12e680ddbd 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-2.6-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-2.6-goalf-1.1.0-no-OFED.eb @@ -16,7 +16,7 @@ dependencies = [('GMP', '5.0.5')] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, - 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb index afeba6c842..b72cd92143 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [('GMP', '5.0.5')] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, - 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb index 264418e53b..e764834b2d 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb @@ -21,7 +21,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, - 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], 'dirs': ['include/nettle'], } -- GitLab From 4f40a85c7cc2a4a406dfa53e4327bc4d8590508f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 14:26:47 +0100 Subject: [PATCH 0489/2133] additional style fixes in Oger easyconfigs --- ...-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 22 ++++++------------- .../Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb | 22 ++++++------------- .../Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb | 19 ++++++---------- .../Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb | 19 ++++++---------- 4 files changed, 28 insertions(+), 54 deletions(-) diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 575449dbbf..26ed184aed 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -2,6 +2,7 @@ easyblock = "PythonPackage" name = 'Oger' version = '1.1.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://reservoir-computing.org/organic/engine' description = """The OrGanic Environment for Reservoir computing (Oger) toolbox is a Python toolbox, released under the @@ -13,27 +14,18 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['http://organic.elis.ugent.be/sites/organic.elis.ugent.be/files'] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - dependencies = [ - (python, pythonversion), - ("MDP", "3.3", versionsuffix), + ('Python', '2.7.3'), + ('MDP', '3.3', versionsuffix), ] options = {'modulename': name} sanity_check_paths = { - 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in - [ - 'datasets', 'evaluation', 'examples', 'gradient', - 'nodes', 'parallel', 'tests', 'utils', - ] - ] + 'files': ['lib/python%(pyshortver)s/site-packages/Oger/__init__.py'], + 'dirs': ['lib/python%%(pyshortver)s/site-packages/Oger/%s' % d for d in ['datasets', 'evaluation', 'examples', + 'gradient', 'nodes', 'parallel', + 'tests', 'utils']], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb index 2492882fca..ccf5582151 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-goolf-1.4.10-Python-2.7.3.eb @@ -2,6 +2,7 @@ easyblock = "PythonPackage" name = 'Oger' version = '1.1.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://reservoir-computing.org/organic/engine' description = """The OrGanic Environment for Reservoir computing (Oger) toolbox is a Python toolbox, released under the @@ -14,27 +15,18 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://organic.elis.ugent.be/sites/organic.elis.ugent.be/files'] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - dependencies = [ - (python, pythonversion), - ("MDP", "3.3", versionsuffix), + ('Python', '2.7.3'), + ('MDP', '3.3', versionsuffix), ] options = {'modulename': name} sanity_check_paths = { - 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in - [ - 'datasets', 'evaluation', 'examples', 'gradient', - 'nodes', 'parallel', 'tests', 'utils', - ] - ] + 'files': ['lib/python%(pyshortver)s/site-packages/Oger/__init__.py'], + 'dirs': ['lib/python%%(pyshortver)s/site-packages/Oger/%s' % d for d in ['datasets', 'evaluation', 'examples', + 'gradient', 'nodes', 'parallel', + 'tests', 'utils']], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb index 5d36b14860..0a7a7d631b 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-4.0.6-Python-2.7.3.eb @@ -2,6 +2,7 @@ easyblock = "PythonPackage" name = 'Oger' version = '1.1.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://reservoir-computing.org/organic/engine' description = """The OrGanic Environment for Reservoir computing (Oger) toolbox is a Python toolbox, released under the @@ -13,24 +14,18 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ['http://organic.elis.ugent.be/sites/organic.elis.ugent.be/files'] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - dependencies = [ - (python, pythonversion), - ("MDP", "3.3", versionsuffix), + ('Python', '2.7.3'), + ('MDP', '3.3', versionsuffix), ] options = {'modulename': name} sanity_check_paths = { - 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in - ['datasets', 'evaluation', 'examples', 'gradient', 'nodes', 'parallel', 'tests', 'utils'] - ] + 'files': ['lib/python%(pyshortver)s/site-packages/Oger/__init__.py'], + 'dirs': ['lib/python%%(pyshortver)s/site-packages/Oger/%s' % d for d in ['datasets', 'evaluation', 'examples', + 'gradient', 'nodes', 'parallel', + 'tests', 'utils']], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb index 8c7ce0f3fb..f44806a8e5 100644 --- a/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/Oger/Oger-1.1.3-ictce-5.3.0-Python-2.7.3.eb @@ -2,6 +2,7 @@ easyblock = "PythonPackage" name = 'Oger' version = '1.1.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://reservoir-computing.org/organic/engine' description = """The OrGanic Environment for Reservoir computing (Oger) toolbox is a Python toolbox, released under the @@ -14,24 +15,18 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://organic.elis.ugent.be/sites/organic.elis.ugent.be/files'] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - dependencies = [ - (python, pythonversion), - ("MDP", "3.3", versionsuffix), + ('Python', '2.7.3'), + ('MDP', '3.3', versionsuffix), ] options = {'modulename': name} sanity_check_paths = { - 'files': ['lib/python2.7/site-packages/Oger/__init__.py'], - 'dirs': ['lib/python%s/site-packages/Oger/%s' % (pythonshortversion, dir) for dir in - ['datasets', 'evaluation', 'examples', 'gradient', 'nodes', 'parallel', 'tests', 'utils'] - ] + 'files': ['lib/python%(pyshortver)s/site-packages/Oger/__init__.py'], + 'dirs': ['lib/python%%(pyshortver)s/site-packages/Oger/%s' % d for d in ['datasets', 'evaluation', 'examples', + 'gradient', 'nodes', 'parallel', + 'tests', 'utils']], } moduleclass = 'data' -- GitLab From 4983db633f39e8f4fbf44da07b988f3a1d4e550a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 14:28:47 +0100 Subject: [PATCH 0490/2133] additional style fixes in OpenFOAM easyconfigs --- .../easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-goolf-1.4.10.eb | 7 ++++--- .../easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-ictce-6.1.5.eb | 7 ++++--- .../o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb | 7 ++++--- .../easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb | 7 ++++--- .../easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb | 7 ++++--- .../easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb | 7 ++++--- 6 files changed, 24 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-goolf-1.4.10.eb index 999d176f1a..f6e2827584 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-goolf-1.4.10.eb @@ -15,9 +15,10 @@ sources = [ 'ThirdParty-%(version)s.gtgz', ] -patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] builddependencies = [('flex', '2.5.35')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-ictce-6.1.5.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-ictce-6.1.5.eb index 65d62e3845..2836d4ab9d 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.0.1-ictce-6.1.5.eb @@ -15,9 +15,10 @@ sources = [ 'ThirdParty-%(version)s.gtgz', ] -patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] builddependencies = [('flex', '2.5.38')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb index 1ac57ee5f3..eeefa3f7b2 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb @@ -15,9 +15,10 @@ sources = [ 'ThirdParty-%(version)s.tgz', ] -patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] builddependencies = [('flex', '2.5.35')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb index 6d09f89ac2..686251e8fe 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb @@ -15,9 +15,10 @@ sources = [ 'ThirdParty-%(version)s.tgz', ] -patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] builddependencies = [('flex', '2.5.35')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb index 9ab942e9ec..1a0fdd7519 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb @@ -15,9 +15,10 @@ sources = [ 'ThirdParty-%(version)s.tgz', ] -patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] builddependencies = [('flex', '2.5.35')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb index 0f4a8e96f8..823efd74ab 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb @@ -15,9 +15,10 @@ sources = [ 'ThirdParty-%(version)s.tgz', ] -patches = ['cleanup-OpenFOAM-%s.patch' % version, - ('cleanup-ThirdParty-%s.patch' % version, "..") # patch should not be applied in OpenFOAM subdir - ] +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] builddependencies = [('flex', '2.5.35')] -- GitLab From eb58f1626044a7efd55b2fb6cee07e3f1e64560f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 14:44:09 +0100 Subject: [PATCH 0491/2133] {vis}[intel/2016a] PyFFmpeg 2.1beta + FFmpeg 0.10.16 --- .../f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb | 30 +++ ...Fmpeg-2.1beta-intel-2016a-Python-2.7.11.eb | 33 +++ .../PyFFmpeg-2.1beta_Cython-fixes.patch | 199 ++++++++++++++++++ .../PyFFmpeg-2.1beta_ffmpegpath.patch | 19 ++ 4 files changed, 281 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_Cython-fixes.patch create mode 100644 easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_ffmpegpath.patch diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb new file mode 100644 index 0000000000..3b9215acdb --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '0.10.16' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.11.08'), + ('zlib', '1.2.8'), + ('x264', '20160114'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f4ffc86816 --- /dev/null +++ b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyFFmpeg' +version = '2.1beta' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/mhaller/pyffmpeg' +description = """Python FFmpeg wrapper""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/pyffmpeg/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'PyFFmpeg-%(version)s_ffmpegpath.patch', + 'PyFFmpeg-%(version)s_Cython-fixes.patch', +] + +dependencies = [ + ('Python', '2.7.11'), + ('FFmpeg', '0.10.16'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_Cython-fixes.patch b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_Cython-fixes.patch new file mode 100644 index 0000000000..30d4848e4f --- /dev/null +++ b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_Cython-fixes.patch @@ -0,0 +1,199 @@ +--- pyffmpeg-2.1beta/pyffmpeg.pyx.orig 2011-01-12 16:49:19.000000000 +0100 ++++ pyffmpeg-2.1beta/pyffmpeg.pyx 2016-02-17 14:09:02.007382083 +0100 +@@ -183,7 +183,6 @@ + # int height + # int pix_fmt + # int frame_number +-# int hurry_up + # int skip_idct + # int skip_frame + +@@ -220,7 +219,6 @@ + float b_quant_factor + int rc_strategy + int b_frame_strategy +- int hurry_up + int rtp_mode + int rtp_payload_size + int mv_bits +@@ -370,12 +368,12 @@ + int skip_loop_filter + + +- enum CodecType: +- CODEC_TYPE_UNKNOWN = -1 +- CODEC_TYPE_VIDEO = 0 +- CODEC_TYPE_AUDIO = 1 +- CODEC_TYPE_DATA = 2 +- CODEC_TYPE_SUBTITLE = 3 ++ enum AVMediaType: ++ AVMEDIA_TYPE_UNKNOWN = -1 ++ AVMEDIA_TYPE_VIDEO = 0 ++ AVMEDIA_TYPE_AUDIO = 1 ++ AVMEDIA_TYPE_DATA = 2 ++ AVMEDIA_TYPE_SUBTITLE = 3 + + struct AVCodec: + char *name +@@ -620,7 +618,7 @@ + AVInputFormat *av_probe_input_format(AVProbeData *pd, int is_opened) + AVInputFormat *av_probe_input_format2(AVProbeData *pd, int is_opened,int * score) + AVFormatContext * avformat_alloc_context() +- AVOutputFormat *guess_format(char *short_name, char *filename,char *mime_type) ++ AVOutputFormat *av_guess_format(char *short_name, char *filename,char *mime_type) + + cdef __registered + __registered = 0 +@@ -703,6 +701,7 @@ + + + def py_av_register_all(): ++ global __registered + if __registered: + return + __registered = 1 +@@ -761,10 +760,10 @@ + ############################################################################### + ## Some common settings + ############################################################################### +-TS_AUDIOVIDEO={'video1':(CODEC_TYPE_VIDEO, -1, {}), 'audio1':(CODEC_TYPE_AUDIO, -1, {})} +-TS_AUDIO={ 'audio1':(CODEC_TYPE_AUDIO, -1, {})} +-TS_VIDEO={ 'video1':(CODEC_TYPE_VIDEO, -1, {})} +-TS_VIDEO_PIL={ 'video1':(CODEC_TYPE_VIDEO, -1, {'outputmode':OUTPUTMODE_PIL})} ++TS_AUDIOVIDEO={'video1':(AVMEDIA_TYPE_VIDEO, -1, {}), 'audio1':(AVMEDIA_TYPE_AUDIO, -1, {})} ++TS_AUDIO={ 'audio1':(AVMEDIA_TYPE_AUDIO, -1, {})} ++TS_VIDEO={ 'video1':(AVMEDIA_TYPE_VIDEO, -1, {})} ++TS_VIDEO_PIL={ 'video1':(AVMEDIA_TYPE_VIDEO, -1, {'outputmode':OUTPUTMODE_PIL})} + + + +@@ -805,13 +804,13 @@ + # self.prepacket=None + # self.packet=&self.packetbufa + +- def __new__(self): ++ def __cinit__(self): + pass + + def dump(self): + pass + +- def open(self,char *filename, track_selector={'video1':(CODEC_TYPE_VIDEO, -1), 'audio1':(CODEC_TYPE_AUDIO, -1)}): ++ def open(self,char *filename, track_selector={'video1':(AVMEDIA_TYPE_VIDEO, -1), 'audio1':(AVMEDIA_TYPE_AUDIO, -1)}): + pass + + def close(self): +@@ -906,7 +905,6 @@ + skip_frame + skip_idct + skip_loop_filter +- hurry_up + dct_algo + idct_algo + +@@ -916,7 +914,7 @@ + self.observer=None + self.support_truncated=support_truncated + for k in args.keys(): +- if k not in [ "skip_frame", "skip_loop_filter", "skip_idct", "hurry_up", "hurry_mode", "dct_algo", "idct_algo", "check_start" ,"check_end"]: ++ if k not in [ "skip_frame", "skip_loop_filter", "skip_idct", "hurry_mode", "dct_algo", "idct_algo", "check_start" ,"check_end"]: + sys.stderr.write("warning unsupported arguments in stream initialization :"+k+"\n") + if self.Codec == NULL: + raise IOError("Unable to get decoder") +@@ -924,7 +922,6 @@ + self.CodecCtx.flags = self.CodecCtx.flags | CODEC_FLAG_TRUNCATED + avcodec_open(self.CodecCtx, self.Codec) + if args.has_key("hurry_mode"): +- self.CodecCtx.hurry_up=2 + self.CodecCtx.skip_loop_filter=32 + self.CodecCtx.skip_frame=32 + self.CodecCtx.skip_idct=32 +@@ -934,8 +931,6 @@ + self.CodecCtx.skip_idct=args["skip_idct"] + if args.has_key("skip_loop_filter"): + self.CodecCtx.skip_loop_filter=args["skip_loop_filter"] +- if args.has_key("hurry_up"): +- self.CodecCtx.skip_loop_filter=args["hurry_up"] + if args.has_key("dct_algo"): + self.CodecCtx.dct_algo=args["dct_algo"] + if args.has_key("idct_algo"): +@@ -1389,7 +1384,6 @@ + skip_frame + skip_idct + skip_loop_filter +- hurry_up + dct_algo + idct_algo + +@@ -1668,12 +1662,10 @@ + if (b) : + self.CodecCtx.skip_idct = AVDISCARD_BIDIR + self.CodecCtx.skip_frame = AVDISCARD_BIDIR +- self.CodecCtx.hurry_up = 1 + self.hurried_frames = 0 + else: + self.CodecCtx.skip_idct = 0 + self.CodecCtx.skip_frame = 0 +- self.CodecCtx.hurry_up = 0 + + ######################################## + ### +@@ -1832,7 +1824,7 @@ + cdef int with_readahead + cdef unsigned long long int seek_before_security_interval + +- def __new__(self,with_readahead=True,seek_before=4000): ++ def __cinit__(self,with_readahead=True,seek_before=4000): + self.filename = None + self.tracks=[] + self.ctracks=NULL +@@ -1902,7 +1894,7 @@ + + if (mode=="w"): + raise Exception,"Not yet supported sorry" +- self.FormatCtx.oformat = guess_format(NULL, filename_, NULL); ++ self.FormatCtx.oformat = av_guess_format(NULL, filename_, NULL); + if (self.FormatCtx.oformat==NULL): + raise Exception, "Unable to find output format for %s\n" + +@@ -1960,7 +1952,7 @@ + cdef AVFormatContext * oc + oc = avformat_alloc_context() + # Guess file format with file extention +- oc.oformat = guess_format(NULL, filename_, NULL); ++ oc.oformat = av_guess_format(NULL, filename_, NULL); + if (oc.oformat==NULL): + raise Exception, "Unable to find output format for %s\n" + # Alloc priv_data for format +@@ -2038,7 +2030,7 @@ + raise IOError("Unable to find specified Track") + + CodecCtx = self.FormatCtx.streams[trackno].codec +- if (s[0]==CODEC_TYPE_VIDEO): ++ if (s[0]==AVMEDIA_TYPE_VIDEO): + try: + vt=VideoTrack() + except: +@@ -2048,7 +2040,7 @@ + vt.init0(self,trackno, CodecCtx) ## here we are passing cpointers so we do a C call + vt.init(**s[2])## here we do a python call + self.tracks.append(vt) +- elif (s[0]==CODEC_TYPE_AUDIO): ++ elif (s[0]==AVMEDIA_TYPE_AUDIO): + try: + at=AudioTrack() + except: +@@ -2171,11 +2163,11 @@ + ## I don't know why it seems that Windows Cython have problem calling the correct virtual function + ## + ## +- if ct.CodecCtx.codec_type==CODEC_TYPE_VIDEO: ++ if ct.CodecCtx.codec_type==AVMEDIA_TYPE_VIDEO: + processed=True + vt=ct + vt.process_packet(self.packet) +- elif ct.CodecCtx.codec_type==CODEC_TYPE_AUDIO: ++ elif ct.CodecCtx.codec_type==AVMEDIA_TYPE_AUDIO: + processed=True + at=ct + at.process_packet(self.packet) diff --git a/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_ffmpegpath.patch b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_ffmpegpath.patch new file mode 100644 index 0000000000..e0487b1d98 --- /dev/null +++ b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_ffmpegpath.patch @@ -0,0 +1,19 @@ +--- pyffmpeg-2.1beta/setup.py.orig 2011-01-12 16:46:15.000000000 +0100 ++++ pyffmpeg-2.1beta/setup.py 2016-02-17 10:52:57.454775826 +0100 +@@ -33,7 +33,7 @@ + + else: + ffmpegpath = '/opt/ffmpeg' +- for x in [ os.environ["HOME"]+"build/ffmpeg", '/usr/local/ffmpeg', '/opt/ffmpeg' ]: ++ for x in [os.environ['EBROOTFFMPEG'], os.environ["HOME"]+"build/ffmpeg", '/usr/local/ffmpeg', '/opt/ffmpeg' ]: + try: + os.stat(x) + ffmpegpath = x +@@ -69,6 +69,7 @@ + map(lambda x: x not in result and result.append(x), deps) + return result + ++print "ffmpegpath: %s" % ffmpegpath + + libs = [ 'avformat', 'avcodec', 'avutil', 'swscale' ] + incdir = [ path_join(ffmpegpath, 'include'), "/usr/include/ffmpeg" , "./include" ] -- GitLab From b2a2d6723ee94ccddce194485a29fc04bcbb34e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 14:47:24 +0100 Subject: [PATCH 0492/2133] add comments in patch files --- .../easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_Cython-fixes.patch | 2 ++ .../easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_ffmpegpath.patch | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_Cython-fixes.patch b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_Cython-fixes.patch index 30d4848e4f..4370508444 100644 --- a/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_Cython-fixes.patch +++ b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_Cython-fixes.patch @@ -1,3 +1,5 @@ +fix compilation issues, cfr. https://code.google.com/archive/p/pyffmpeg/issues/44 +author: Kenneth Hoste (HPC-UGent) --- pyffmpeg-2.1beta/pyffmpeg.pyx.orig 2011-01-12 16:49:19.000000000 +0100 +++ pyffmpeg-2.1beta/pyffmpeg.pyx 2016-02-17 14:09:02.007382083 +0100 @@ -183,7 +183,6 @@ diff --git a/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_ffmpegpath.patch b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_ffmpegpath.patch index e0487b1d98..8196e01135 100644 --- a/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_ffmpegpath.patch +++ b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta_ffmpegpath.patch @@ -1,3 +1,5 @@ +specify FFmpeg install location in PyFFmpeg's setup.py +author: Kenneth Hoste (HPC-UGent) --- pyffmpeg-2.1beta/setup.py.orig 2011-01-12 16:46:15.000000000 +0100 +++ pyffmpeg-2.1beta/setup.py 2016-02-17 10:52:57.454775826 +0100 @@ -33,7 +33,7 @@ -- GitLab From a42c01e4c575fcabe8ef9ee7b182234edcd22bf1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 14:55:32 +0100 Subject: [PATCH 0493/2133] additional style fixes in ParMETIS easyconfigs --- .../p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb | 6 ++++-- .../easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb | 6 ++++-- .../easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb | 6 ++++-- .../easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb | 6 ++++-- .../easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb | 6 ++++-- .../p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb | 6 ++++-- .../easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb | 6 ++++-- .../easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb | 6 ++++-- .../easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb | 6 ++++-- 9 files changed, 36 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb index 42da94d19e..dbaf1f39f5 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goalf-1.1.0-no-OFED.eb @@ -11,8 +11,10 @@ description = """ParMETIS is an MPI-based parallel library that implements a var toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] sources = ['ParMetis-%s.tar.gz' % version] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb index 9da0a95728..8183de649d 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb @@ -11,8 +11,10 @@ description = """ParMETIS is an MPI-based parallel library that implements a var toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] sources = ['ParMetis-%s.tar.gz' % version] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb index 4357d1d8af..d03b34a63f 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-4.0.6.eb @@ -11,8 +11,10 @@ description = """ParMETIS is an MPI-based parallel library that implements a var toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] sources = ['ParMetis-%s.tar.gz' % version] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb index 2cb2e02d6a..11db9fe038 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb @@ -12,8 +12,10 @@ description = """ParMETIS is an MPI-based parallel library that implements a var toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] sources = ['ParMetis-%s.tar.gz' % version] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb index 9adb21d10a..529f9810e3 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb @@ -11,8 +11,10 @@ description = """ParMETIS is an MPI-based parallel library that implements a var toolchain = {'name': 'gmpolf', 'version': '1.4.8'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb index 7ab94b866f..48d813595b 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb @@ -11,8 +11,10 @@ description = """ParMETIS is an MPI-based parallel library that implements a var toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb index f751a31515..f4413be294 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb @@ -11,8 +11,10 @@ description = """ParMETIS is an MPI-based parallel library that implements a var toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb index a91e416ba0..10dc438149 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb @@ -11,8 +11,10 @@ description = """ParMETIS is an MPI-based parallel library that implements a var toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.4')] diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb index 904b9fb5ff..a32790b7f1 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb @@ -12,8 +12,10 @@ description = """ParMETIS is an MPI-based parallel library that implements a var toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', - 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.4')] -- GitLab From e283b9f2752a692f27940d5da9fcfdc41b07f168 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 15:03:39 +0100 Subject: [PATCH 0494/2133] additional style fixes in Python easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 4 +--- easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb | 4 +--- 17 files changed, 17 insertions(+), 51 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 91a293153e..2110e24871 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -43,9 +43,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index 0f080708a5..76db705ebd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -43,9 +43,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb index d4350dca92..a5549be298 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb @@ -42,9 +42,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb index eef0597d02..1156ffc2af 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -43,9 +43,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb index 09bb245d3a..56b2274143 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -43,9 +43,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 6af31b5b60..2661d5c96a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -43,9 +43,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb index 147a7cab13..94c61afabc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -42,9 +42,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 1ea0118d0c..ec5aac3306 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -43,9 +43,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index b890f8cb1b..d8572b5d59 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -43,9 +43,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 0f80537c01..8090f32031 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -43,9 +43,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index 4df02bbcfe..012b08cef6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -40,9 +40,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb index 4645a18ca8..0d23383202 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -41,9 +41,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb index 9c11f0e5c3..029f3682d4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -41,9 +41,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb index cab707ec57..950a1d4aea 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -41,9 +41,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 42e834b9da..188046b969 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -41,9 +41,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 67e92c7ae0..f8a3851092 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -39,9 +39,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index 7a1cf602ae..ae86e7bce7 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -39,9 +39,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], -- GitLab From f2e7347e0f57714c39566bee0a17c9ff26108641 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 15:04:46 +0100 Subject: [PATCH 0495/2133] additional style fixes in psmpi easyconfigs --- easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 2 -- .../easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb | 1 - 2 files changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index f1eb61bd5b..3e04c7775f 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -25,7 +25,6 @@ configopts = '--with-confset=gcc --enable-shared --enable-static' dependencies = [('pscom', '5.0.44-1')] - sanity_check_paths = { 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', @@ -40,5 +39,4 @@ sanity_check_paths = { 'dirs': [], } - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index 16c0c9ffc3..4bb1ff6f7a 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -25,7 +25,6 @@ configopts = '--with-confset=intel --enable-shared --enable-static --enable-romi dependencies = [('pscom', '5.0.44-1')] - sanity_check_paths = { 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', -- GitLab From 4447352acc3ab0b4fd227a3b2035c444e226ffa2 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 17 Feb 2016 15:13:32 +0100 Subject: [PATCH 0496/2133] Don't use %(perl)s and add Perl as a dep. Perl needs to be a dep so perlver is introduced as a variable where we can use %(perlver)s --- .../Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb | 6 +++--- .../Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb | 5 +++-- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb index 8102a2d352..d05f4f9c7a 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb @@ -23,13 +23,13 @@ toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} sources = ['%(namelower)s_%(version)s.tgz'] source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] -perl = 'Perl' perlver = '5.20.3' kmer = '100' -versionsuffix = '-mt-kmer_%s-%%(perl)s-%%(perlver)s' % kmer +versionsuffix = '-mt-kmer_%s-Perl-%%(perlver)s' % kmer dependencies = [ - ('BioPerl', '1.6.923', '-%(perl)s-%(perlver)s'), + ('Perl', perlver), + ('BioPerl', '1.6.923', '-Perl-%(perlver)s'), ] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % kmer diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb index 15491a3ef4..fe2df81ad0 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb @@ -26,10 +26,11 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] perl = 'Perl' perlver = '5.20.3' kmer = '31' -versionsuffix = '-mt-kmer_%s-%%(perl)s-%%(perlver)s' % kmer +versionsuffix = '-mt-kmer_%s-Perl-%%(perlver)s' % kmer dependencies = [ - ('BioPerl', '1.6.923', '-%(perl)s-%(perlver)s'), + ('Perl', perlver), + ('BioPerl', '1.6.923', '-Perl-%(perlver)s'), ] # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous -- GitLab From c950d94d6855882bbeec92838498d997ab58c302 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 15:20:52 +0100 Subject: [PATCH 0497/2133] additional style fixes in TCC, Vampir, VampirServer and ViennaRNA easyconfigs --- easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb | 2 -- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb | 4 ++-- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb | 4 ++-- .../v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb | 4 ++-- .../v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 4 ++-- 7 files changed, 12 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb b/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb index 35f352db69..c502d5385e 100644 --- a/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb +++ b/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb @@ -11,8 +11,6 @@ easyblock = 'ConfigureMake' name = 'TCC' version = '0.9.26' -# altversions = ['0.9.21', '0.9.22', '0.9.23', '0.9.24', '0.9.25', -# '0.9.26'] # older versions may require more special handling homepage = 'http://bellard.org/tcc/' description = """The Tiny C Compiler (aka TCC, tCc, or TinyCC) is an x86 and x86-64 C compiler diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb index 4ebcf299af..85c8901493 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb @@ -30,8 +30,8 @@ sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] # Adjust this variable to point to the location of your Vampir license file license_file = '/example/licenses/path/vampir.license' -install_cmd = "./" + sources[0] + \ - " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s " +install_cmd += "--no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb index 80a6746a4c..a25a9d20e8 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb @@ -33,8 +33,8 @@ checksums = [ # Adjust this variable to point to the location of your Vampir license file license_file = '/example/licenses/path/vampir.license' -install_cmd = "./" + sources[0] + \ - " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s " +install_cmd += "--no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb index 0d946c3eca..6a97299365 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -34,8 +34,8 @@ checksums = [ # Adjust this variable to point to the location of your Vampir license file license_file = '/example/licenses/path/vampir.license' -install_cmd = "./" + sources[0] + \ - " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && " +install_cmd += "%(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf", "lib/vampirserver-driver.%s" % SHLIB_EXT], diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb index 7c6cf538ad..740784c812 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb @@ -35,8 +35,8 @@ sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', 'paln', 'duplex', 'alifold', 'plfold', 'up', - 'aliduplex', 'Lalifold', '2Dfold', 'parconv', - 'PKplex', 'plex', 'snoop', 'forester']] + + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + ['bin/Kinfold'], 'dirs': [] } diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb index 9c115491a3..375b58016f 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb @@ -37,8 +37,8 @@ sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', 'paln', 'duplex', 'alifold', 'plfold', 'up', - 'aliduplex', 'Lalifold', '2Dfold', 'parconv', - 'PKplex', 'plex', 'snoop', 'forester']] + + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + ['bin/Kinfold'], 'dirs': [] } diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index b0f11b9ddd..316c43df98 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -38,8 +38,8 @@ sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', 'paln', 'duplex', 'alifold', 'plfold', 'up', - 'aliduplex', 'Lalifold', '2Dfold', 'parconv', - 'PKplex', 'plex', 'snoop', 'forester']] + + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + ['bin/Kinfold'], 'dirs': [] } -- GitLab From ca2e4830b3403de42ac78cb24b86cad7ec192096 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 15:27:28 +0100 Subject: [PATCH 0498/2133] additional style fixes in xtrans easyconfigs --- .../easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb | 10 ++++------ .../easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb | 10 ++++------ .../easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb | 10 ++++------ .../easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb | 10 ++++------ .../easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb | 10 ++++------ .../easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb | 10 ++++------ .../easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb | 10 ++++------ .../easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb | 10 ++++------ .../easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb | 10 ++++------ .../easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb | 10 ++++------ 10 files changed, 40 insertions(+), 60 deletions(-) diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb index d4d9f7b97d..6694ef584a 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb @@ -15,12 +15,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in [ - 'transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', - 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' - ] - ], - 'dirs': [] + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb index a2a0755c9f..7ac7af4a53 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb @@ -15,12 +15,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in [ - 'transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', - 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' - ] - ], - 'dirs': [] + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb index e0801c0268..ec378cd83c 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb @@ -14,12 +14,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in [ - 'transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', - 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' - ] - ], - 'dirs': [] + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb index 90167fba75..98cc20e543 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb @@ -15,12 +15,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in [ - 'transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', - 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' - ] - ], - 'dirs': [] + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb index 70ff99da7d..1d6eb396ed 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb @@ -15,12 +15,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in [ - 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', - 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' - ] - ], - 'dirs': [] + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb index ec215c7fbf..23de4f9f86 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb @@ -15,12 +15,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in [ - 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', - 'Xtranssock.c', 'Xtransutil.c' - ] - ], - 'dirs': [] + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb index 1793db7b6f..f7ff52f126 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb @@ -15,12 +15,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in [ - 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', - 'Xtranssock.c', 'Xtransutil.c' - ] - ], - 'dirs': [] + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb index 9f200617fa..aba9aa9dae 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb @@ -15,12 +15,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in [ - 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', - 'Xtranssock.c', 'Xtransutil.c' - ] - ], - 'dirs': [] + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb index 06cbd1c8ee..3b75c81b7b 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb @@ -15,12 +15,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in [ - 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', - 'Xtranssock.c', 'Xtransutil.c' - ] - ], - 'dirs': [] + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb index 886f7c9bbf..bfcb216ed9 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb @@ -15,12 +15,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in [ - 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', - 'Xtranssock.c', 'Xtransutil.c' - ] - ], - 'dirs': [] + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], } moduleclass = 'devel' -- GitLab From ceb26f6847fd690ba95e2f093f13bdce770ee7e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 15:35:53 +0100 Subject: [PATCH 0499/2133] disable optarch toolchain option to dance around internal compiler error --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb index 3b9215acdb..3e71d0c50e 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb @@ -7,6 +7,8 @@ homepage = 'https://www.ffmpeg.org/' description = """A complete, cross-platform solution to record, convert and stream audio and video.""" toolchain = {'name': 'intel', 'version': '2016a'} +# disable use of -xHOST, since it can trigger an internal compiler error in this case +toolchainopts = {'optarch': False} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] -- GitLab From 39a8b1f806e2ba2a602cc0f1566489538cb98730 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Feb 2016 16:28:37 +0100 Subject: [PATCH 0500/2133] consistently use %(perlver)s --- .../BioPerl-1.6.923-intel-2015b-Perl-5.20.3.eb | 7 ++----- .../DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb | 11 +++-------- 2 files changed, 5 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-intel-2015b-Perl-5.20.3.eb index 13d2badd18..0b4fbe276a 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-intel-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-intel-2015b-Perl-5.20.3.eb @@ -2,6 +2,7 @@ easyblock = 'PerlModule' name = 'BioPerl' version = '1.6.923' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://www.bioperl.org/' description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. @@ -12,12 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] sources = ['release-%s.tar.gz' % version.replace('.', '-')] -perl = 'Perl' -perlver = '5.20.3' -versionsuffix = '-%s-%s' % (perl, perlver) - dependencies = [ - (perl, perlver), + ('Perl', '5.20.3'), ('DB_File', '1.831', versionsuffix), ] diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb index 051ab1254e..cfa6ec1084 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb @@ -2,6 +2,7 @@ easyblock = 'PerlModule' name = 'DB_File' version = '1.831' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://perldoc.perl.org/DB_File.html' description = """Perl5 access to Berkeley DB version 1.x.""" @@ -13,19 +14,13 @@ sources = [SOURCE_TAR_GZ] dependencies = [('DB', '2.7.7')] -perl = 'Perl' -perlver = '5.20.3' -versionsuffix = '-%s-%s' % (perl, perlver) - dependencies = [ - (perl, perlver), + ('Perl', '5.20.3'), ] -perlmajver = perlver.split('.')[0] sanity_check_paths = { - 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DB_File.pm' % (perlmajver, perlver)], + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], } moduleclass = 'data' - -- GitLab From 21415a9341ea1216a0dca9456b441baa4d1dfa8d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 17 Feb 2016 23:13:47 +0000 Subject: [PATCH 0501/2133] Working versiion with upstream Boost 1.60 fix --- ...ynchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb diff --git a/easybuild/easyconfigs/r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb b/easybuild/easyconfigs/r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb new file mode 100644 index 0000000000..b8f1d5f134 --- /dev/null +++ b/easybuild/easyconfigs/r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'synchronicity' +version = '1.1.9.1' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """synchronicity: Boost mutex functionality in R""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.2.3' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('BH', '1.60.0-1', '-R-3.2.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['synchronicity'], +} + +moduleclass = 'lang' -- GitLab From 8e33fd247dff9201fd3ab371560068869e5639e9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 17 Feb 2016 23:21:19 +0000 Subject: [PATCH 0502/2133] Add author information --- .../r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb b/easybuild/easyconfigs/r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb index b8f1d5f134..f056af2b4f 100644 --- a/easybuild/easyconfigs/r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb +++ b/easybuild/easyconfigs/r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb @@ -1,3 +1,8 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# The Francis Crick Institute + easyblock = 'RPackage' name = 'synchronicity' -- GitLab From 829d4bce5aa38d6444c4eb516969f6264205b4d3 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 18 Feb 2016 13:33:41 +1300 Subject: [PATCH 0503/2133] Reinstate Open MPI version --- easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb index bd3a091b31..9110e61a28 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb @@ -1,7 +1,8 @@ easyblock = "PackedBinary" name = "ORCA" -version = '3_0_0-linux_x86-64' +openmpiversion = '1.6.5' +version = '3_0_0-linux_x86-64_openmpi_%s' % ''.join(openmpiversion.split('.')) homepage = 'http://www.thch.uni-bonn.de/tc/orca/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry @@ -15,7 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] # ORCA 3.0.0 is compiled only against OpenMPI 1.6.5 for Linux -dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] +dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', -- GitLab From 85f72adb9620c063da36e6874d1a53fc882be7d3 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 18 Feb 2016 13:43:01 +1300 Subject: [PATCH 0504/2133] New EasyConfig for PyZMQ --- ...MQ-15.1.0-foss-2015a-Python-2.7.11-zmq4.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.1.0-foss-2015a-Python-2.7.11-zmq4.eb diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.1.0-foss-2015a-Python-2.7.11-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.1.0-foss-2015a-Python-2.7.11-zmq4.eb new file mode 100644 index 0000000000..308e3beea4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.1.0-foss-2015a-Python-2.7.11-zmq4.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.1.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.11' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '4.1.4' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' -- GitLab From b0056c579fe968b204c48d2b2e7959317d70f721 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 18 Feb 2016 14:08:16 +1300 Subject: [PATCH 0505/2133] New EasyConfig for libsodium 1.0.8 with the foss-2015a toolchain --- .../l/libsodium/libsodium-1.0.8-foss-2015a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2015a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2015a.eb new file mode 100644 index 0000000000..50ea0fca74 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.8' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From ba4d135f7c216e87ffbed1fa4d49e0893a2f1c04 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 18 Feb 2016 14:15:47 +1300 Subject: [PATCH 0506/2133] New EasyConfig for util-linux-2.27.1 with the foss-2015a toolchain --- .../util-linux-2.27.1-foss-2015a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb new file mode 100644 index 0000000000..50b1fff058 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.27.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From ea8e1ef7e004f4120de794c0f87f987e40e9c0a6 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 18 Feb 2016 14:19:16 +1300 Subject: [PATCH 0507/2133] New EasyConfig for ZeroMQ 4.1.4 with the foss-2015a toolchain --- .../z/ZeroMQ/ZeroMQ-4.1.4-foss-2015a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2015a.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2015a.eb new file mode 100644 index 0000000000..1de09786b7 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.1.4' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.27.1'), + ('libsodium', '1.0.6'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From ccb9f32e4fcb8fa19af29e2725033f15d92932b2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 18 Feb 2016 14:21:50 +1300 Subject: [PATCH 0508/2133] Use PyZMQ 15.2.0 instead of PyZMQ 15.1.0 --- ...11-zmq4.eb => PyZMQ-15.2.0-foss-2015a-Python-2.7.11-zmq4.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/PyZMQ/{PyZMQ-15.1.0-foss-2015a-Python-2.7.11-zmq4.eb => PyZMQ-15.2.0-foss-2015a-Python-2.7.11-zmq4.eb} (97%) diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.1.0-foss-2015a-Python-2.7.11-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2015a-Python-2.7.11-zmq4.eb similarity index 97% rename from easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.1.0-foss-2015a-Python-2.7.11-zmq4.eb rename to easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2015a-Python-2.7.11-zmq4.eb index 308e3beea4..b6f32ee0fc 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.1.0-foss-2015a-Python-2.7.11-zmq4.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2015a-Python-2.7.11-zmq4.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'PyZMQ' -version = '15.1.0' +version = '15.2.0' homepage = 'http://www.zeromq.org/bindings:python' description = """Python bindings for ZeroMQ""" -- GitLab From 46c819dc7ea43d0794393a487264a925d22da65f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 18 Feb 2016 14:26:29 +1300 Subject: [PATCH 0509/2133] New EasyConfig for IPython 3.2.3 with Python 2.7.11 and the foss-2015a toolchain --- .../IPython-3.2.3-foss-2015a-Python-2.7.11.eb | 90 +++++++++++++++++++ 1 file changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb new file mode 100644 index 0000000000..6a2901ff52 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb @@ -0,0 +1,90 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '3.2.3' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +python = 'Python' +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), +] + +moduleclass = 'tools' -- GitLab From c41d3d1d1750f9a7e145e8b3c0ecf651c1635647 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 13:55:49 +0100 Subject: [PATCH 0510/2133] minor style fixes in Python/libsodium easyconfigs --- .../easyconfigs/l/libsodium/libsodium-1.0.8-foss-2015a.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 8 +++----- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2015a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2015a.eb index 50ea0fca74..9293b733b8 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2015a.eb @@ -13,7 +13,7 @@ source_urls = ['https://download.libsodium.org/libsodium/releases/'] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], 'dirs': ['include/sodium', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index 7f06897c75..34c45f4ac7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -23,8 +23,8 @@ dependencies = [ ('SQLite', '3.10.0'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), # required for pycrypto -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] @@ -43,9 +43,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], -- GitLab From 039b9d674e98bfcbec8f6bf8109430b8d0950178 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 14:52:53 +0100 Subject: [PATCH 0511/2133] {vis}[gimkl/2.11.5] PyFFmpeg 2.1beta --- .../f/FFmpeg/FFmpeg-0.10.16-gimkl-2.11.5.eb | 30 +++++++++++++++++ .../n/NASM/NASM-2.11.08-gimkl-2.11.5.eb | 31 +++++++++++++++++ ...mpeg-2.1beta-gimkl-2.11.5-Python-2.7.10.eb | 33 +++++++++++++++++++ .../x/x264/x264-20160114-gimkl-2.11.5.eb | 24 ++++++++++++++ .../y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb | 31 +++++++++++++++++ 5 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.08-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-gimkl-2.11.5-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20160114-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-gimkl-2.11.5.eb new file mode 100644 index 0000000000..7c1be39c96 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-gimkl-2.11.5.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '0.10.16' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.11.08'), + ('zlib', '1.2.8'), + ('x264', '20160114'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-gimkl-2.11.5.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-gimkl-2.11.5.eb new file mode 100644 index 0000000000..60a507ddb8 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-gimkl-2.11.5.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-gimkl-2.11.5-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-gimkl-2.11.5-Python-2.7.10.eb new file mode 100644 index 0000000000..c6aa562ded --- /dev/null +++ b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-gimkl-2.11.5-Python-2.7.10.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyFFmpeg' +version = '2.1beta' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/mhaller/pyffmpeg' +description = """Python FFmpeg wrapper""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'usempi': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/pyffmpeg/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'PyFFmpeg-%(version)s_ffmpegpath.patch', + 'PyFFmpeg-%(version)s_Cython-fixes.patch', +] + +dependencies = [ + ('Python', '2.7.10'), + ('FFmpeg', '0.10.16'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x264/x264-20160114-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/x264/x264-20160114-gimkl-2.11.5.eb new file mode 100644 index 0000000000..c6c378ce92 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160114-gimkl-2.11.5.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160114' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = ['ftp://ftp.videolan.org/pub/videolan/x264/snapshots/'] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb new file mode 100644 index 0000000000..b2b7c412d9 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 52ad0d5711da3c786090c4359296dae3961a2701 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 18 Feb 2016 15:11:18 +0100 Subject: [PATCH 0512/2133] Add support for GATE-7.0 for intel-2016a --- .../Autotools-20150119-intel-2016a.eb | 17 +++ .../b/Bison/Bison-3.0.2-intel-2016a.eb | 22 ++++ .../c/CFITSIO/CFITSIO-3.37-intel-2016a.eb | 22 ++++ .../c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb | 24 ++++ .../c/CMake/CMake-3.1.3-intel-2016a.eb | 22 ++++ .../c/CMake/CMake-3.2.3-intel-2016a.eb | 31 +++++ .../e/eudev/eudev-3.0-intel-2016a.eb | 33 +++++ .../fixesproto/fixesproto-5.0-intel-2016a.eb | 19 +++ .../fontconfig-2.11.93-intel-2016a.eb | 22 ++++ .../fontsproto-2.1.3-intel-2016a.eb | 20 +++ .../f/freetype/freetype-2.5.5-intel-2016a.eb | 21 ++++ .../g/GATE/GATE-7.0-intel-2016a.eb | 29 +++++ .../easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb | 18 +++ .../g/Geant4/Geant4-9.6.p04-intel-2016a.eb | 24 ++++ .../g/gettext/gettext-0.19.4-intel-2016a.eb | 18 +++ .../g/glproto/glproto-1.4.17-intel-2016a.eb | 20 +++ .../g/gperf/gperf-3.0.4-intel-2016a.eb | 22 ++++ .../inputproto-2.3.1-intel-2016a.eb | 19 +++ .../k/kbproto/kbproto-1.0.6-intel-2016a.eb | 19 +++ .../k/kbproto/kbproto-1.0.7-intel-2016a.eb | 19 +++ .../LLVM-3.6.2-intel-2016a-Python-2.7.9.eb | 38 ++++++ .../libX11-1.6.3-intel-2016a-Python-2.7.9.eb | 37 ++++++ .../l/libXau/libXau-1.0.8-intel-2016a.eb | 25 ++++ .../libXdamage-1.1.4-intel-2016a.eb | 26 ++++ .../l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb | 25 ++++ .../l/libXext/libXext-1.3.3-intel-2016a.eb | 34 +++++ .../libXfixes/libXfixes-5.0.1-intel-2016a.eb | 24 ++++ .../l/libXfont/libXfont-1.5.1-intel-2016a.eb | 29 +++++ .../libXft-2.3.2-intel-2016a-libX11-1.6.3.eb | 34 +++++ .../l/libXpm/libXpm-3.5.11-intel-2016a.eb | 22 ++++ .../libXrender-0.9.9-intel-2016a.eb | 28 +++++ .../l/libdrm/libdrm-2.4.59-intel-2016a.eb | 25 ++++ .../libfontenc-1.1.3-intel-2016a.eb | 23 ++++ .../libpciaccess-0.13.1-intel-2016a.eb | 26 ++++ .../l/libpng/libpng-1.6.16-intel-2016a.eb | 19 +++ .../libpthread-stubs-0.3-intel-2016a.eb | 20 +++ .../l/libtool/libtool-2.4.5-intel-2016a.eb | 17 +++ .../libxcb-1.11-intel-2016a-Python-2.7.9.eb | 34 +++++ .../libxml2-2.9.2-intel-2016a-Python-2.7.9.eb | 28 +++++ .../Mesa-10.4.5-intel-2016a-Python-2.7.9.eb | 75 +++++++++++ .../makedepend-1.0.5-intel-2016a.eb | 20 +++ .../n/ncurses/ncurses-5.9-intel-2016a.eb | 36 ++++++ .../p/PCRE/PCRE-8.36-intel-2016a.eb | 18 +++ .../p/Python/Python-2.7.9-intel-2016a.eb | 117 ++++++++++++++++++ .../pkg-config/pkg-config-0.28-intel-2016a.eb | 27 ++++ .../r/ROOT/ROOT-v5.34.26-intel-2016a.eb | 57 +++++++++ .../renderproto-0.11-intel-2016a.eb | 20 +++ .../s/SQLite/SQLite-3.8.8.1-intel-2016a.eb | 38 ++++++ .../t/Tcl/Tcl-8.6.3-intel-2016a.eb | 25 ++++ .../t/Tk/Tk-8.6.3-intel-2016a-no-X11.eb | 24 ++++ ...xcb-proto-1.11-intel-2016a-Python-2.7.9.eb | 27 ++++ .../xextproto/xextproto-7.3.0-intel-2016a.eb | 25 ++++ .../xorg-macros-1.17-intel-2016a.eb | 22 ++++ .../x/xproto/xproto-7.0.27-intel-2016a.eb | 24 ++++ .../x/xtrans/xtrans-1.3.5-intel-2016a.eb | 24 ++++ 55 files changed, 1534 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2016a.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2016a.eb create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2016a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2016a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2016a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2016a.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2016a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2016a-no-X11.eb create mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2016a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2016a.eb new file mode 100644 index 0000000000..8d512386b5 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2016a.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150119' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.5'), # 20150119 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2016a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2016a.eb new file mode 100644 index 0000000000..4fdbf98d8f --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2016a.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2016a.eb new file mode 100644 index 0000000000..7af022d137 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.37' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +srcversion = '%s0' % version.replace('.', '') +source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +sources = ['%%(namelower)s%s.tar.gz' % srcversion] + +sanity_check_paths = { + 'files': ["lib/libcfitsio.a"], + 'dirs': ["include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb new file mode 100644 index 0000000000..42f08bd8d9 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.1.3.1' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '3.1.3')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb new file mode 100644 index 0000000000..45251dfaf6 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.1.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb new file mode 100644 index 0000000000..34313f0a0f --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2016a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2016a.eb new file mode 100644 index 0000000000..246e9d0730 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.0' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-%(version)s_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb new file mode 100644 index 0000000000..33951308af --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2016a.eb new file mode 100644 index 0000000000..f906761e9b --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.93' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb new file mode 100644 index 0000000000..5b1c1517ba --- /dev/null +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'fontsproto' +version = '2.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X11 font extension wire protocol" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2016a.eb new file mode 100644 index 0000000000..35f4da2da2 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2016a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.16')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb new file mode 100644 index 0000000000..a0a092ac93 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb @@ -0,0 +1,29 @@ +name = 'GATE' +version = '7.0' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [('%(namelower)s_v%(version)s.tar_.gz', "tar xfvz %s")] +source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/'] + +patches = [ + 'GATE-%(version)s_Makefile-prefix.patch', + 'GATE-%(version)s_unistdh.patch', +] + +builddependencies = [ + ('CMake', '3.1.3'), +] + +dependencies = [ + ('Geant4', '9.6.p04'), + ('CLHEP', '2.1.3.1'), + ('ROOT', 'v5.34.26'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb new file mode 100644 index 0000000000..75f289b550 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb new file mode 100644 index 0000000000..0496cd5322 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb @@ -0,0 +1,24 @@ +name = 'Geant4' +version = '9.6.p04' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + ('CLHEP', '2.1.3.1'), +] + +builddependencies = [('CMake', '3.1.3')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += "-DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2016a.eb new file mode 100644 index 0000000000..069f899a71 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.4' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb new file mode 100644 index 0000000000..c26a1ac08a --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'glproto' +version = '1.4.17' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016a.eb new file mode 100644 index 0000000000..5938576aa7 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb new file mode 100644 index 0000000000..323816dd0b --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2016a.eb new file mode 100644 index 0000000000..3a33382528 --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb new file mode 100644 index 0000000000..29d6a6987a --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb new file mode 100644 index 0000000000..6139d93743 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.6.2' +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.2.3'), + (python, pyver), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a-Python-2.7.9.eb new file mode 100644 index 0000000000..060a6e35d0 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a-Python-2.7.9.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' +versionsuffix = '-Python-2.7.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', versionsuffix), + ('inputproto', '2.3.1'), + ('xproto', '7.0.27'), + ('kbproto', '1.0.6'), +] + +dependencies = [ + ('libxcb', '1.11', versionsuffix), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb new file mode 100644 index 0000000000..5a623c350f --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xproto', '7.0.27'), +] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000..420c8c2f42 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libXdamage' +version = '1.1.4' +pyver = '-Python-2.7.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Damage extension library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3', pyver), + ('libxcb', '1.11', pyver), + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xdamage.h', 'lib/libXdamage.so', 'lib/libXdamage.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb new file mode 100644 index 0000000000..a7153188df --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.27'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb new file mode 100644 index 0000000000..b08a10bd51 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.27'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb new file mode 100644 index 0000000000..50734ffc1f --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a.eb new file mode 100644 index 0000000000..58e597f6b8 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.27'), + ('xtrans', '1.3.5'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.so', 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb new file mode 100644 index 0000000000..ab04e0520c --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.6'), + ('renderproto', '0.11'), +] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver + +dependencies = [ + ('libX11', libx11ver, '-Python-2.7.9'), + ('libXrender', '0.9.9'), + ('freetype', '2.5.5'), + ('fontconfig', '2.11.93'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb new file mode 100644 index 0000000000..39b2ff6653 --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libXpm' +version = '3.5.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [('gettext', '0.19.4', '', ('GCC', '4.9.2'))] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb new file mode 100644 index 0000000000..06b460f5f2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2016a.eb new file mode 100644 index 0000000000..8d7f8591ba --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.59' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb new file mode 100644 index 0000000000..d93ab58f1d --- /dev/null +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfontenc' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/xlibs/' +description = """X11 font encoding library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.27'), +] + +sanity_check_paths = { + 'files': ['include/X11/fonts/fontenc.h', 'lib/libfontenc.%s' % SHLIB_EXT, 'lib/libfontenc.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2016a.eb new file mode 100644 index 0000000000..eeafddf420 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.1' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +builddependencies = [ + ('Autotools', '20150119', '', ('GCC', '4.9.2')), + ('xorg-macros', '1.17'), +] + +preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2016a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2016a.eb new file mode 100644 index 0000000000..d9a7ed9527 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.16' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016a.eb new file mode 100644 index 0000000000..afc1225690 --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2016a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2016a.eb new file mode 100644 index 0000000000..4219e58cfd --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2016a.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.5' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2016a-Python-2.7.9.eb new file mode 100644 index 0000000000..4279354d1f --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2016a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('xcb-proto', '1.11', versionsuffix), + ('libXau', '1.0.8'), + ('libpthread-stubs', '0.3'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2016a-Python-2.7.9.eb new file mode 100644 index 0000000000..e000b25261 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2016a-Python-2.7.9.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2016a-Python-2.7.9.eb new file mode 100644 index 0000000000..712aaf2f8b --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2016a-Python-2.7.9.eb @@ -0,0 +1,75 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '10.4.5' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = ['%(name)sLib-%(version)s.tar.gz'] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +patches = ['Mesa-%(version)s_sse4_1.patch'] + +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), + ('Automake', '1.15'), + ('makedepend', '1.0.5'), + ('kbproto', '1.0.6'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.27'), + ('libtool', '2.4.5'), + ('pkg-config', '0.28'), + ('glproto', '1.4.17'), + ('M4', '1.4.17') +] + +dependencies = [ + ('Python', pythonver), + ('libxml2', '2.9.2', versionsuffix), + ('libdrm', '2.4.59'), + ('libX11', '1.6.3', versionsuffix), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1'), + ('LLVM', '3.6.2', versionsuffix), + ('eudev', '3.0'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --disable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" +configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl""" + +# package-config files for os dependencies are in an os specific place +#preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' + +prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/wglext.h', 'include/GL/gl.h', + 'include/GL/glxext.h', 'include/GL/glx_mangle.h', + 'include/GL/wmesa.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb new file mode 100644 index 0000000000..1158bd68be --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016a.eb new file mode 100644 index 0000000000..f16049293d --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2016a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2016a.eb new file mode 100644 index 0000000000..dabda6ed92 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.36' + +homepage = 'http://www.pcre.org/' +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb new file mode 100644 index 0000000000..1d8106ab4e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb @@ -0,0 +1,117 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2016a.eb new file mode 100644 index 0000000000..9a712cb3b4 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.28' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +# don't use PAX, it might break. +tar_config_opts = True + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2016a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2016a.eb new file mode 100644 index 0000000000..face3c9641 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2016a.eb @@ -0,0 +1,57 @@ +name = 'ROOT' +version = 'v5.34.26' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', + 'ROOT-v5.34.26_libX.patch', +] + +python = 'Python' +pyver = '2.7.9' + +dependencies = [ + ('GSL', '1.16'), + ('Mesa', '10.4.5', '-%s-%s' % (python, pyver)), + ('libxml2', '2.9.2', '-%s-%s' % (python, pyver)), + ('PCRE', '8.36'), + ('CFITSIO', '3.37'), + ('freetype', '2.5.5'), + (python, pyver), + ('zlib', '1.2.8'), + ('libXft', '2.3.2', '-libX11-1.6.3'), + ('libXpm', '3.5.11'), + ('libXext', '1.3.3'), +] + +# use external ZLIB +preconfigopts = 'ZLIB=$EBROOTZLIB ' + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xrootd --disable-mysql --disable-krb5 --disable-odbc ' +configopts += ' --disable-oracle --disable-pgsql --disable-qt --disable-sqlite' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +configopts += ' --with-cfitsio-incdir=$EBROOTCFITSIO/include --with-cfitsio-libdir=$EBROOTCFITSIO/lib' +configopts += ' --with-opengl-incdir=$EBROOTMESA/include --with-opengl-libdir=$EBROOTMESA/lib' +configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLIBXEXT/lib' +configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' +configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb new file mode 100644 index 0000000000..37b516e535 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2016a.eb new file mode 100644 index 0000000000..4421de3277 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2016a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2016a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2016a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2016a.eb new file mode 100644 index 0000000000..e368b2b5ef --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2016a-no-X11.eb new file mode 100644 index 0000000000..c673514d37 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2016a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb new file mode 100644 index 0000000000..7cbfd9e916 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-proto' +version = '1.11' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[0:2]) + +sanity_check_paths = { + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb new file mode 100644 index 0000000000..dcc6160700 --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2016a.eb new file mode 100644 index 0000000000..f26da7ae49 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.17' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +dependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2016a.eb new file mode 100644 index 0000000000..2f1b41c474 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.27' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb new file mode 100644 index 0000000000..8366af681c --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', + 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', + 'Xtranstli.c', 'Xtransutil.c']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From bbe3efb4a29bb9a1b15636cff2b4cbc516792d96 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 18 Feb 2016 15:25:27 +0100 Subject: [PATCH 0513/2133] Add GATE-6.2 support for intel-2016a. --- .../c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb | 20 +++++ .../c/CMake/CMake-2.8.4-intel-2016a.eb | 22 +++++ .../g/GATE/GATE-6.2-intel-2016a.eb | 26 ++++++ .../easyconfigs/g/GSL/GSL-1.15-intel-2016a.eb | 18 ++++ .../g/Geant4/Geant4-9.5.p01-intel-2016a.eb | 24 +++++ .../libreadline-6.2-intel-2016a.eb | 30 +++++++ .../libxml2-2.8.0-intel-2016a-Python-2.7.3.eb | 33 +++++++ .../p/Python/Python-2.7.3-intel-2016a.eb | 89 +++++++++++++++++++ .../r/ROOT/ROOT-v5.34.01-intel-2016a.eb | 39 ++++++++ 9 files changed, 301 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2016a-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb new file mode 100644 index 0000000000..ceed3e9cd3 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'CLHEP' +version = '2.1.1.0' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +# CLHEP compiles with icc instead of icpc +configopts = 'CXX="$CC" CXXFLAGS="$CXXFLAGS -gcc"' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb new file mode 100644 index 0000000000..62574e2454 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '2.8.4' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb new file mode 100644 index 0000000000..502c8f56f7 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb @@ -0,0 +1,26 @@ +name = 'GATE' +version = '6.2' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [('%%(namelower)s_v%s_tar_gz_15843.gz' % '_'.join(version.split('.')), "tar xfvz %s")] +source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/gate_release/2012/08/'] + +patches = [ + 'GATE-%(version)s_Makefile-prefix.patch', + 'GATE-%(version)s_GCC-4.7.patch', +] + +dependencies = [ + ('Geant4', '9.5.p01'), + ('CLHEP', '2.1.1.0'), + ('ROOT', 'v5.34.01'), +] +builddependencies = [('CMake', '2.8.4')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2016a.eb new file mode 100644 index 0000000000..714d2f9de8 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb new file mode 100644 index 0000000000..5b065cc9f0 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb @@ -0,0 +1,24 @@ +name = 'Geant4' +version = '9.5.p01' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + ('CLHEP', '2.1.1.0'), +] + +builddependencies = [('CMake', '2.8.4')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += "-DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb new file mode 100644 index 0000000000..3d2c4263e5 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.2' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2016a-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2016a-Python-2.7.3.eb new file mode 100644 index 0000000000..d4cc4b5eb1 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2016a-Python-2.7.3.eb @@ -0,0 +1,33 @@ +name = 'libxml2' +version = '2.8.0' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb new file mode 100644 index 0000000000..96ff3e825b --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb @@ -0,0 +1,89 @@ +name = 'Python' +version = '2.7.3' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.6.1' +scipyversion = '0.10.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +exts_list = [ + ('setuptools', '0.6c11', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('mpi4py', '1.3', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.17.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.1', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '1.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.12.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2016a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2016a.eb new file mode 100644 index 0000000000..a76d8e6f3c --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2016a.eb @@ -0,0 +1,39 @@ +name = 'ROOT' +version = 'v5.34.01' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['%s_%s.source.tar.gz' % (name.lower(), version)] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-%(version)s_recent-ifort.patch', +] + +python = 'Python' +pyver = '2.7.3' + +dependencies = [ + ('GSL', '1.15'), + ('libxml2', '2.8.0', '-%s-%s' % (python, pyver)), + (python, pyver), +] + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' + +moduleclass = 'data' -- GitLab From 8e83769f3ce54088a63c872a8ca6f89bfbabb260 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 18 Feb 2016 15:40:28 +0100 Subject: [PATCH 0514/2133] Fix up xcb-proto mis-import. --- .../xcb-proto-1.11-intel-2016a-Python-2.7.9.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/x/xcb-proto/{xcb-proto-1.11-intel-2016a-Python-2.7.9.eb => }/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb (100%) diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb similarity index 100% rename from easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb rename to easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb -- GitLab From 0496a6bd9d329ae1748ca82b211a7a63380dd151 Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 18 Feb 2016 17:10:39 +0200 Subject: [PATCH 0515/2133] add easyconfig Boost-1.59.0-intel-2015b.eb --- .../b/Boost/Boost-1.59.0-intel-2015b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb new file mode 100644 index 0000000000..7461992321 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.59.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 8ad5823fa146d339ad0d9bd4b5e6f4f3a1eeb7b0 Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 18 Feb 2016 17:11:56 +0200 Subject: [PATCH 0516/2133] add easyconfig OpenFOAM-3.0.0-intel-2015b.eb --- .../o/OpenFOAM/OpenFOAM-3.0.0-intel-2015b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-intel-2015b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-intel-2015b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-intel-2015b.eb new file mode 100644 index 0000000000..eb8704d554 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-intel-2015b.eb @@ -0,0 +1,40 @@ +name = 'OpenFOAM' +version = '3.0.0' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'cstd': 'c++14'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-%(version)s_libreadline.patch', + ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0', '-32bitIDX'), + ('ncurses', '5.9'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.59.0'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.3.2'), + ('flex', '2.5.39'), +] + +moduleclass = 'cae' -- GitLab From b7c41c51db22fa2cfc380b3ca6d96e8c0433059b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 17:14:00 +0100 Subject: [PATCH 0517/2133] use newer version of Cython --- ...ython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb | 24 +++++++++++++++++++ ...mpeg-2.1beta-gimkl-2.11.5-Python-2.7.10.eb | 1 + 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb b/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb new file mode 100644 index 0000000000..426fedf887 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.23.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/Cython/' +description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.10')] + +cythonlibdir = 'lib/python%(pyshortver)s/site-packages/Cython-%(version)s-py%(pyshortver)s-linux-x86_64.egg' +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': [cythonlibdir + '/%(name)s'] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-gimkl-2.11.5-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-gimkl-2.11.5-Python-2.7.10.eb index c6aa562ded..3f9ec175b0 100644 --- a/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-gimkl-2.11.5-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PyFFmpeg/PyFFmpeg-2.1beta-gimkl-2.11.5-Python-2.7.10.eb @@ -20,6 +20,7 @@ patches = [ dependencies = [ ('Python', '2.7.10'), + ('Cython', '0.23.4', versionsuffix), ('FFmpeg', '0.10.16'), ] -- GitLab From 491137525e581d1164af4658e1c8d6eeb9842643 Mon Sep 17 00:00:00 2001 From: John-Paul Robinson Date: Thu, 18 Feb 2016 12:36:08 -0600 Subject: [PATCH 0518/2133] Update BFAST to use goolf-1.7.20 This updates to using a newer GCC 4.8.4 via goolf-1.7.20 in order to avoid a build failure for GCC 4.7.2 in goolf-1.4.10. The build failes due to a texinfo parsing bug in GCC documentation files. This problem appears on systems like CentOS 7 due to stricter parsing in newer versions of texinfo (5+) supplied by the system environment. See the bug report for GCC 4.7.2 and patch description https://gcc.gnu.org/bugzilla/show_bug.cgi?id=52903 --- .../b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb new file mode 100644 index 0000000000..a5c3af2f9a --- /dev/null +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BFAST' +version = '0.7.0a' + +homepage = 'http://bfast.sourceforge.net/' +description = """BFAST facilitates the fast and accurate mapping of short reads to reference sequences. + Some advantages of BFAST include: + 1) Speed: enables billions of short reads to be mapped quickly. + 2) Accuracy: A priori probabilities for mapping reads with defined set of variants. + 3) An easy way to measurably tune accuracy at the expense of speed.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +import string +swdir = version.rstrip(string.lowercase + string.uppercase) +# eg. http://sourceforge.net/projects/bfast/files/bfast/0.7.0/bfast-0.7.0a.tar.gz/download +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % swdir, 'download'] + +dependencies = [('bzip2', '1.0.6')] + +sanity_check_paths = { + 'files': ["bin/bfast"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c08bd4a87dc921af2bf10fe29a6f8a604787ddeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 20:19:42 +0100 Subject: [PATCH 0519/2133] {toolchain}[dummy] intel 2016.02 --- .../easyconfigs/i/intel/intel-2016.02.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel/intel-2016.02.eb diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02.eb b/easybuild/easyconfigs/i/intel/intel-2016.02.eb new file mode 100644 index 0000000000..4c2ff105d6 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.02.eb @@ -0,0 +1,25 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'intel' +version = '2016.02' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.2.181' +gccver = '4.9.3' +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.2.181', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' -- GitLab From 3807a518db8659408f9261906b69c3a819a3b98f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 20:55:57 +0100 Subject: [PATCH 0520/2133] bump GCC to 5.3.0 --- easybuild/easyconfigs/i/intel/intel-2016.02.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02.eb b/easybuild/easyconfigs/i/intel/intel-2016.02.eb index 4c2ff105d6..47932a57f9 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02.eb @@ -10,7 +10,7 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.2.181' -gccver = '4.9.3' +gccver = '5.3.0' binutilsver = '2.26' gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ -- GitLab From c0ea345ba8147c1884077157db1bcd921e71ea15 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 10:14:51 +1300 Subject: [PATCH 0521/2133] Corrected inappropriate version of libsodium dependency --- easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2015a.eb index 1de09786b7..344b95ebc3 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2015a.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2015a.eb @@ -24,7 +24,7 @@ configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' dependencies = [ ('OpenPGM', '5.2.122'), ('util-linux', '2.27.1'), - ('libsodium', '1.0.6'), + ('libsodium', '1.0.8'), ] sanity_check_paths = { -- GitLab From 96e9028c4aa356bde6671e7b1f30069137b5d124 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 10:21:08 +1300 Subject: [PATCH 0522/2133] Ensure that Doxygen depends on the same Bison as flex does --- easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb index 3b682b018a..95861d4eca 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb @@ -12,7 +12,7 @@ source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] builddependencies = [ ('flex', '2.6.0'), - ('Bison', '3.0.3'), + ('Bison', '3.0.4'), ] moduleclass = 'devel' -- GitLab From bd034850f4692606c7b408fba1f4ad56c6d9275e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 11:01:09 +1300 Subject: [PATCH 0523/2133] Updated source URL for FreeXL downloads --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb | 3 +-- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb index c7a2ae14f5..3db020fd06 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'usempi': False, 'pic': True} download_suffix = '' -source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '2.8.10.2')] diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb index 727ab2cbec..74e839a8b5 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'usempi': False, 'pic': True} download_suffix = '' -source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb index c84e5dcc81..c38933ad4f 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb @@ -9,8 +9,7 @@ description = "FreeXL is an open source library to extract valid data from withi toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'usempi': False, 'pic': True} -download_suffix = '' -source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [('CMake', '3.4.1')] -- GitLab From 83406376b7edcd2ea11e6bb459faa6da2e9bcc84 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 11:02:16 +1300 Subject: [PATCH 0524/2133] Remove unnecessary download_suffix --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb | 1 - easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb index 3db020fd06..69c610cd3f 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb @@ -9,7 +9,6 @@ description = "FreeXL is an open source library to extract valid data from withi toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'usempi': False, 'pic': True} -download_suffix = '' source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb index 74e839a8b5..0401395acc 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb @@ -9,7 +9,6 @@ description = "FreeXL is an open source library to extract valid data from withi toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'usempi': False, 'pic': True} -download_suffix = '' source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 0907ea3fd1c6bbeaeb6064ba47eddb79851b6551 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 23:12:00 +0100 Subject: [PATCH 0525/2133] {compiler}[dummp] GCC 5.3.0-2.26 --- .../b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb | 27 + .../b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 41 + .../easyconfigs/b/binutils/binutils-2.26.eb | 39 + .../f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 16 + easybuild/easyconfigs/f/flex/flex-2.6.0.eb | 16 + easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb | 25 + .../easyconfigs/g/GCCcore/GCCcore-4.9.3.eb | 3 +- .../easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 54 + .../mpfr-3.1.3-allpatches-20151029.patch | 1830 +++++++++++++++++ .../m/M4/M4-1.4.17-GCCcore-5.3.0.eb | 26 + .../z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb | 25 + 11 files changed, 2100 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..b7cebec049 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.26', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..ca71c5f04e --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb new file mode 100644 index 0000000000..5145e1becd --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), +] + +# statically link with zlib, to avoid runtime dependency on zlib +# further, add the system library path in the rpath: this should 'harden' the +# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' +prebuildopts = preconfigopts + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..f20e1d0126 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb new file mode 100644 index 0000000000..e7580df4ae --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..34bf1f36a8 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '5.3.0' + +binutilsver = '2.26' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index 268b052687..40449db3d5 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -10,7 +10,6 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' -gcc_name = 'GCC' source_urls = [ 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror @@ -19,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ - '%s-%s.tar.bz2' % (gcc_name.lower(), version), + 'gcc-%(version)s.tar.bz2', 'gmp-6.0.0a.tar.bz2', 'mpfr-%s.tar.gz' % mpfr_version, 'mpc-1.0.2.tar.gz', diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb new file mode 100644 index 0000000000..e7aac86863 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '5.3.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.3' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.0.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.15.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20151029.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [ + ('binutils', '2.26'), + ('M4', '1.4.17'), +] + +checksums = [ + 'c9616fd448f980259c31de613e575719', # gcc-5.3.0.tar.bz2 + '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 + '7b650781f0a7c4a62e9bc8bdaaa0018b', # mpfr-3.1.3.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + '8428efbbc6f6e2810ce5c1ba73ecf98c', # isl-0.15.tar.bz2 + '6476b450c3db177b2250f3549362380e', # mpfr-3.1.3-allpatches-20151029.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch new file mode 100644 index 0000000000..891831f521 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch @@ -0,0 +1,1830 @@ +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:49:23.950112879 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:49:24.042113845 +0000 +@@ -0,0 +1 @@ ++lngamma-and-doc +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-06-19 19:55:09.000000000 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:49:24.042113845 +0000 +@@ -1 +1 @@ +-3.1.3 ++3.1.3-p1 +diff -Naurd mpfr-3.1.3-a/doc/mpfr.texi mpfr-3.1.3-b/doc/mpfr.texi +--- mpfr-3.1.3-a/doc/mpfr.texi 2015-06-19 19:55:11.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.texi 2015-07-02 10:49:24.018113593 +0000 +@@ -810,13 +810,17 @@ + When the input point is in the closure of the domain of the mathematical + function and an input argument is +0 (resp.@: @minus{}0), one considers + the limit when the corresponding argument approaches 0 from above +-(resp.@: below). If the limit is not defined (e.g., @code{mpfr_log} on +-@minus{}0), the behavior is specified in the description of the MPFR function. ++(resp.@: below), if possible. If the limit is not defined (e.g., ++@code{mpfr_sqrt} and @code{mpfr_log} on @minus{}0), the behavior is ++specified in the description of the MPFR function, but must be consistent ++with the rule from the above paragraph (e.g., @code{mpfr_log} on @pom{}0 ++gives @minus{}Inf). + + When the result is equal to 0, its sign is determined by considering the + limit as if the input point were not in the domain: If one approaches 0 + from above (resp.@: below), the result is +0 (resp.@: @minus{}0); +-for example, @code{mpfr_sin} on +0 gives +0. ++for example, @code{mpfr_sin} on @minus{}0 gives @minus{}0 and ++@code{mpfr_acos} on 1 gives +0 (in all rounding modes). + In the other cases, the sign is specified in the description of the MPFR + function; for example @code{mpfr_max} on @minus{}0 and +0 gives +0. + +@@ -832,8 +836,8 @@ + @c that advantages in practice), like for any bug fix. + Example: @code{mpfr_hypot} on (NaN,0) gives NaN, but @code{mpfr_hypot} + on (NaN,+Inf) gives +Inf (as specified in @ref{Special Functions}), +-since for any finite input @var{x}, @code{mpfr_hypot} on (@var{x},+Inf) +-gives +Inf. ++since for any finite or infinite input @var{x}, @code{mpfr_hypot} on ++(@var{x},+Inf) gives +Inf. + + @node Exceptions, Memory Handling, Floating-Point Values on Special Numbers, MPFR Basics + @comment node-name, next, previous, up +@@ -1581,7 +1585,8 @@ + @deftypefunx int mpfr_add_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_add_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} + @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) + 0 = (+0) and (@minus{}0) + 0 = (@minus{}0)). + The @code{mpfr_add_d} function assumes that the radix of the @code{double} type + is a power of 2, with a precision at most that declared by the C implementation +@@ -1599,7 +1604,8 @@ + @deftypefunx int mpfr_sub_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sub_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} - @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) @minus{} 0 = (+0), (@minus{}0) @minus{} 0 = (@minus{}0), + 0 @minus{} (+0) = (@minus{}0) and 0 @minus{} (@minus{}0) = (+0)). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_sub} +@@ -1615,7 +1621,7 @@ + Set @var{rop} to @math{@var{op1} @GMPtimes{} @var{op2}} rounded in the + direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_mul_d}. + @end deftypefun + +@@ -1635,7 +1641,7 @@ + @deftypefunx int mpfr_div_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1}/@var{op2}} rounded in the direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_div} + and @code{mpfr_div_d}. + @end deftypefun +@@ -1643,15 +1649,18 @@ + @deftypefun int mpfr_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sqrt_ui (mpfr_t @var{rop}, unsigned long int @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{\sqrt{@var{op}}, the square root of @var{op}} +-rounded in the direction @var{rnd} (set @var{rop} to @minus{}0 if @var{op} is +-@minus{}0, to be consistent with the IEEE 754 standard). ++rounded in the direction @var{rnd}. Set @var{rop} to @minus{}0 if ++@var{op} is @minus{}0, to be consistent with the IEEE 754 standard. + Set @var{rop} to NaN if @var{op} is negative. + @end deftypefun + + @deftypefun int mpfr_rec_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{1/\sqrt{@var{op}}, the reciprocal square root of @var{op}} +-rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is +-@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. ++rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is ++@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. Warning! ++Therefore the result on @minus{}0 is different from the one of the rSqrt ++function recommended by the IEEE 754-2008 standard (Section 9.2.1), which ++is @minus{}Inf instead of +Inf. + @end deftypefun + + @deftypefun int mpfr_cbrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -1832,7 +1841,9 @@ + @m{\log_2 @var{op}, log2(@var{op})} or + @m{\log_{10} @var{op}, log10(@var{op})}, respectively, + rounded in the direction @var{rnd}. +-Set @var{rop} to @minus{}Inf if @var{op} is @minus{}0 ++Set @var{rop} to +0 if @var{op} is 1 (in all rounding modes), ++for consistency with the ISO C99 and IEEE 754-2008 standards. ++Set @var{rop} to @minus{}Inf if @var{op} is @pom{}0 + (i.e., the sign of the zero has no influence on the result). + @end deftypefun + +@@ -2003,8 +2014,11 @@ + @deftypefun int mpfr_lngamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to the value of the logarithm of the Gamma function on @var{op}, + rounded in the direction @var{rnd}. +-When @math{@minus{}2@var{k}@minus{}1 @le{} @var{op} @le{} @minus{}2@var{k}}, +-@var{k} being a non-negative integer, @var{rop} is set to NaN. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf, ++following the general rules on special values. ++When @math{@minus{}2@var{k}@minus{}1 < @var{op} < @minus{}2@var{k}}, ++@var{k} being a nonnegative integer, set @var{rop} to NaN@. + See also @code{mpfr_lgamma}. + @end deftypefun + +@@ -2012,10 +2026,11 @@ + Set @var{rop} to the value of the logarithm of the absolute value of the + Gamma function on @var{op}, rounded in the direction @var{rnd}. The sign + (1 or @minus{}1) of Gamma(@var{op}) is returned in the object pointed to +-by @var{signp}. When @var{op} is an infinity or a non-positive integer, set +-@var{rop} to +Inf. When @var{op} is NaN, @minus{}Inf or a negative integer, +-*@var{signp} is undefined, and when @var{op} is @pom{}0, *@var{signp} is +-the sign of the zero. ++by @var{signp}. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf. ++When @var{op} is NaN, @minus{}Inf or a negative integer, *@var{signp} is ++undefined, and when @var{op} is @pom{}0, *@var{signp} is the sign of the zero. + @end deftypefun + + @deftypefun int mpfr_digamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -2064,7 +2079,10 @@ + @deftypefunx int mpfr_fms (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_t @var{op3}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{(@var{op1} @GMPtimes{} @var{op2}) + @var{op3}} + (resp.@: @math{(@var{op1} @GMPtimes{} @var{op2}) - @var{op3}}) +-rounded in the direction @var{rnd}. ++rounded in the direction @var{rnd}. Concerning special values (signed zeros, ++infinities, NaN), these functions behave like a multiplication followed by a ++separate addition or subtraction. That is, the fused operation matters only ++for rounding. + @end deftypefun + + @deftypefun int mpfr_agm (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_rnd_t @var{rnd}) +@@ -2089,8 +2107,8 @@ + i.e., $\sqrt{x^2+y^2}$, + @end tex + rounded in the direction @var{rnd}. +-Special values are handled as described in Section F.9.4.3 of +-the ISO C99 and IEEE 754-2008 standards: ++Special values are handled as described in the ISO C99 (Section F.9.4.3) ++and IEEE 754-2008 (Section 9.2.1) standards: + If @var{x} or @var{y} is an infinity, then +Inf is returned in @var{rop}, + even if the other number is NaN. + @end deftypefun +diff -Naurd mpfr-3.1.3-a/doc/mpfr.info mpfr-3.1.3-b/doc/mpfr.info +--- mpfr-3.1.3-a/doc/mpfr.info 2015-06-19 19:55:53.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.info 2015-07-02 10:49:38.718267817 +0000 +@@ -1,4 +1,4 @@ +-This is mpfr.info, produced by makeinfo version 5.2 from mpfr.texi. ++This is mpfr.info, produced by makeinfo version 6.0 from mpfr.texi. + + This manual documents how to install and use the Multiple Precision + Floating-Point Reliable Library, version 3.1.3. +@@ -55,7 +55,7 @@ + MPFR Copying Conditions + *********************** + +-The GNU MPFR library (or MPFR for short) is "free"; this means that ++The GNU MPFR library (or MPFR for short) is “free”; this means that + everyone is free to use it and free to redistribute it on a free basis. + The library is not in the public domain; it is copyrighted and there are + restrictions on its distribution, but these restrictions are designed to +@@ -418,7 +418,7 @@ + 4.2 Nomenclature and Types + ========================== + +-A "floating-point number", or "float" for short, is an arbitrary ++A “floating-point number”, or “float” for short, is an arbitrary + precision significand (also called mantissa) with a limited precision + exponent. The C data type for such objects is ‘mpfr_t’ (internally + defined as a one-element array of a structure, and ‘mpfr_ptr’ is the C +@@ -432,7 +432,7 @@ + to the other functions supported by MPFR. Unless documented otherwise, + the sign bit of a NaN is unspecified. + +-The "precision" is the number of bits used to represent the significand ++The “precision” is the number of bits used to represent the significand + of a floating-point number; the corresponding C data type is + ‘mpfr_prec_t’. The precision can be any integer between ‘MPFR_PREC_MIN’ + and ‘MPFR_PREC_MAX’. In the current implementation, ‘MPFR_PREC_MIN’ is +@@ -446,7 +446,7 @@ + may abort, crash or have undefined behavior (depending on your C + implementation). + +-The "rounding mode" specifies the way to round the result of a ++The “rounding mode” specifies the way to round the result of a + floating-point operation, in case the exact result can not be + represented exactly in the destination significand; the corresponding C + data type is ‘mpfr_rnd_t’. +@@ -499,14 +499,14 @@ + representable numbers, it is rounded to the one with the least + significant bit set to zero. For example, the number 2.5, which is + represented by (10.1) in binary, is rounded to (10.0)=2 with a precision +-of two bits, and not to (11.0)=3. This rule avoids the "drift" ++of two bits, and not to (11.0)=3. This rule avoids the “drift” + phenomenon mentioned by Knuth in volume 2 of The Art of Computer + Programming (Section 4.2.2). + + Most MPFR functions take as first argument the destination variable, + as second and following arguments the input variables, as last argument + a rounding mode, and have a return value of type ‘int’, called the +-"ternary value". The value stored in the destination variable is ++“ternary value”. The value stored in the destination variable is + correctly rounded, i.e., MPFR behaves as if it computed the result with + an infinite precision, then rounded it to the precision of this + variable. The input variables are regarded as exact (in particular, +@@ -572,15 +572,18 @@ + When the input point is in the closure of the domain of the + mathematical function and an input argument is +0 (resp. −0), one + considers the limit when the corresponding argument approaches 0 from +-above (resp. below). If the limit is not defined (e.g., ‘mpfr_log’ on +-−0), the behavior is specified in the description of the MPFR function. ++above (resp. below), if possible. If the limit is not defined (e.g., ++‘mpfr_sqrt’ and ‘mpfr_log’ on −0), the behavior is specified in the ++description of the MPFR function, but must be consistent with the rule ++from the above paragraph (e.g., ‘mpfr_log’ on ±0 gives −Inf). + + When the result is equal to 0, its sign is determined by considering + the limit as if the input point were not in the domain: If one + approaches 0 from above (resp. below), the result is +0 (resp. −0); for +-example, ‘mpfr_sin’ on +0 gives +0. In the other cases, the sign is +-specified in the description of the MPFR function; for example +-‘mpfr_max’ on −0 and +0 gives +0. ++example, ‘mpfr_sin’ on −0 gives −0 and ‘mpfr_acos’ on 1 gives +0 (in all ++rounding modes). In the other cases, the sign is specified in the ++description of the MPFR function; for example ‘mpfr_max’ on −0 and +0 ++gives +0. + + When the input point is not in the closure of the domain of the + function, the result is NaN. Example: ‘mpfr_sqrt’ on −17 gives NaN. +@@ -590,8 +593,8 @@ + numbers; such a case is always explicitly specified in *note MPFR + Interface::. Example: ‘mpfr_hypot’ on (NaN,0) gives NaN, but + ‘mpfr_hypot’ on (NaN,+Inf) gives +Inf (as specified in *note Special +-Functions::), since for any finite input X, ‘mpfr_hypot’ on (X,+Inf) +-gives +Inf. ++Functions::), since for any finite or infinite input X, ‘mpfr_hypot’ on ++(X,+Inf) gives +Inf. + +  + File: mpfr.info, Node: Exceptions, Next: Memory Handling, Prev: Floating-Point Values on Special Numbers, Up: MPFR Basics +@@ -1253,8 +1256,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_add_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 + OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) + 0 = ++ Set ROP to OP1 + OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) + 0 = + (+0) and (−0) + 0 = (−0)). The ‘mpfr_add_d’ function assumes that + the radix of the ‘double’ type is a power of 2, with a precision at + most that declared by the C implementation (macro +@@ -1280,8 +1284,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_sub_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 - OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) − 0 = ++ Set ROP to OP1 - OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) − 0 = + (+0), (−0) − 0 = (−0), 0 − (+0) = (−0) and 0 − (−0) = (+0)). The + same restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_sub’ and + ‘mpfr_sub_d’. +@@ -1300,7 +1305,7 @@ + mpfr_rnd_t RND) + Set ROP to OP1 times OP2 rounded in the direction RND. When a + result is zero, its sign is the product of the signs of the +- operands (for types having no signed zero, it is considered ++ operands (for types having no signed zeros, 0 is considered + positive). The same restrictions than for ‘mpfr_add_d’ apply to + ‘mpfr_mul_d’. + +@@ -1327,21 +1332,24 @@ + mpfr_rnd_t RND) + Set ROP to OP1/OP2 rounded in the direction RND. When a result is + zero, its sign is the product of the signs of the operands (for +- types having no signed zero, it is considered positive). The same ++ types having no signed zeros, 0 is considered positive). The same + restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_div’ and + ‘mpfr_div_d’. + + -- Function: int mpfr_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_sqrt_ui (mpfr_t ROP, unsigned long int OP, + mpfr_rnd_t RND) +- Set ROP to the square root of OP rounded in the direction RND (set +- ROP to −0 if OP is −0, to be consistent with the IEEE 754 +- standard). Set ROP to NaN if OP is negative. ++ Set ROP to the square root of OP rounded in the direction RND. Set ++ ROP to −0 if OP is −0, to be consistent with the IEEE 754 standard. ++ Set ROP to NaN if OP is negative. + + -- Function: int mpfr_rec_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the reciprocal square root of OP rounded in the + direction RND. Set ROP to +Inf if OP is ±0, +0 if OP is +Inf, and +- NaN if OP is negative. ++ NaN if OP is negative. Warning! Therefore the result on −0 is ++ different from the one of the rSqrt function recommended by the ++ IEEE 754-2008 standard (Section 9.2.1), which is −Inf instead of ++ +Inf. + + -- Function: int mpfr_cbrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_root (mpfr_t ROP, mpfr_t OP, unsigned long int K, +@@ -1515,8 +1523,10 @@ + -- Function: int mpfr_log2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_log10 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the natural logarithm of OP, log2(OP) or log10(OP), +- respectively, rounded in the direction RND. Set ROP to −Inf if OP +- is −0 (i.e., the sign of the zero has no influence on the result). ++ respectively, rounded in the direction RND. Set ROP to +0 if OP is ++ 1 (in all rounding modes), for consistency with the ISO C99 and ++ IEEE 754-2008 standards. Set ROP to −Inf if OP is ±0 (i.e., the ++ sign of the zero has no influence on the result). + + -- Function: int mpfr_exp (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_exp2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) +@@ -1649,17 +1659,21 @@ + + -- Function: int mpfr_lngamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the Gamma function on OP, +- rounded in the direction RND. When −2K−1 <= OP <= −2K, K being a +- non-negative integer, ROP is set to NaN. See also ‘mpfr_lgamma’. ++ rounded in the direction RND. When OP is 1 or 2, set ROP to +0 (in ++ all rounding modes). When OP is an infinity or a nonpositive ++ integer, set ROP to +Inf, following the general rules on special ++ values. When −2K−1 < OP < −2K, K being a nonnegative integer, set ++ ROP to NaN. See also ‘mpfr_lgamma’. + + -- Function: int mpfr_lgamma (mpfr_t ROP, int *SIGNP, mpfr_t OP, + mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the absolute value of the + Gamma function on OP, rounded in the direction RND. The sign (1 or + −1) of Gamma(OP) is returned in the object pointed to by SIGNP. +- When OP is an infinity or a non-positive integer, set ROP to +Inf. +- When OP is NaN, −Inf or a negative integer, *SIGNP is undefined, +- and when OP is ±0, *SIGNP is the sign of the zero. ++ When OP is 1 or 2, set ROP to +0 (in all rounding modes). When OP ++ is an infinity or a nonpositive integer, set ROP to +Inf. When OP ++ is NaN, −Inf or a negative integer, *SIGNP is undefined, and when ++ OP is ±0, *SIGNP is the sign of the zero. + + -- Function: int mpfr_digamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the Digamma (sometimes also called Psi) +@@ -1703,7 +1717,10 @@ + -- Function: int mpfr_fms (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, mpfr_t + OP3, mpfr_rnd_t RND) + Set ROP to (OP1 times OP2) + OP3 (resp. (OP1 times OP2) - OP3) +- rounded in the direction RND. ++ rounded in the direction RND. Concerning special values (signed ++ zeros, infinities, NaN), these functions behave like a ++ multiplication followed by a separate addition or subtraction. ++ That is, the fused operation matters only for rounding. + + -- Function: int mpfr_agm (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, + mpfr_rnd_t RND) +@@ -1717,9 +1734,10 @@ + RND) + Set ROP to the Euclidean norm of X and Y, i.e., the square root of + the sum of the squares of X and Y, rounded in the direction RND. +- Special values are handled as described in Section F.9.4.3 of the +- ISO C99 and IEEE 754-2008 standards: If X or Y is an infinity, then +- +Inf is returned in ROP, even if the other number is NaN. ++ Special values are handled as described in the ISO C99 (Section ++ F.9.4.3) and IEEE 754-2008 (Section 9.2.1) standards: If X or Y is ++ an infinity, then +Inf is returned in ROP, even if the other number ++ is NaN. + + -- Function: int mpfr_ai (mpfr_t ROP, mpfr_t X, mpfr_rnd_t RND) + Set ROP to the value of the Airy function Ai on X, rounded in the +@@ -2670,7 +2688,7 @@ + 5.16 Internals + ============== + +-A "limb" means the part of a multi-precision number that fits in a ++A “limb” means the part of a multi-precision number that fits in a + single word. Usually a limb contains 32 or 64 bits. The C data type + for a limb is ‘mp_limb_t’. + +@@ -3140,7 +3158,7 @@ + 0. PREAMBLE + + The purpose of this License is to make a manual, textbook, or other +- functional and useful document "free" in the sense of freedom: to ++ functional and useful document “free” in the sense of freedom: to + assure everyone the effective freedom to copy and redistribute it, + with or without modifying it, either commercially or + noncommercially. Secondarily, this License preserves for the +@@ -3655,9 +3673,9 @@ + * Menu: + + * mpfr_abs: Basic Arithmetic Functions. +- (line 160) +-* mpfr_acos: Special Functions. (line 51) +-* mpfr_acosh: Special Functions. (line 115) ++ (line 165) ++* mpfr_acos: Special Functions. (line 53) ++* mpfr_acosh: Special Functions. (line 117) + * mpfr_add: Basic Arithmetic Functions. + (line 6) + * mpfr_add_d: Basic Arithmetic Functions. +@@ -3670,15 +3688,15 @@ + (line 8) + * mpfr_add_z: Basic Arithmetic Functions. + (line 14) +-* mpfr_agm: Special Functions. (line 210) +-* mpfr_ai: Special Functions. (line 226) +-* mpfr_asin: Special Functions. (line 52) +-* mpfr_asinh: Special Functions. (line 116) ++* mpfr_agm: Special Functions. (line 219) ++* mpfr_ai: Special Functions. (line 236) ++* mpfr_asin: Special Functions. (line 54) ++* mpfr_asinh: Special Functions. (line 118) + * mpfr_asprintf: Formatted Output Functions. + (line 193) +-* mpfr_atan: Special Functions. (line 53) +-* mpfr_atan2: Special Functions. (line 63) +-* mpfr_atanh: Special Functions. (line 117) ++* mpfr_atan: Special Functions. (line 55) ++* mpfr_atan2: Special Functions. (line 65) ++* mpfr_atanh: Special Functions. (line 119) + * mpfr_buildopt_decimal_p: Miscellaneous Functions. + (line 162) + * mpfr_buildopt_gmpinternals_p: Miscellaneous Functions. +@@ -3690,7 +3708,7 @@ + * mpfr_can_round: Rounding Related Functions. + (line 39) + * mpfr_cbrt: Basic Arithmetic Functions. +- (line 108) ++ (line 113) + * mpfr_ceil: Integer Related Functions. + (line 7) + * mpfr_check_range: Exception Related Functions. +@@ -3735,18 +3753,18 @@ + (line 27) + * mpfr_cmp_z: Comparison Functions. + (line 11) +-* mpfr_const_catalan: Special Functions. (line 237) +-* mpfr_const_euler: Special Functions. (line 236) +-* mpfr_const_log2: Special Functions. (line 234) +-* mpfr_const_pi: Special Functions. (line 235) ++* mpfr_const_catalan: Special Functions. (line 247) ++* mpfr_const_euler: Special Functions. (line 246) ++* mpfr_const_log2: Special Functions. (line 244) ++* mpfr_const_pi: Special Functions. (line 245) + * mpfr_copysign: Miscellaneous Functions. + (line 109) +-* mpfr_cos: Special Functions. (line 29) +-* mpfr_cosh: Special Functions. (line 95) +-* mpfr_cot: Special Functions. (line 47) +-* mpfr_coth: Special Functions. (line 111) +-* mpfr_csc: Special Functions. (line 46) +-* mpfr_csch: Special Functions. (line 110) ++* mpfr_cos: Special Functions. (line 31) ++* mpfr_cosh: Special Functions. (line 97) ++* mpfr_cot: Special Functions. (line 49) ++* mpfr_coth: Special Functions. (line 113) ++* mpfr_csc: Special Functions. (line 48) ++* mpfr_csch: Special Functions. (line 112) + * mpfr_custom_get_exp: Custom Interface. (line 75) + * mpfr_custom_get_kind: Custom Interface. (line 65) + * mpfr_custom_get_significand: Custom Interface. (line 70) +@@ -3756,47 +3774,47 @@ + * mpfr_custom_move: Custom Interface. (line 82) + * MPFR_DECL_INIT: Initialization Functions. + (line 74) +-* mpfr_digamma: Special Functions. (line 166) ++* mpfr_digamma: Special Functions. (line 172) + * mpfr_dim: Basic Arithmetic Functions. +- (line 166) ++ (line 171) + * mpfr_div: Basic Arithmetic Functions. +- (line 72) ++ (line 74) + * mpfr_divby0_p: Exception Related Functions. + (line 134) + * mpfr_div_2exp: Compatibility with MPF. + (line 49) + * mpfr_div_2si: Basic Arithmetic Functions. +- (line 181) ++ (line 186) + * mpfr_div_2ui: Basic Arithmetic Functions. +- (line 179) ++ (line 184) + * mpfr_div_d: Basic Arithmetic Functions. +- (line 84) ++ (line 86) + * mpfr_div_q: Basic Arithmetic Functions. +- (line 88) ++ (line 90) + * mpfr_div_si: Basic Arithmetic Functions. +- (line 80) ++ (line 82) + * mpfr_div_ui: Basic Arithmetic Functions. +- (line 76) ++ (line 78) + * mpfr_div_z: Basic Arithmetic Functions. +- (line 86) ++ (line 88) + * mpfr_d_div: Basic Arithmetic Functions. +- (line 82) ++ (line 84) + * mpfr_d_sub: Basic Arithmetic Functions. +- (line 35) +-* mpfr_eint: Special Functions. (line 133) ++ (line 36) ++* mpfr_eint: Special Functions. (line 135) + * mpfr_eq: Compatibility with MPF. + (line 28) + * mpfr_equal_p: Comparison Functions. + (line 59) + * mpfr_erangeflag_p: Exception Related Functions. + (line 137) +-* mpfr_erf: Special Functions. (line 177) +-* mpfr_erfc: Special Functions. (line 178) +-* mpfr_exp: Special Functions. (line 23) +-* mpfr_exp10: Special Functions. (line 25) +-* mpfr_exp2: Special Functions. (line 24) +-* mpfr_expm1: Special Functions. (line 129) +-* mpfr_fac_ui: Special Functions. (line 121) ++* mpfr_erf: Special Functions. (line 183) ++* mpfr_erfc: Special Functions. (line 184) ++* mpfr_exp: Special Functions. (line 25) ++* mpfr_exp10: Special Functions. (line 27) ++* mpfr_exp2: Special Functions. (line 26) ++* mpfr_expm1: Special Functions. (line 131) ++* mpfr_fac_ui: Special Functions. (line 123) + * mpfr_fits_intmax_p: Conversion Functions. + (line 150) + * mpfr_fits_sint_p: Conversion Functions. +@@ -3815,20 +3833,20 @@ + (line 147) + * mpfr_floor: Integer Related Functions. + (line 8) +-* mpfr_fma: Special Functions. (line 203) ++* mpfr_fma: Special Functions. (line 209) + * mpfr_fmod: Integer Related Functions. + (line 92) +-* mpfr_fms: Special Functions. (line 205) ++* mpfr_fms: Special Functions. (line 211) + * mpfr_fprintf: Formatted Output Functions. + (line 157) + * mpfr_frac: Integer Related Functions. + (line 76) +-* mpfr_free_cache: Special Functions. (line 244) ++* mpfr_free_cache: Special Functions. (line 254) + * mpfr_free_str: Conversion Functions. + (line 137) + * mpfr_frexp: Conversion Functions. + (line 45) +-* mpfr_gamma: Special Functions. (line 148) ++* mpfr_gamma: Special Functions. (line 150) + * mpfr_get_d: Conversion Functions. + (line 7) + * mpfr_get_decimal64: Conversion Functions. +@@ -3887,7 +3905,7 @@ + (line 56) + * mpfr_greater_p: Comparison Functions. + (line 55) +-* mpfr_hypot: Special Functions. (line 218) ++* mpfr_hypot: Special Functions. (line 227) + * mpfr_inexflag_p: Exception Related Functions. + (line 136) + * mpfr_inf_p: Comparison Functions. +@@ -3922,21 +3940,21 @@ + (line 31) + * mpfr_integer_p: Integer Related Functions. + (line 119) +-* mpfr_j0: Special Functions. (line 182) +-* mpfr_j1: Special Functions. (line 183) +-* mpfr_jn: Special Functions. (line 184) ++* mpfr_j0: Special Functions. (line 188) ++* mpfr_j1: Special Functions. (line 189) ++* mpfr_jn: Special Functions. (line 190) + * mpfr_lessequal_p: Comparison Functions. + (line 58) + * mpfr_lessgreater_p: Comparison Functions. + (line 64) + * mpfr_less_p: Comparison Functions. + (line 57) +-* mpfr_lgamma: Special Functions. (line 157) +-* mpfr_li2: Special Functions. (line 143) +-* mpfr_lngamma: Special Functions. (line 152) ++* mpfr_lgamma: Special Functions. (line 162) ++* mpfr_li2: Special Functions. (line 145) ++* mpfr_lngamma: Special Functions. (line 154) + * mpfr_log: Special Functions. (line 16) + * mpfr_log10: Special Functions. (line 18) +-* mpfr_log1p: Special Functions. (line 125) ++* mpfr_log1p: Special Functions. (line 127) + * mpfr_log2: Special Functions. (line 17) + * mpfr_max: Miscellaneous Functions. + (line 22) +@@ -3947,29 +3965,29 @@ + * mpfr_modf: Integer Related Functions. + (line 82) + * mpfr_mul: Basic Arithmetic Functions. +- (line 51) ++ (line 53) + * mpfr_mul_2exp: Compatibility with MPF. + (line 47) + * mpfr_mul_2si: Basic Arithmetic Functions. +- (line 174) ++ (line 179) + * mpfr_mul_2ui: Basic Arithmetic Functions. +- (line 172) ++ (line 177) + * mpfr_mul_d: Basic Arithmetic Functions. +- (line 57) ++ (line 59) + * mpfr_mul_q: Basic Arithmetic Functions. +- (line 61) ++ (line 63) + * mpfr_mul_si: Basic Arithmetic Functions. +- (line 55) ++ (line 57) + * mpfr_mul_ui: Basic Arithmetic Functions. +- (line 53) ++ (line 55) + * mpfr_mul_z: Basic Arithmetic Functions. +- (line 59) ++ (line 61) + * mpfr_nanflag_p: Exception Related Functions. + (line 135) + * mpfr_nan_p: Comparison Functions. + (line 39) + * mpfr_neg: Basic Arithmetic Functions. +- (line 159) ++ (line 164) + * mpfr_nextabove: Miscellaneous Functions. + (line 15) + * mpfr_nextbelow: Miscellaneous Functions. +@@ -3983,13 +4001,13 @@ + * mpfr_overflow_p: Exception Related Functions. + (line 133) + * mpfr_pow: Basic Arithmetic Functions. +- (line 116) ++ (line 121) + * mpfr_pow_si: Basic Arithmetic Functions. +- (line 120) ++ (line 125) + * mpfr_pow_ui: Basic Arithmetic Functions. +- (line 118) ++ (line 123) + * mpfr_pow_z: Basic Arithmetic Functions. +- (line 122) ++ (line 127) + * mpfr_prec_round: Rounding Related Functions. + (line 13) + * ‘mpfr_prec_t’: Nomenclature and Types. +@@ -3999,7 +4017,7 @@ + * mpfr_print_rnd_mode: Rounding Related Functions. + (line 71) + * mpfr_rec_sqrt: Basic Arithmetic Functions. +- (line 103) ++ (line 105) + * mpfr_regular_p: Comparison Functions. + (line 43) + * mpfr_reldiff: Compatibility with MPF. +@@ -4021,11 +4039,11 @@ + * ‘mpfr_rnd_t’: Nomenclature and Types. + (line 34) + * mpfr_root: Basic Arithmetic Functions. +- (line 109) ++ (line 114) + * mpfr_round: Integer Related Functions. + (line 9) +-* mpfr_sec: Special Functions. (line 45) +-* mpfr_sech: Special Functions. (line 109) ++* mpfr_sec: Special Functions. (line 47) ++* mpfr_sech: Special Functions. (line 111) + * mpfr_set: Assignment Functions. + (line 9) + * mpfr_setsign: Miscellaneous Functions. +@@ -4100,57 +4118,57 @@ + (line 49) + * mpfr_signbit: Miscellaneous Functions. + (line 99) +-* mpfr_sin: Special Functions. (line 30) +-* mpfr_sinh: Special Functions. (line 96) +-* mpfr_sinh_cosh: Special Functions. (line 101) +-* mpfr_sin_cos: Special Functions. (line 35) ++* mpfr_sin: Special Functions. (line 32) ++* mpfr_sinh: Special Functions. (line 98) ++* mpfr_sinh_cosh: Special Functions. (line 103) ++* mpfr_sin_cos: Special Functions. (line 37) + * mpfr_si_div: Basic Arithmetic Functions. +- (line 78) ++ (line 80) + * mpfr_si_sub: Basic Arithmetic Functions. +- (line 31) ++ (line 32) + * mpfr_snprintf: Formatted Output Functions. + (line 180) + * mpfr_sprintf: Formatted Output Functions. + (line 170) + * mpfr_sqr: Basic Arithmetic Functions. +- (line 69) ++ (line 71) + * mpfr_sqrt: Basic Arithmetic Functions. +- (line 96) ++ (line 98) + * mpfr_sqrt_ui: Basic Arithmetic Functions. +- (line 97) ++ (line 99) + * mpfr_strtofr: Assignment Functions. + (line 80) + * mpfr_sub: Basic Arithmetic Functions. +- (line 25) ++ (line 26) + * mpfr_subnormalize: Exception Related Functions. + (line 60) + * mpfr_sub_d: Basic Arithmetic Functions. +- (line 37) ++ (line 38) + * mpfr_sub_q: Basic Arithmetic Functions. +- (line 43) ++ (line 44) + * mpfr_sub_si: Basic Arithmetic Functions. +- (line 33) ++ (line 34) + * mpfr_sub_ui: Basic Arithmetic Functions. +- (line 29) ++ (line 30) + * mpfr_sub_z: Basic Arithmetic Functions. +- (line 41) +-* mpfr_sum: Special Functions. (line 252) ++ (line 42) ++* mpfr_sum: Special Functions. (line 262) + * mpfr_swap: Assignment Functions. + (line 150) + * ‘mpfr_t’: Nomenclature and Types. + (line 6) +-* mpfr_tan: Special Functions. (line 31) +-* mpfr_tanh: Special Functions. (line 97) ++* mpfr_tan: Special Functions. (line 33) ++* mpfr_tanh: Special Functions. (line 99) + * mpfr_trunc: Integer Related Functions. + (line 10) + * mpfr_ui_div: Basic Arithmetic Functions. +- (line 74) ++ (line 76) + * mpfr_ui_pow: Basic Arithmetic Functions. +- (line 126) ++ (line 131) + * mpfr_ui_pow_ui: Basic Arithmetic Functions. +- (line 124) ++ (line 129) + * mpfr_ui_sub: Basic Arithmetic Functions. +- (line 27) ++ (line 28) + * mpfr_underflow_p: Exception Related Functions. + (line 132) + * mpfr_unordered_p: Comparison Functions. +@@ -4181,61 +4199,61 @@ + (line 182) + * mpfr_vsprintf: Formatted Output Functions. + (line 171) +-* mpfr_y0: Special Functions. (line 193) +-* mpfr_y1: Special Functions. (line 194) +-* mpfr_yn: Special Functions. (line 195) ++* mpfr_y0: Special Functions. (line 199) ++* mpfr_y1: Special Functions. (line 200) ++* mpfr_yn: Special Functions. (line 201) + * mpfr_zero_p: Comparison Functions. + (line 42) +-* mpfr_zeta: Special Functions. (line 171) +-* mpfr_zeta_ui: Special Functions. (line 172) ++* mpfr_zeta: Special Functions. (line 177) ++* mpfr_zeta_ui: Special Functions. (line 178) + * mpfr_z_sub: Basic Arithmetic Functions. +- (line 39) ++ (line 40) + + +  + Tag Table: + Node: Top775 + Node: Copying2007 +-Node: Introduction to MPFR3766 +-Node: Installing MPFR5880 +-Node: Reporting Bugs11323 +-Node: MPFR Basics13353 +-Node: Headers and Libraries13669 +-Node: Nomenclature and Types16828 +-Node: MPFR Variable Conventions18874 +-Node: Rounding Modes20418 +-Ref: ternary value21544 +-Node: Floating-Point Values on Special Numbers23526 +-Node: Exceptions26572 +-Node: Memory Handling29749 +-Node: MPFR Interface30894 +-Node: Initialization Functions33008 +-Node: Assignment Functions40318 +-Node: Combined Initialization and Assignment Functions49673 +-Node: Conversion Functions50974 +-Node: Basic Arithmetic Functions60035 +-Node: Comparison Functions69200 +-Node: Special Functions72687 +-Node: Input and Output Functions86672 +-Node: Formatted Output Functions88644 +-Node: Integer Related Functions98431 +-Node: Rounding Related Functions105051 +-Node: Miscellaneous Functions108888 +-Node: Exception Related Functions117568 +-Node: Compatibility with MPF124386 +-Node: Custom Interface127127 +-Node: Internals131526 +-Node: API Compatibility133066 +-Node: Type and Macro Changes134995 +-Node: Added Functions137844 +-Node: Changed Functions141132 +-Node: Removed Functions145545 +-Node: Other Changes145973 +-Node: Contributors147576 +-Node: References150219 +-Node: GNU Free Documentation License151973 +-Node: Concept Index174562 +-Node: Function and Type Index180659 ++Node: Introduction to MPFR3770 ++Node: Installing MPFR5884 ++Node: Reporting Bugs11327 ++Node: MPFR Basics13357 ++Node: Headers and Libraries13673 ++Node: Nomenclature and Types16832 ++Node: MPFR Variable Conventions18894 ++Node: Rounding Modes20438 ++Ref: ternary value21568 ++Node: Floating-Point Values on Special Numbers23554 ++Node: Exceptions26813 ++Node: Memory Handling29990 ++Node: MPFR Interface31135 ++Node: Initialization Functions33249 ++Node: Assignment Functions40559 ++Node: Combined Initialization and Assignment Functions49914 ++Node: Conversion Functions51215 ++Node: Basic Arithmetic Functions60276 ++Node: Comparison Functions69777 ++Node: Special Functions73264 ++Node: Input and Output Functions87862 ++Node: Formatted Output Functions89834 ++Node: Integer Related Functions99621 ++Node: Rounding Related Functions106241 ++Node: Miscellaneous Functions110078 ++Node: Exception Related Functions118758 ++Node: Compatibility with MPF125576 ++Node: Custom Interface128317 ++Node: Internals132716 ++Node: API Compatibility134260 ++Node: Type and Macro Changes136189 ++Node: Added Functions139038 ++Node: Changed Functions142326 ++Node: Removed Functions146739 ++Node: Other Changes147167 ++Node: Contributors148770 ++Node: References151413 ++Node: GNU Free Documentation License153167 ++Node: Concept Index175760 ++Node: Function and Type Index181857 +  + End Tag Table + +diff -Naurd mpfr-3.1.3-a/src/lngamma.c mpfr-3.1.3-b/src/lngamma.c +--- mpfr-3.1.3-a/src/lngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/lngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -603,16 +603,17 @@ + mpfr_get_prec (y), mpfr_log_prec, y, inex)); + + /* special cases */ +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x) || ++ (MPFR_IS_NEG (x) && mpfr_integer_p (x)))) + { +- if (MPFR_IS_NAN (x) || MPFR_IS_NEG (x)) ++ if (MPFR_IS_NAN (x)) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; + } +- else /* lngamma(+Inf) = lngamma(+0) = +Inf */ ++ else /* lngamma(+/-Inf) = lngamma(nonpositive integer) = +Inf */ + { +- if (MPFR_IS_ZERO (x)) ++ if (!MPFR_IS_INF (x)) + mpfr_set_divby0 (); + MPFR_SET_INF (y); + MPFR_SET_POS (y); +@@ -620,8 +621,8 @@ + } + } + +- /* if x < 0 and -2k-1 <= x <= -2k, then lngamma(x) = NaN */ +- if (MPFR_IS_NEG (x) && (unit_bit (x) == 0 || mpfr_integer_p (x))) ++ /* if -2k-1 < x < -2k <= 0, then lngamma(x) = NaN */ ++ if (MPFR_IS_NEG (x) && unit_bit (x) == 0) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3" ++#define MPFR_VERSION_STRING "3.1.3-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:49:24.042113845 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3"; ++ return "3.1.3-p1"; + } +diff -Naurd mpfr-3.1.3-a/tests/tlngamma.c mpfr-3.1.3-b/tests/tlngamma.c +--- mpfr-3.1.3-a/tests/tlngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tlngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -33,7 +33,7 @@ + special (void) + { + mpfr_t x, y; +- int inex; ++ int i, inex; + + mpfr_init (x); + mpfr_init (y); +@@ -46,25 +46,29 @@ + exit (1); + } + +- mpfr_set_inf (x, -1); ++ mpfr_set_inf (x, 1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(-Inf)\n"); ++ printf ("Error for lngamma(+Inf)\n"); + exit (1); + } + +- mpfr_set_inf (x, 1); ++ mpfr_set_inf (x, -1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(+Inf)\n"); ++ printf ("Error for lngamma(-Inf)\n"); + exit (1); + } + + mpfr_set_ui (x, 0, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(+0)\n"); + exit (1); +@@ -72,32 +76,58 @@ + + mpfr_set_ui (x, 0, MPFR_RNDN); + mpfr_neg (x, x, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(-0)\n"); + exit (1); + } + + mpfr_set_ui (x, 1, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(1)\n"); + exit (1); + } + +- mpfr_set_si (x, -1, MPFR_RNDN); +- mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ for (i = 1; i <= 5; i++) + { +- printf ("Error for lngamma(-1)\n"); +- exit (1); ++ int c; ++ ++ mpfr_set_si (x, -i, MPFR_RNDN); ++ mpfr_clear_flags (); ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) ++ { ++ printf ("Error for lngamma(-%d)\n", i); ++ exit (1); ++ } ++ if (i & 1) ++ { ++ mpfr_nextabove (x); ++ c = '+'; ++ } ++ else ++ { ++ mpfr_nextbelow (x); ++ c = '-'; ++ } ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_nan_p (y)) ++ { ++ printf ("Error for lngamma(-%d%cepsilon)\n", i, c); ++ exit (1); ++ } + } + + mpfr_set_ui (x, 2, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(2)\n"); + exit (1); +@@ -127,7 +157,7 @@ + mpfr_set_str (x, CHECK_X2, 10, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str (x, CHECK_Y2, 10, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp (y, x)) ++ if (mpfr_cmp0 (y, x)) + { + printf ("mpfr_lngamma("CHECK_X2") is wrong:\n" + "expected "); +@@ -143,7 +173,7 @@ + mpfr_lngamma (y, x, MPFR_RNDU); + mpfr_set_prec (x, 175); + mpfr_set_str_binary (x, "0.1010001100011101101011001101110010100001000001000001110011000001101100001111001001000101011011100100010101011110100111110101010100010011010010000101010111001100011000101111E7"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (1)\n"); + exit (1); +@@ -155,7 +185,7 @@ + mpfr_lngamma (x, y, MPFR_RNDZ); + mpfr_set_prec (y, 21); + mpfr_set_str_binary (y, "0.111000101000001100101E9"); +- if (MPFR_IS_NAN (x) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (120)\n"); + printf ("Expected "); mpfr_print_binary (y); puts (""); +@@ -169,7 +199,7 @@ + inex = mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 206); + mpfr_set_str_binary (x, "0.10000111011000000011100010101001100110001110000111100011000100100110110010001011011110101001111011110110000001010100111011010000000011100110110101100111000111010011110010000100010111101010001101000110101001E13"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (768)\n"); + exit (1); +@@ -185,7 +215,7 @@ + mpfr_set_str_binary (x, "0.1100E-66"); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str_binary (x, "0.1100E6"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(0.1100E-66)\n"); + exit (1); +@@ -199,7 +229,7 @@ + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 32); + mpfr_set_str_binary (x, "-0.10001000111011111011000010100010E207"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(-2^199+0.5)\n"); + printf ("Got "); +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:50:08.046573308 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:50:08.126574142 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-overflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:50:08.126574142 +0000 +@@ -1 +1 @@ +-3.1.3-p1 ++3.1.3-p2 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -49,7 +49,7 @@ + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +- else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || ++ else if (MPFR_UNLIKELY(n <= 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || + exp > __gmpfr_emax + n)) ) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 +@@ -32,7 +32,7 @@ + rnd_mode), + ("y[%Pu]=%.*Rg inexact=%d", mpfr_get_prec(y), mpfr_log_prec, y, inexact)); + +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (n == 0 || MPFR_IS_SINGULAR (x))) + return mpfr_set (y, x, rnd_mode); + else + { +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p1" ++#define MPFR_VERSION_STRING "3.1.3-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -39,7 +39,7 @@ + { + mpfr_exp_t exp = MPFR_GET_EXP (x); + MPFR_SETRAW (inexact, y, x, exp, rnd_mode); +- if (MPFR_UNLIKELY( n > 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || ++ if (MPFR_UNLIKELY(n >= 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || + exp > __gmpfr_emax - n))) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emin > MPFR_EMAX_MAX + n || +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:50:08.126574142 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p1"; ++ return "3.1.3-p2"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 +@@ -242,6 +242,76 @@ + large (MPFR_EMAX_MAX); + } + ++/* Cases where the function overflows on n = 0 when rounding is like ++ away from zero. */ ++static void ++overflow0 (mpfr_exp_t emax) ++{ ++ mpfr_exp_t old_emax; ++ mpfr_t x, y1, y2; ++ int neg, r, op; ++ static char *sop[4] = { "mul_2ui", "mul_2si", "div_2ui", "div_2si" }; ++ ++ old_emax = mpfr_get_emax (); ++ set_emax (emax); ++ ++ mpfr_init2 (x, 8); ++ mpfr_inits2 (6, y1, y2, (mpfr_ptr) 0); ++ ++ mpfr_set_inf (x, 1); ++ mpfr_nextbelow (x); ++ ++ for (neg = 0; neg <= 1; neg++) ++ { ++ RND_LOOP (r) ++ { ++ int inex1, inex2; ++ unsigned int flags1, flags2; ++ ++ /* Even if there isn't an overflow (rounding ~ toward zero), ++ the result is the same as the one of an overflow. */ ++ inex1 = mpfr_overflow (y1, (mpfr_rnd_t) r, neg ? -1 : 1); ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (mpfr_inf_p (y1)) ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ for (op = 0; op < 4; op++) ++ { ++ mpfr_clear_flags (); ++ inex2 = ++ op == 0 ? mpfr_mul_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 1 ? mpfr_mul_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 2 ? mpfr_div_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 3 ? mpfr_div_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ (MPFR_ASSERTN (0), 0); ++ flags2 = __gmpfr_flags; ++ if (!(mpfr_equal_p (y1, y2) && ++ SAME_SIGN (inex1, inex2) && ++ flags1 == flags2)) ++ { ++ printf ("Error in overflow0 for %s, mpfr_%s, emax = %" ++ MPFR_EXP_FSPEC "d,\nx = ", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r), sop[op], ++ (mpfr_eexp_t) emax); ++ mpfr_dump (x); ++ printf ("Expected "); ++ mpfr_dump (y1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (y2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } ++ mpfr_neg (x, x, MPFR_RNDN); ++ } ++ ++ mpfr_clears (x, y1, y2, (mpfr_ptr) 0); ++ set_emax (old_emax); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -334,6 +404,11 @@ + underflow0 (); + large0 (); + ++ if (mpfr_get_emax () != MPFR_EMAX_MAX) ++ overflow0 (mpfr_get_emax ()); ++ overflow0 (MPFR_EMAX_MAX); ++ overflow0 (-1); ++ + tests_end_mpfr (); + return 0; + } +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-17 08:54:48.592799981 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-17 08:54:48.616811495 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-underflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-17 08:54:48.616811495 +0000 +@@ -1 +1 @@ +-3.1.3-p2 ++3.1.3-p3 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -45,7 +45,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX - (n - 1) || + exp < __gmpfr_emin + (n - 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-17 08:54:48.608807656 +0000 +@@ -44,7 +44,9 @@ + if (MPFR_UNLIKELY (n >= diffexp)) /* exp - n <= emin - 1 */ + { + if (rnd_mode == MPFR_RNDN && +- (n > diffexp || (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ (n > diffexp || ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN (y)); + } +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-17 08:54:48.616811495 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p2" ++#define MPFR_VERSION_STRING "3.1.3-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -48,7 +48,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX + (n + 1) || + exp < __gmpfr_emin - (n + 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-17 08:54:48.616811495 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p2"; ++ return "3.1.3-p3"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-17 08:54:48.608807656 +0000 +@@ -50,77 +50,82 @@ + { + mpfr_t x, y, z1, z2; + mpfr_exp_t emin; +- int i, k; ++ int i, k, s; + int prec; + int rnd; + int div; + int inex1, inex2; + unsigned int flags1, flags2; + +- /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) +- * with emin = e, x = 1 + i/16, i in { -1, 0, 1 }, and k = 1 to 4, +- * by comparing the result with the one of a simple division. ++ /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) with ++ * emin = e, x = s * (1 + i/16), i in { -1, 0, 1 }, s in { -1, 1 }, and ++ * k = 1 to 4, by comparing the result with the one of a simple division. + */ + emin = mpfr_get_emin (); + set_emin (e); + mpfr_inits2 (8, x, y, (mpfr_ptr) 0); + for (i = 15; i <= 17; i++) +- { +- inex1 = mpfr_set_ui_2exp (x, i, -4, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- for (prec = 6; prec >= 3; prec -= 3) +- { +- mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); +- RND_LOOP (rnd) +- for (k = 1; k <= 4; k++) +- { +- /* The following one is assumed to be correct. */ +- inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- mpfr_clear_flags (); +- /* Do not use mpfr_div_ui to avoid the optimization +- by mpfr_div_2si. */ +- inex1 = mpfr_div (z1, y, z1, (mpfr_rnd_t) rnd); +- flags1 = __gmpfr_flags; +- +- for (div = 0; div <= 2; div++) ++ for (s = 1; s >= -1; s -= 2) ++ { ++ inex1 = mpfr_set_si_2exp (x, s * i, -4, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ for (prec = 6; prec >= 3; prec -= 3) ++ { ++ mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); ++ RND_LOOP (rnd) ++ for (k = 1; k <= 4; k++) + { ++ /* The following one is assumed to be correct. */ ++ inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); + mpfr_clear_flags (); +- inex2 = div == 0 ? +- mpfr_mul_2si (z2, x, e - k, (mpfr_rnd_t) rnd) : div == 1 ? +- mpfr_div_2si (z2, x, k - e, (mpfr_rnd_t) rnd) : +- mpfr_div_2ui (z2, x, k - e, (mpfr_rnd_t) rnd); +- flags2 = __gmpfr_flags; +- if (flags1 == flags2 && SAME_SIGN (inex1, inex2) && +- mpfr_equal_p (z1, z2)) +- continue; +- printf ("Error in underflow("); +- if (e == MPFR_EMIN_MIN) +- printf ("MPFR_EMIN_MIN"); +- else if (e == emin) +- printf ("default emin"); +- else if (e >= LONG_MIN) +- printf ("%ld", (long) e); +- else +- printf ("= LONG_MIN) ++ printf ("%ld", (long) e); ++ else ++ printf ("d1 or (np[n-1]=d1 and np[n-2]>=d0) here, ++ since we truncate the divisor at each step, but since {np,n} < D ++ originally, the largest possible partial quotient is B-1. */ ++ if (MPFR_UNLIKELY(np[n-1] > d1 || (np[n-1] == d1 && np[n-2] >= d0))) + q2 = ~ (mp_limb_t) 0; + else + udiv_qr_3by2 (q2, q1, q0, np[n - 1], np[n - 2], np[n - 3], +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-17 08:58:21.118986898 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-10-29 13:47:46.763900609 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p4"; ++ return "3.1.3-p5"; + } +diff -Naurd mpfr-3.1.3-a/tests/tdiv.c mpfr-3.1.3-b/tests/tdiv.c +--- mpfr-3.1.3-a/tests/tdiv.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tdiv.c 2015-10-29 13:47:46.751900855 +0000 +@@ -1099,6 +1099,69 @@ + mpfr_set_emax (old_emax); + } + ++/* Bug in mpfr_divhigh_n_basecase when all limbs of q (except the most ++ significant one) are B-1 where B=2^GMP_NUMB_BITS. Since we truncate ++ the divisor at each step, it might happen at some point that ++ (np[n-1],np[n-2]) > (d1,d0), and not only the equality. ++ Reported by Ricky Farr ++ ++ To get a failure, a MPFR_DIVHIGH_TAB entry below the MPFR_DIV_THRESHOLD ++ limit must have a value 0. With most mparam.h files, this cannot occur. */ ++static void ++test_20151023 (void) ++{ ++ mpfr_prec_t p; ++ mpfr_t n, d, q, q0; ++ int inex, i; ++ ++ for (p = GMP_NUMB_BITS; p <= 2000; p++) ++ { ++ mpfr_init2 (n, 2*p); ++ mpfr_init2 (d, p); ++ mpfr_init2 (q, p); ++ mpfr_init2 (q0, GMP_NUMB_BITS); ++ ++ /* generate a random divisor of p bits */ ++ mpfr_urandomb (d, RANDS); ++ /* generate a random quotient of GMP_NUMB_BITS bits */ ++ mpfr_urandomb (q0, RANDS); ++ /* zero-pad the quotient to p bits */ ++ inex = mpfr_prec_round (q0, p, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ ++ for (i = 0; i < 3; i++) ++ { ++ /* i=0: try with the original quotient xxx000...000 ++ i=1: try with the original quotient minus one ulp ++ i=2: try with the original quotient plus one ulp */ ++ if (i == 1) ++ mpfr_nextbelow (q0); ++ else if (i == 2) ++ { ++ mpfr_nextabove (q0); ++ mpfr_nextabove (q0); ++ } ++ ++ inex = mpfr_mul (n, d, q0, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_nextabove (n); ++ mpfr_div (q, n, d, MPFR_RNDN); ++ MPFR_ASSERTN(mpfr_cmp (q, q0) == 0); ++ ++ inex = mpfr_mul (n, d, q0, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_nextbelow (n); ++ mpfr_div (q, n, d, MPFR_RNDN); ++ MPFR_ASSERTN(mpfr_cmp (q, q0) == 0); ++ } ++ ++ mpfr_clear (n); ++ mpfr_clear (d); ++ mpfr_clear (q); ++ mpfr_clear (q0); ++ } ++} ++ + #define TEST_FUNCTION test_div + #define TWO_ARGS + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) +@@ -1219,6 +1282,7 @@ + consistency (); + test_20070603 (); + test_20070628 (); ++ test_20151023 (); + test_generic (2, 800, 50); + test_extreme (); + diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..0a925c97ef --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..f4a9aac776 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From acef6c27bfc6728047e208dab35ac30bc57051c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 23:20:43 +0100 Subject: [PATCH 0526/2133] use libxml2 easyblock --- .../libxml2-2.9.3-foss-2015a-Python-2.7.11.eb | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb index 8052162f58..28c3bb06af 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb @@ -1,12 +1,9 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' homepage = 'http://xmlsoft.org/' -description = """Libxml2 is the XML C parser and -toolchain developed for the Gnome project - (but usable outside of the Gnome platform).""" +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True} @@ -28,9 +25,4 @@ dependencies = [ ('Python', pythonver), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' -- GitLab From 8ffcb6f65566c0fcaaf037e0b3a63c3b3894d2ed Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 11:36:17 +1300 Subject: [PATCH 0527/2133] Add CMake build dep --- easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb index 95861d4eca..5adccf48d7 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb @@ -11,6 +11,7 @@ sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] builddependencies = [ + ('CMake', '3.4.1'), ('flex', '2.6.0'), ('Bison', '3.0.4'), ] -- GitLab From 7b700637e99545fbf22bc1ee7ecad9f0452de3ef Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 11:47:17 +1300 Subject: [PATCH 0528/2133] New EasyConfig for CMake 3.4.1 with GCC 4.9.2 --- .../c/CMake/CMake-3.4.1-GCC-4.9.2.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..cb117db322 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 00ed67d354c2d17c962bc355c79a1aff6d7f5867 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 18 Feb 2016 23:27:38 +0000 Subject: [PATCH 0529/2133] VCFtools update to 0.1.14 for foss-2015b --- .../v/VCFtools/VCFtools-0.1.14-foss-2015b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb new file mode 100644 index 0000000000..038d96046c --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'VCFtools' +version = '0.1.14' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +perl = 'Perl' +perlver = '5.16.3' +dependencies = [ + (perl, perlver), +] + +files_to_copy = ["bin", "lib", "examples", (["bin/man1"], 'man')] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 25234cabe1eec2a8655bb8f3dc8793590f1ecfc2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 18 Feb 2016 23:33:32 +0000 Subject: [PATCH 0530/2133] Use ConfigureMake and fix sources --- .../easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb index 038d96046c..e54dd8f2d4 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb @@ -6,7 +6,7 @@ # adam.huffman@crick.ac.uk # The Francis Crick Institute -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'VCFtools' version = '0.1.14' @@ -20,7 +20,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'optarch': True} source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] -sources = ['%(namelower)s_%(version)s.tar.gz'] +sources = ['%(namelower)s-%(version)s.tar.gz'] perl = 'Perl' perlver = '5.16.3' -- GitLab From 29bdfe711f830e92f3442131f7b11f95fe9020d2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 13:51:40 +1300 Subject: [PATCH 0531/2133] Patch needed for older versions of libspatialite --- .../l/libspatialite/libspatialite-configure.ac.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch new file mode 100644 index 0000000000..aacff1481f --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch @@ -0,0 +1,12 @@ +diff -urN libspatialite-4.1.1.orig/configure libspatialite-4.1.1/configure +--- libspatialite-4.1.1.orig/configure 2013-06-29 08:53:15.000000000 +0200 ++++ libspatialite-4.1.1/configure 2014-04-02 11:37:56.484423000 +0200 +@@ -263,7 +263,7 @@ + LIBS="$GEOS_LDFLAGS" + AC_SEARCH_LIBS(GEOSTopologyPreserveSimplify,geos_c,,AC_MSG_ERROR([could not find libgeos_c - you may need to specify the directory of a geos-config file using --with-geosconfig])) + LIBS="$LIBS_SAVE" +- LIBS=$LIBS$GEOS_LDFLAGS' -lgeos_c' ++ LIBS="$LIBS $GEOS_LDFLAGS -lgeos_c" + + #----------------------------------------------------------------------- + # --enable-geosadvanced -- GitLab From b49f76d9db0d68b541194ce6cc77a92667c6027a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 15:27:04 +1300 Subject: [PATCH 0532/2133] Deleted libspatialite-4.1.1 and associated files --- .../libspatialite-4.1.1-goolf-1.5.14.eb | 27 ------------------- .../libspatialite-configure.ac.patch | 12 --------- 2 files changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb delete mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb deleted file mode 100644 index 8132d40673..0000000000 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libspatialite' -version = '4.1.1' - -homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" -description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." - -toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'usempi': False, 'pic': True} - -download_suffix = '' -source_urls = ['http://www.gaia-gis.it/gaia-sins/'] -sources = [SOURCE_TAR_GZ] - -patches = ['libspatialite-configure.ac.patch'] - -dependencies = [('FreeXL','1.0.0g'),('GEOS','3.3.5'), ('SQLite', '3.8.4.3'), ('PROJ', '4.8.0')] -configopts = '--disable-geosadvanced' -builddependencies = [('CMake', '2.8.10.2')] - -sanity_check_paths = { - 'files': ["lib/libspatialite.la"], - 'dirs': ["lib","include"] - } - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch deleted file mode 100644 index aacff1481f..0000000000 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -urN libspatialite-4.1.1.orig/configure libspatialite-4.1.1/configure ---- libspatialite-4.1.1.orig/configure 2013-06-29 08:53:15.000000000 +0200 -+++ libspatialite-4.1.1/configure 2014-04-02 11:37:56.484423000 +0200 -@@ -263,7 +263,7 @@ - LIBS="$GEOS_LDFLAGS" - AC_SEARCH_LIBS(GEOSTopologyPreserveSimplify,geos_c,,AC_MSG_ERROR([could not find libgeos_c - you may need to specify the directory of a geos-config file using --with-geosconfig])) - LIBS="$LIBS_SAVE" -- LIBS=$LIBS$GEOS_LDFLAGS' -lgeos_c' -+ LIBS="$LIBS $GEOS_LDFLAGS -lgeos_c" - - #----------------------------------------------------------------------- - # --enable-geosadvanced -- GitLab From d67d88a99ac9860c6a57151d3c5ce24e73c20c7f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 15:37:10 +1300 Subject: [PATCH 0533/2133] Rename ORCA-3.0.0 EasyConfig to that which is expected given version string --- ...0_0-linux_x86-64.eb => ORCA-3_0_0-linux_x86-64_openmpi_165.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_0-linux_x86-64.eb => ORCA-3_0_0-linux_x86-64_openmpi_165.eb} (100%) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb similarity index 100% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb -- GitLab From d447397f4f05bb119f8f6068323e7a5ec3e83e68 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 15:44:45 +1300 Subject: [PATCH 0534/2133] Older version of libspatialite, reinstated --- .../libspatialite-4.1.1-goolf-1.5.14.eb | 27 +++++++++++++++++++ .../libspatialite-configure.ac.patch | 12 +++++++++ 2 files changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..8132d40673 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.1.1' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +patches = ['libspatialite-configure.ac.patch'] + +dependencies = [('FreeXL','1.0.0g'),('GEOS','3.3.5'), ('SQLite', '3.8.4.3'), ('PROJ', '4.8.0')] +configopts = '--disable-geosadvanced' +builddependencies = [('CMake', '2.8.10.2')] + +sanity_check_paths = { + 'files': ["lib/libspatialite.la"], + 'dirs': ["lib","include"] + } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch new file mode 100644 index 0000000000..aacff1481f --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch @@ -0,0 +1,12 @@ +diff -urN libspatialite-4.1.1.orig/configure libspatialite-4.1.1/configure +--- libspatialite-4.1.1.orig/configure 2013-06-29 08:53:15.000000000 +0200 ++++ libspatialite-4.1.1/configure 2014-04-02 11:37:56.484423000 +0200 +@@ -263,7 +263,7 @@ + LIBS="$GEOS_LDFLAGS" + AC_SEARCH_LIBS(GEOSTopologyPreserveSimplify,geos_c,,AC_MSG_ERROR([could not find libgeos_c - you may need to specify the directory of a geos-config file using --with-geosconfig])) + LIBS="$LIBS_SAVE" +- LIBS=$LIBS$GEOS_LDFLAGS' -lgeos_c' ++ LIBS="$LIBS $GEOS_LDFLAGS -lgeos_c" + + #----------------------------------------------------------------------- + # --enable-geosadvanced -- GitLab From 21d05c9574074a7c3dd736dd87e3754f98036012 Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 19 Feb 2016 09:56:21 +0200 Subject: [PATCH 0535/2133] modify easyconfig Boost-1.59.0-intel-2015b.eb --- easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb index 7461992321..61f63ebb4e 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb @@ -4,6 +4,7 @@ version = '1.59.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" +configopts = '--without-libraries=python' toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'pic': True, 'usempi': True} -- GitLab From 089fb0470f3460c6dbb1159e7d7bc29860d3a3bc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2016 09:33:10 +0000 Subject: [PATCH 0536/2133] Update Perl dep to 5.20.2 --- easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb | 15 + ...dle-Bioconductor-3.2-foss-2015b-R-3.2.3.eb | 259 ++++++++++++++++++ .../v/VCFtools/VCFtools-0.1.14-foss-2015b.eb | 2 +- 3 files changed, 275 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2015b-R-3.2.3.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb new file mode 100644 index 0000000000..c9ef30b97e --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_74' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2015b-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2015b-R-3.2.3.eb new file mode 100644 index 0000000000..604873bafd --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2015b-R-3.2.3.eb @@ -0,0 +1,259 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.2' +rver = '3.2.3' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', rver)] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +bioconductor_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/data/experiment/src/contrib/', + # for hexbin + 'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.16.1', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.8.1', bioconductor_options), + ('IRanges', '2.4.1', bioconductor_options), + ('GenomeInfoDb', '1.6.1', bioconductor_options), + ('AnnotationDbi', '1.32.0', bioconductor_options), + ('zlibbioc', '1.16.0', bioconductor_options), + ('XVector', '0.10.0', bioconductor_options), + ('Biostrings', '2.38.0', 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bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.12.0', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), + ('perm', '1.0-0.0', bioconductor_options), + ('baySeq', '2.2.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), + ('samr', '2.0', bioconductor_options), + ('DEGseq', '1.22.0', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), + ('rtracklayer', '1.30.1', bioconductor_options), + ('biomaRt', '2.26.0', bioconductor_options), + ('GenomicFeatures', '1.22.4', bioconductor_options), + ('bumphunter', '1.10.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), + ('NOISeq', '2.14.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), + ('annotate', '1.48.0', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('BSgenome', '1.38.0', bioconductor_options), + ('VariantAnnotation', '1.16.3', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.1', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.10.0', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), + ('KEGGREST', '1.10.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('GEOquery', '2.34.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), + ('GenomicFiles', '1.4.0', bioconductor_options), + ('derfinderHelper', '1.4.1', bioconductor_options), + ('derfinder', '1.4.4', bioconductor_options), + ('polyester', '1.4.0', bioconductor_options), + ('Rsubread', '1.18.0', bioconductor_options), + # New packages for Bioconductor 3.2 + ('ABAData', '1.0.0', bioconductor_options), + ('ABAEnrichment', '1.0.0', bioconductor_options), + ('acde', '1.0.0', bioconductor_options), + ('DNAcopy','1.44.0', bioconductor_options), + ('pixmap','0.4-11', ext_options), + ('strucchange','1.5-1', ext_options), + ('hexbin', '1.24.1', bioconductor_options), + ('vsn','3.38.0', bioconductor_options), + ('tilingArray','1.48.0', bioconductor_options), + ('GLAD','2.34.0', bioconductor_options), + ('aCGH','1.48.0', bioconductor_options), + ('snapCGH','1.40.0', bioconductor_options), + ('ADaCGH2', '2.10.0', bioconductor_options), + ('affxparser', '1.42.0', bioconductor_options), + ('AllelicImbalance', '1.8.0', bioconductor_options), + ('AnnotationHub', '2.2.2', bioconductor_options), + ('AnnotationHubData', '1.0.0', bioconductor_options), + ('antiProfiles', '1.10.0', bioconductor_options), + ('aroma.light', '3.0.0', bioconductor_options), + ('ballgown', '2.2.0', bioconductor_options), + ('BaseSpaceR', '1.14.0', bioconductor_options), + ('BBCAnalyzer', '1.0.0', bioconductor_options), + ('biobroom', '1.2.0', bioconductor_options), + ('BiocStyle', '1.8.0', bioconductor_options), + ('caOmicsV', '1.0.0', bioconductor_options), + ('CausalR', '0.99.12', bioconductor_options), + ('ChIPComp', '1.0.0', bioconductor_options), + ('CNPBayes', '1.0.0', bioconductor_options), + ('CNVPanelizer', '1.0.0', bioconductor_options), + ('DAPAR', '1.0.0', bioconductor_options), + ('DChIPRep', '1.0.3', bioconductor_options), + ('DeMAND', '1.0.0', bioconductor_options), + ('destiny', '1.0.0', bioconductor_options), + ('DiffLogo', '1.0.0', bioconductor_options), + ('DNABarcodes', '1.0.0', bioconductor_options), + ('dupRadar', '1.0.0', bioconductor_options), + ('ELMER', '1.2.0', bioconductor_options), + ('EnrichedHeatmap', '1.0.0', bioconductor_options), + ('erma', '0.2.0', bioconductor_options), + ('eudysbiome', '1.0.0', bioconductor_options), + ('fCI', '1.0.0', bioconductor_options), + ('FindMyFriends', '1.0.1', bioconductor_options), + ('gcatest', '1.0.0', bioconductor_options), + ('GeneBreak', '1.0.0', bioconductor_options), + ('genotypeeval', '1.0.0', bioconductor_options), + ('GEOsearch', '1.0.0', bioconductor_options), + ('GUIDEseq', '1.0.4', bioconductor_options), + ('Guitar', '1.7.0', bioconductor_options), + ('hierGWAS', '1.0.0', bioconductor_options), + ('HilbertCurve', '1.0.0', bioconductor_options), + ('iCheck', '1.0.0', bioconductor_options), + ('iGC', '1.0.0', bioconductor_options), + ('Imetagene', '1.0.0', bioconductor_options), + ('INSPEcT', '1.0.0', bioconductor_options), + ('IONiseR', '1.0.0', bioconductor_options), + ('ldblock', '1.0.0', bioconductor_options), + ('LedPred', '1.2.0', bioconductor_options), + ('lfa', '1.0.0', bioconductor_options), + ('LOLA', '1.0.0', bioconductor_options), + ('MEAL', '1.0.1', bioconductor_options), + ('metagenomeFeatures', '1.0.0', bioconductor_options), + ('metaX', '1.0.0', bioconductor_options), + ('miRcomp', '1.0.0', bioconductor_options), + ('mirIntegrator', '1.0.0', bioconductor_options), + ('miRLAB', '1.0.0', bioconductor_options), + ('motifbreakR', '1.0.1', bioconductor_options), + ('myvariant', '1.0.1', bioconductor_options), + ('NanoStringDiff', '1.0.0', bioconductor_options), + ('OGSA', '1.0.0', bioconductor_options), + ('OperaMate', '1.2.0', bioconductor_options), + ('Oscope', '1.0.0', bioconductor_options), + ('Path2PPI', '1.0.0', bioconductor_options), + ('pathVar', '1.0.0', bioconductor_options), + ('PGA', '1.0.0', bioconductor_options), + ('Prize', '1.0.0', bioconductor_options), + ('Prostar', '1.0.1', bioconductor_options), + ('ProteomicsAnnotationHubData', '1.0.0', bioconductor_options), + ('RareVariantVis', '1.2.0', bioconductor_options), + ('rCGH', '1.0.2', bioconductor_options), + ('RCy3', '0.99.25', bioconductor_options), + ('RiboProfiling', '1.0.0', bioconductor_options), + ('rnaseqcomp', '1.0.0', bioconductor_options), + ('ropls', '1.2.2', bioconductor_options), + ('RTCGA', '1.0.0', bioconductor_options), + ('RTCGAToolbox', '2.0.0', bioconductor_options), + ('sbgr', '1.0.0', bioconductor_options), + ('SEPA', '1.0.0', bioconductor_options), + ('SICtools', '1.0.0', bioconductor_options), + ('SISPA', '1.0.0', bioconductor_options), + ('SNPhood', '1.0.1', bioconductor_options), + ('subSeq', '1.0.1', bioconductor_options), + ('SummarizedExperiment', '1.0.1', bioconductor_options), + ('SWATH2stats', '1.0.1', bioconductor_options), + ('synlet', '1.0.0', bioconductor_options), + ('TarSeqQC', '1.0.0', bioconductor_options), + ('TCGAbiolinks', '1.0.1', bioconductor_options), + ('traseR', '1.0.0', bioconductor_options), + ('variancePartition', '1.0.0', bioconductor_options), + ('XBSeq', '1.0.0', bioconductor_options), + +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb index e54dd8f2d4..ae66406e49 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb @@ -23,7 +23,7 @@ source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download sources = ['%(namelower)s-%(version)s.tar.gz'] perl = 'Perl' -perlver = '5.16.3' +perlver = '5.20.2' dependencies = [ (perl, perlver), ] -- GitLab From 1dea727507990444d75d21ec14dd5c9182798732 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2016 09:36:51 +0000 Subject: [PATCH 0537/2133] Add correct suffix to Perl dep --- easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb index ae66406e49..4e998968a7 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb @@ -24,8 +24,9 @@ sources = ['%(namelower)s-%(version)s.tar.gz'] perl = 'Perl' perlver = '5.20.2' +perlsuffix = '-bare' dependencies = [ - (perl, perlver), + (perl, perlver, perlsuffix), ] files_to_copy = ["bin", "lib", "examples", (["bin/man1"], 'man')] -- GitLab From 99edd6535a3ed99cee84432c865a84ef132eee31 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2016 10:22:17 +0000 Subject: [PATCH 0538/2133] Remove inadvertently added changes from another branch --- easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb | 15 - ...dle-Bioconductor-3.2-foss-2015b-R-3.2.3.eb | 259 ------------------ 2 files changed, 274 deletions(-) delete mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb delete mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2015b-R-3.2.3.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb deleted file mode 100644 index c9ef30b97e..0000000000 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb +++ /dev/null @@ -1,15 +0,0 @@ -name = 'Java' -version = '1.8.0_74' - -homepage = 'http://java.com/' -description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy - Java applications on desktops and servers.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html -(vp, vs) = version.split('_') -altver = '%su%s' % (vp.split('.')[1], vs) -sources = ['jdk-%s-linux-x64.tar.gz' % altver] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2015b-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2015b-R-3.2.3.eb deleted file mode 100644 index 604873bafd..0000000000 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2015b-R-3.2.3.eb +++ /dev/null @@ -1,259 +0,0 @@ -easyblock = 'Bundle' - -name = 'R-bundle-Bioconductor' -version = '3.2' -rver = '3.2.3' -versionsuffix = '-R-%s' % rver - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -toolchain = {'name': 'foss', 'version': '2015b'} - -# these are extensions for R -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -dependencies = [('R', rver)] - -name_tmpl = '%(name)s_%(version)s.tar.gz' -bioconductor_options = { - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib/', # current version of packages - 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': name_tmpl, -} -bioconductor_options = { - 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', - 'http://www.bioconductor.org/packages/3.2/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.2/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.2/data/experiment/src/contrib/', - # for hexbin - 'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/', - ], - 'source_tmpl': name_tmpl, -} - -name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib/', # current version of packages - 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': name_tmpl, -} - -# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends -# !! order of packages is important !! -exts_list = [ - ('BiocGenerics', '0.16.1', bioconductor_options), - ('Biobase', '2.28.0', bioconductor_options), - ('S4Vectors', '0.8.1', bioconductor_options), - ('IRanges', '2.4.1', bioconductor_options), - ('GenomeInfoDb', '1.6.1', bioconductor_options), - ('AnnotationDbi', '1.32.0', bioconductor_options), - ('zlibbioc', '1.16.0', bioconductor_options), - ('XVector', '0.10.0', bioconductor_options), - ('Biostrings', '2.38.0', bioconductor_options), - ('GenomicRanges', '1.22.1', bioconductor_options), - ('lambda.r', '1.1.7', bioconductor_options), - ('futile.options', '1.0.0', bioconductor_options), - ('futile.logger', '1.4.1', bioconductor_options), - ('BiocParallel', '1.4.0', bioconductor_options), - ('Rsamtools', '1.22.0', bioconductor_options), - ('SummarizedExperiment', '1.0.1', bioconductor_options), - ('GenomicAlignments', '1.6.1', bioconductor_options), - ('ShortRead', '1.28.0', bioconductor_options), - ('graph', '1.46.0', bioconductor_options), - ('affyio', '1.36.0', bioconductor_options), - ('BiocInstaller', '1.20.0', bioconductor_options), - ('preprocessCore', '1.30.0', bioconductor_options), - ('affy', '1.46.1', bioconductor_options), - ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.15', bioconductor_options), - ('RBGL', '1.44.0', bioconductor_options), - ('org.Hs.eg.db', '3.1.2', bioconductor_options), - ('AnnotationForge', '1.10.1', bioconductor_options), - ('KEGG.db', '3.1.2', bioconductor_options), - ('annaffy', '1.40.0', bioconductor_options), - ('gcrma', '2.40.0', bioconductor_options), - ('oligoClasses', '1.30.0', bioconductor_options), - ('edgeR', '3.12.0', bioconductor_options), - ('PFAM.db', '3.1.2', bioconductor_options), - ('perm', '1.0-0.0', bioconductor_options), - ('baySeq', '2.2.0', bioconductor_options), - ('qvalue', '2.0.0', bioconductor_options), - ('impute', '1.42.0', bioconductor_options), - ('samr', '2.0', bioconductor_options), - ('DEGseq', '1.22.0', bioconductor_options), - ('hgu133plus2.db', '3.1.3', bioconductor_options), - ('illuminaio', '0.10.0', bioconductor_options), - ('rtracklayer', '1.30.1', bioconductor_options), - ('biomaRt', '2.26.0', bioconductor_options), - ('GenomicFeatures', '1.22.4', bioconductor_options), - ('bumphunter', '1.10.0', bioconductor_options), - ('multtest', '2.24.0', bioconductor_options), - ('siggenes', '1.42.0', bioconductor_options), - ('DynDoc', '1.46.0', bioconductor_options), - ('genoset', '1.22.0', bioconductor_options), - ('NOISeq', '2.14.0', bioconductor_options), - ('Rgraphviz', '2.12.0', bioconductor_options), - ('RNASeqPower', '1.8.0', bioconductor_options), - ('annotate', '1.48.0', bioconductor_options), - ('GSEABase', '1.30.2', bioconductor_options), - ('genefilter', '1.50.0', bioconductor_options), - ('Category', '2.34.2', bioconductor_options), - ('GOstats', '2.34.0', bioconductor_options), - ('BSgenome', '1.38.0', bioconductor_options), - ('VariantAnnotation', '1.16.3', bioconductor_options), - ('biovizBase', '1.16.0', bioconductor_options), - ('OrganismDbi', '1.10.0', bioconductor_options), - ('ggbio', '1.16.1', bioconductor_options), - ('geneplotter', '1.46.0', bioconductor_options), - ('DESeq2', '1.10.0', bioconductor_options), - ('ReportingTools', '2.8.0', bioconductor_options), - ('affycoretools', '1.40.5', bioconductor_options), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), - ('Homo.sapiens', '1.1.2', bioconductor_options), - ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), - ('AgiMicroRna', '2.18.0', bioconductor_options), - ('GenomeGraphs', '1.28.0', bioconductor_options), - ('geneLenDataBase', '1.4.0', bioconductor_options), - ('goseq', '1.20.0', bioconductor_options), - ('KEGGREST', '1.10.0', bioconductor_options), - ('KEGGgraph', '1.26.0', bioconductor_options), - ('KEGGprofile', '1.10.0', bioconductor_options), - ('GEOquery', '2.34.0', bioconductor_options), - ('minfi', '1.14.0', bioconductor_options), - ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), - ('methylumi', '2.14.0', bioconductor_options), - ('lumi', '2.20.2', bioconductor_options), - ('widgetTools', '1.46.0', bioconductor_options), - ('tkWidgets', '1.46.0', bioconductor_options), - ('Mfuzz', '2.28.0', bioconductor_options), - ('maSigPro', '1.40.0', bioconductor_options), - ('SPIA', '2.20.0', bioconductor_options), - ('Gviz', '1.12.1', bioconductor_options), - ('cummeRbund', '2.10.0', bioconductor_options), - ('GenomicFiles', '1.4.0', bioconductor_options), - ('derfinderHelper', '1.4.1', bioconductor_options), - ('derfinder', '1.4.4', bioconductor_options), - ('polyester', '1.4.0', bioconductor_options), - ('Rsubread', '1.18.0', bioconductor_options), - # New packages for Bioconductor 3.2 - ('ABAData', '1.0.0', bioconductor_options), - ('ABAEnrichment', '1.0.0', bioconductor_options), - ('acde', '1.0.0', bioconductor_options), - ('DNAcopy','1.44.0', bioconductor_options), - ('pixmap','0.4-11', ext_options), - ('strucchange','1.5-1', ext_options), - ('hexbin', '1.24.1', bioconductor_options), - ('vsn','3.38.0', bioconductor_options), - ('tilingArray','1.48.0', bioconductor_options), - ('GLAD','2.34.0', bioconductor_options), - ('aCGH','1.48.0', bioconductor_options), - ('snapCGH','1.40.0', bioconductor_options), - ('ADaCGH2', '2.10.0', bioconductor_options), - ('affxparser', '1.42.0', bioconductor_options), - ('AllelicImbalance', '1.8.0', bioconductor_options), - ('AnnotationHub', '2.2.2', bioconductor_options), - ('AnnotationHubData', '1.0.0', bioconductor_options), - ('antiProfiles', '1.10.0', bioconductor_options), - ('aroma.light', '3.0.0', bioconductor_options), - ('ballgown', '2.2.0', bioconductor_options), - ('BaseSpaceR', '1.14.0', bioconductor_options), - ('BBCAnalyzer', '1.0.0', bioconductor_options), - ('biobroom', '1.2.0', bioconductor_options), - ('BiocStyle', '1.8.0', bioconductor_options), - ('caOmicsV', '1.0.0', bioconductor_options), - ('CausalR', '0.99.12', bioconductor_options), - ('ChIPComp', '1.0.0', bioconductor_options), - ('CNPBayes', '1.0.0', bioconductor_options), - ('CNVPanelizer', '1.0.0', bioconductor_options), - ('DAPAR', '1.0.0', bioconductor_options), - ('DChIPRep', '1.0.3', bioconductor_options), - ('DeMAND', '1.0.0', bioconductor_options), - ('destiny', '1.0.0', bioconductor_options), - ('DiffLogo', '1.0.0', bioconductor_options), - ('DNABarcodes', '1.0.0', bioconductor_options), - ('dupRadar', '1.0.0', bioconductor_options), - ('ELMER', '1.2.0', bioconductor_options), - ('EnrichedHeatmap', '1.0.0', bioconductor_options), - ('erma', '0.2.0', bioconductor_options), - ('eudysbiome', '1.0.0', bioconductor_options), - ('fCI', '1.0.0', bioconductor_options), - ('FindMyFriends', '1.0.1', bioconductor_options), - ('gcatest', '1.0.0', bioconductor_options), - ('GeneBreak', '1.0.0', bioconductor_options), - ('genotypeeval', '1.0.0', bioconductor_options), - ('GEOsearch', '1.0.0', bioconductor_options), - ('GUIDEseq', '1.0.4', bioconductor_options), - ('Guitar', '1.7.0', bioconductor_options), - ('hierGWAS', '1.0.0', bioconductor_options), - ('HilbertCurve', '1.0.0', bioconductor_options), - ('iCheck', '1.0.0', bioconductor_options), - ('iGC', '1.0.0', bioconductor_options), - ('Imetagene', '1.0.0', bioconductor_options), - ('INSPEcT', '1.0.0', bioconductor_options), - ('IONiseR', '1.0.0', bioconductor_options), - ('ldblock', '1.0.0', bioconductor_options), - ('LedPred', '1.2.0', bioconductor_options), - ('lfa', '1.0.0', bioconductor_options), - ('LOLA', '1.0.0', bioconductor_options), - ('MEAL', '1.0.1', bioconductor_options), - ('metagenomeFeatures', '1.0.0', bioconductor_options), - ('metaX', '1.0.0', bioconductor_options), - ('miRcomp', '1.0.0', bioconductor_options), - ('mirIntegrator', '1.0.0', bioconductor_options), - ('miRLAB', '1.0.0', bioconductor_options), - ('motifbreakR', '1.0.1', bioconductor_options), - ('myvariant', '1.0.1', bioconductor_options), - ('NanoStringDiff', '1.0.0', bioconductor_options), - ('OGSA', '1.0.0', bioconductor_options), - ('OperaMate', '1.2.0', bioconductor_options), - ('Oscope', '1.0.0', bioconductor_options), - ('Path2PPI', '1.0.0', bioconductor_options), - ('pathVar', '1.0.0', bioconductor_options), - ('PGA', '1.0.0', bioconductor_options), - ('Prize', '1.0.0', bioconductor_options), - ('Prostar', '1.0.1', bioconductor_options), - ('ProteomicsAnnotationHubData', '1.0.0', bioconductor_options), - ('RareVariantVis', '1.2.0', bioconductor_options), - ('rCGH', '1.0.2', bioconductor_options), - ('RCy3', '0.99.25', bioconductor_options), - ('RiboProfiling', '1.0.0', bioconductor_options), - ('rnaseqcomp', '1.0.0', bioconductor_options), - ('ropls', '1.2.2', bioconductor_options), - ('RTCGA', '1.0.0', bioconductor_options), - ('RTCGAToolbox', '2.0.0', bioconductor_options), - ('sbgr', '1.0.0', bioconductor_options), - ('SEPA', '1.0.0', bioconductor_options), - ('SICtools', '1.0.0', bioconductor_options), - ('SISPA', '1.0.0', bioconductor_options), - ('SNPhood', '1.0.1', bioconductor_options), - ('subSeq', '1.0.1', bioconductor_options), - ('SummarizedExperiment', '1.0.1', bioconductor_options), - ('SWATH2stats', '1.0.1', bioconductor_options), - ('synlet', '1.0.0', bioconductor_options), - ('TarSeqQC', '1.0.0', bioconductor_options), - ('TCGAbiolinks', '1.0.1', bioconductor_options), - ('traseR', '1.0.0', bioconductor_options), - ('variancePartition', '1.0.0', bioconductor_options), - ('XBSeq', '1.0.0', bioconductor_options), - -] - -modextrapaths = {'R_LIBS': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], -} - -moduleclass = 'bio' -- GitLab From ed00667eab043229c937957918f0e8e42a500506 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2016 10:47:00 +0000 Subject: [PATCH 0539/2133] Add missing easybuild for BH, required by R-synchronicity --- .../b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb diff --git a/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb b/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb new file mode 100644 index 0000000000..b605c4cd2e --- /dev/null +++ b/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb @@ -0,0 +1,32 @@ + +easyblock = 'RPackage' + +name = 'BH' +version = '1.60.0-1' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """BH: Boost C++ Header Files for R""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.2.3' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('Boost', '1.58.0', '-Python-2.7.10'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['BH'], +} + +moduleclass = 'lang' -- GitLab From aa545b351e213e22c78fe1f2d561f972aaa4b37c Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Fri, 19 Feb 2016 11:53:13 +0100 Subject: [PATCH 0540/2133] Roll ncurses forward to 6.0. --- easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb index 62574e2454..6e790f2a9a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('ncurses', '5.9')] +dependencies = [('ncurses', '6.0')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb index 45251dfaf6..afe0d69bd0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('ncurses', '5.9')] +dependencies = [('ncurses', '6.0')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb index 34313f0a0f..bf57c1d381 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' dependencies = [ - ('ncurses', '5.9'), + ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons #('OpenSSL', '1.0.1k'), diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb index 3d2c4263e5..3c775612ac 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb @@ -15,7 +15,7 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] -dependencies = [('ncurses', '5.9')] +dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses preconfigopts = "LDFLAGS='-lncurses'" diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb index 96ff3e825b..2d8bea6dd7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), ('libreadline', '6.2'), - ('ncurses', '5.9'), + ('ncurses', '6.0'), # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb index 1d8106ab4e..37aa3417d0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), ('libreadline', '6.3'), - ('ncurses', '5.9'), + ('ncurses', '6.0'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -- GitLab From e6329248abe0877a7cb9d03a8854fd60b1477927 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 19 Feb 2016 11:56:32 +0100 Subject: [PATCH 0541/2133] added StringTie-1.2.2-goolf-1.4.10.eb --- .../StringTie/StringTie-1.2.2-goolf-1.4.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..70ca06ed76 --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '1.2.2' + +homepage = 'http://ccb.jhu.edu/software/stringtie/' +description = """StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] +sources = [SOURCELOWER_TAR_GZ] + +files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/stringtie'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 987fd3082e4a43c9c8cf69201529407b05c4095e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2016 10:57:10 +0000 Subject: [PATCH 0542/2133] Add authorship comments --- easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb b/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb index b605c4cd2e..314d4d2d26 100644 --- a/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb +++ b/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb @@ -1,3 +1,7 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# The Francis Crick Institute easyblock = 'RPackage' -- GitLab From 428ae828445f94eb093f89b33a88475efbb0416b Mon Sep 17 00:00:00 2001 From: Danilo Guerrera Date: Fri, 19 Feb 2016 17:12:47 +0100 Subject: [PATCH 0543/2133] fix: added M4 as builddependency --- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 1 + easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.5.39.eb | 4 +++- 4 files changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 5fcc8fc6b3..8efdae380a 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -12,6 +12,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] builddependencies = [ + ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), # zlib required, but being linked instatically, so not a runtime dep diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 3a95cee4b6..246106ec92 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -12,6 +12,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] builddependencies = [ + ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), # zlib required, but being linked instatically, so not a runtime dep diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb index bd9f2b71e7..ce96075acd 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb @@ -11,6 +11,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.25', '', True) +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb index 53eb8f6c78..e4d83f163c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb @@ -5,10 +5,12 @@ homepage = 'http://flex.sourceforge.net/' description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +builddependencies = [('M4', '1.4.17')] + moduleclass = 'lang' -- GitLab From bcef1a374db2931bf6ba5dd7848906c665386f18 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 19 Feb 2016 17:56:34 +0100 Subject: [PATCH 0544/2133] added jModelTest-2.1.9r20160115 and deps --- ...1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 36 ++++++++++++++ ...Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 48 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb create mode 100644 easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb new file mode 100644 index 0000000000..91946b388e --- /dev/null +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PackedBinary' + +name = 'jModelTest' +version = '2.1.9r20160115' + +homepage = 'https://github.com/ddarriba/jmodeltest2' +description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/ddarriba/jmodeltest2/archive/'] +sources = ['v%(version)s.tar.gz'] + +java = 'Java' +javaver = '1.7.0_75' +versionsuffix = '-%s-%s' % (java, javaver) + +builddependencies = [('ant', '1.9.6', '-Java-1.7.0_75', True)] + +dependencies = [('MPJ-Express', '0.44', '%(versionsuffix)s')] + +install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" + +modloadmsg = """To execute jModelTest run: java -jar \\$EBROOTJMODELTEST/jModelTest.jar""" + +sanity_check_paths = { + 'files': ['jModelTest.jar'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb new file mode 100644 index 0000000000..25c03b4120 --- /dev/null +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'MPJ-Express' +version = '0.44' + +homepage = 'http://mpj-express.org/' +description = """MPJ Express is an open source Java message passing library that allows application + developers to write and execute parallel applications for multicore processors and compute clusters/clouds.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://sourceforge.net/projects/mpjexpress/files/releases/'] +sources = ['mpj-v%s.tar.gz' % (version.replace('.','_'))] + +java = 'Java' +javaver = '1.7.0_75' +versionsuffix = '-%s-%s' % (java, javaver) + +builddependencies = [('CMake', '2.8.12')] + +dependencies = [ + (java, javaver, '', True), +] + +# compile JNI wrapper library as described in docs +# http://mpj-express.org/docs/readme/README +postinstallcmds = ["mkdir %(installdir)s/src/mpjdev/natmpjdev/lib/build", + "cd %(installdir)s/src/mpjdev/natmpjdev/lib/build && cmake .. && make && make install DESTDIR=%(installdir)s",] + +modextrapaths = { + 'CLASSPATH': 'lib', +} + +modextravars = { + 'MPJ_HOME': '$root', # MPJ_HOME points to install directory +} + +sanity_check_paths = { + 'files': ['lib/libnativempjdev.so', 'bin/mpjrun.sh'], + 'dirs': [] +} + +moduleclass = 'lib' -- GitLab From 6e5d1de12140d0319e1b54807fd2416362f3e765 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Feb 2016 19:06:04 +0100 Subject: [PATCH 0545/2133] fix determining list of easyconfigs, don't assume locations are correct --- test/easyconfigs/easyconfigs.py | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d77b78e436..ab6bf2ab2c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -338,19 +338,21 @@ def template_easyconfig_test(self, spec): def suite(): """Return all easyblock initialisation tests.""" - - # dynamically generate a separate test for each of the available easyblocks - easyconfigs_path = get_paths_for("easyconfigs")[0] - specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) - - for spec in specs: - # dynamically define new inner functions that can be added as class methods to InitTest - exec("def innertest(self): template_easyconfig_test(self, '%s')" % spec) - spec = os.path.basename(spec) - innertest.__doc__ = "Test for parsing of easyconfig %s" % spec - innertest.__name__ = "test__parse_easyconfig_%s" % spec # double underscore so parsing tests are run first - setattr(EasyConfigTest, innertest.__name__, innertest) - + # dynamically generate a separate test for each of the available easyconfigs + # define new inner functions that can be added as class methods to InitTest + easyconfigs_path = get_paths_for('easyconfigs')[0] + cnt = 0 + for (subpath, _, specs) in os.walk(easyconfigs_path, topdown=True): + for spec in specs: + if spec.endswith('.eb'): + cnt += 1 + exec("def innertest(self): template_easyconfig_test(self, '%s')" % os.path.join(subpath, spec)) + innertest.__doc__ = "Test for parsing of easyconfig %s" % spec + # double underscore so parsing tests are run first + innertest.__name__ = "test__parse_easyconfig_%s" % spec + setattr(EasyConfigTest, innertest.__name__, innertest) + + print "Found %s easyconfigs..." % cnt return TestLoader().loadTestsFromTestCase(EasyConfigTest) if __name__ == '__main__': -- GitLab From 46e9ac65cdde767919eb1083bdcd83fbc625fc51 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Feb 2016 19:19:22 +0100 Subject: [PATCH 0546/2133] exclude template easyconfig --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index ab6bf2ab2c..e2e81c58df 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -344,7 +344,7 @@ def suite(): cnt = 0 for (subpath, _, specs) in os.walk(easyconfigs_path, topdown=True): for spec in specs: - if spec.endswith('.eb'): + if spec.endswith('.eb') and spec != 'TEMPLATE.eb': cnt += 1 exec("def innertest(self): template_easyconfig_test(self, '%s')" % os.path.join(subpath, spec)) innertest.__doc__ = "Test for parsing of easyconfig %s" % spec -- GitLab From b0d79ea7c64b6afd599aed88c22d3eef04509edb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Feb 2016 19:23:16 +0100 Subject: [PATCH 0547/2133] non-parallel build of flex 2.6.0 --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index f20e1d0126..0c9f4d80a4 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -13,4 +13,6 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] dependencies = [('Bison', '3.0.4')] +parallel = 1 + moduleclass = 'lang' -- GitLab From 1de66628f9550887de03b5ce3a5cffbb69e3846e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2016 22:41:42 +0000 Subject: [PATCH 0548/2133] Remove R- prefix from filename --- .../synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/r/{R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb => R/synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb} (100%) diff --git a/easybuild/easyconfigs/r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb b/easybuild/easyconfigs/r/R/synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb similarity index 100% rename from easybuild/easyconfigs/r/R-synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb rename to easybuild/easyconfigs/r/R/synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb -- GitLab From 68f3c25bdbf0c97c7084e96413b145abf6917536 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 Feb 2016 23:04:49 +0000 Subject: [PATCH 0549/2133] Fix typo in renamed file --- ...15b-R.3.2.3.eb => synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/r/R/{synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb => synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb} (100%) diff --git a/easybuild/easyconfigs/r/R/synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb b/easybuild/easyconfigs/r/R/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb similarity index 100% rename from easybuild/easyconfigs/r/R/synchronicity-1.1.9.1-foss-2015b-R.3.2.3.eb rename to easybuild/easyconfigs/r/R/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb -- GitLab From b337156069c68689680c8c0230fe2738e2d23d40 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 20 Feb 2016 08:59:27 +0000 Subject: [PATCH 0550/2133] At last move synchronicity to the correct location --- .../synchronicity}/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{r/R => s/synchronicity}/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb (100%) diff --git a/easybuild/easyconfigs/r/R/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb b/easybuild/easyconfigs/s/synchronicity/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb similarity index 100% rename from easybuild/easyconfigs/r/R/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb rename to easybuild/easyconfigs/s/synchronicity/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb -- GitLab From a5e64a2034139001d5c858a3b65491060711b7a2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 20 Feb 2016 09:11:45 +0000 Subject: [PATCH 0551/2133] Port Perl-5.20.3 to foss/2015b, for vcftools --- .../p/Perl/Perl-5.20.3-foss-2015b.eb | 909 ++++++++++++++++++ 1 file changed, 909 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2015b.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2015b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2015b.eb new file mode 100644 index 0000000000..35f20adfa3 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2015b.eb @@ -0,0 +1,909 @@ +name = 'Perl' +version = '5.20.3' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.58', { + 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('TAP::Harness::Env', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.021', { + 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '0.46', { + 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.93', { + 'source_tmpl': 'DateTime-TimeZone-1.93.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.22', { + 'source_tmpl': 'Try-Tiny-0.22.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Params::Validate', '1.21', { + 'source_tmpl': 'Params-Validate-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.20', { + 'source_tmpl': 'DateTime-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Module::Build', '0.4214', { + 'source_tmpl': 'Module-Build-0.4214.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Readonly', '2.00', { + 'source_tmpl': 'Readonly-2.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.27', { + 'source_tmpl': 'Tree-DAG_Node-1.27.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.48', { + 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.72', { + 'source_tmpl': 'Shell-0.72.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.47', { + 'source_tmpl': 'PathTools-3.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::WrapTie', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.40', { + 'source_tmpl': 'Test-Exception-0.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.11', { + 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.69', { + 'source_tmpl': 'URI-1.69.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.00', { + 'source_tmpl': 'Pod-POM-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.43', { + 'source_tmpl': 'Text-Diff-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.020', { + 'source_tmpl': 'IO-Socket-SSL-2.020.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Getopt::Long', '2.47', { + 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '0.117', { + 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.000002', { + 'source_tmpl': 'Moo-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.05', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.63', { + 'source_tmpl': 'Test-Differences-0.63.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.14', { + 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9912', { + 'source_tmpl': 'version-0.9912.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + # fails: uses 'gcc' + #('XML::Bare', '0.53', { + # 'source_tmpl': 'XML-Bare-0.53.tar.gz', + # 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + #}), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.30', { + 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.11', { + 'source_tmpl': 'AnyEvent-7.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0609', { + 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::Tester', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967012', { + 'source_tmpl': 'Parse-RecDescent-1.967012.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.36', { + 'source_tmpl': 'Carp-1.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.13', { + 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT'], + }), + ('Capture::Tiny', '0.30', { + 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('LWP', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000001', { + 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.19', { + 'source_tmpl': 'File-Which-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.39', { + 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.42', { + 'source_tmpl': 'Scalar-List-Utils-1.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('IO::Scalar', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.87', { + 'source_tmpl': 'Log-Handler-0.87.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Devel::StackTrace', '2.00', { + 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1603', { + 'source_tmpl': 'Moose-2.1603.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.33', { + 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9154', { + 'source_tmpl': 'CPANPLUS-0.9154.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Harness', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.04', { + 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.14', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' -- GitLab From 62bede9ecde18020cc5b6e1cc6da723692d46a44 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 20 Feb 2016 09:22:54 +0000 Subject: [PATCH 0552/2133] Require full version of Perl, handled by #2531 --- .../easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb index 4e998968a7..926d8c8707 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb @@ -23,10 +23,11 @@ source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download sources = ['%(namelower)s-%(version)s.tar.gz'] perl = 'Perl' -perlver = '5.20.2' -perlsuffix = '-bare' +perlver = '5.20.3' +versionsuffix = '-%s-%s' % (perl, perlver) + dependencies = [ - (perl, perlver, perlsuffix), + (perl, perlver), ] files_to_copy = ["bin", "lib", "examples", (["bin/man1"], 'man')] -- GitLab From 4a4141c5f7dbcdb3ab2d02739db1f031e8ee2373 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 20 Feb 2016 10:25:27 +0000 Subject: [PATCH 0553/2133] Update OpenSSL to 1.0.1r --- .../o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb new file mode 100644 index 0000000000..9c3838a1b7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb @@ -0,0 +1,19 @@ +name = 'OpenSSL' +version = '1.0.1r' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From 395bc0f0bf229ffb5587c331d3aa82faa90d9bd0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 20 Feb 2016 17:50:03 +0100 Subject: [PATCH 0554/2133] sync OCaml 4.01.0 ictce/5.5.0 easyconfig wrt deps & extensions --- .../a/Automake/Automake-1.15-ictce-5.5.0.eb | 33 +++++++++++++++++++ .../Autotools-20150215-ictce-5.5.0.eb | 17 ++++++++++ .../libreadline-6.3-ictce-5.5.0.eb | 32 ++++++++++++++++++ .../l/libtool/libtool-2.4.6-ictce-5.5.0.eb | 17 ++++++++++ .../o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 16 +++++++-- 5 files changed, 113 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb new file mode 100644 index 0000000000..25677b6f64 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.5.0.eb new file mode 100644 index 0000000000..72e186977d --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.5.0.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..128a4b2314 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """ The GNU Readline library provides a set of functions for use + by applications that allow users to edit command lines as they are typed + in. Both Emacs and vi editing modes are available. The Readline library + includes additional functions to maintain a list of previously-entered + command lines, to recall and perhaps reedit those lines, and perform + csh-like history expansion on previous commands.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb new file mode 100644 index 0000000000..1a6a78bca6 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb index 51e6fb3d9d..8fc41ecd35 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -30,10 +30,22 @@ sources = [ patches = ['OCaml-%(version)s_icc-fixes.patch'] -builddependencies = [('Autoconf', '2.69')] -dependencies = [('ncurses', '5.9')] +builddependencies = [('Autotools', '20150215')] +dependencies = [ + ('ncurses', '5.9'), + ('libreadline', '6.3'), + ('GSL', '1.16'), +] # parallel build tends to break parallel = 1 +# handled by OPAM, order matters! +exts_list = [ + ('ocamlfind', '1.5.5'), + ('batteries', '2.3.1'), + ('ocaml+twt', '0.94.0'), + ('gsl', '1.18.5'), +] + moduleclass = 'lang' -- GitLab From 56fde423f5ec58a7f19990c3fe5b2901705785d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 20 Feb 2016 18:02:30 +0100 Subject: [PATCH 0555/2133] fix M4 version --- easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb index 1a6a78bca6..cbd60cd24a 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb @@ -12,6 +12,6 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -dependencies = [('M4', '1.4.17')] +dependencies = [('M4', '1.4.16')] moduleclass = 'lib' -- GitLab From ff978f31b074e078fbfa85cd7d7219f3491f4aaf Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 21 Feb 2016 06:48:13 +0000 Subject: [PATCH 0556/2133] Add versionsuffix --- ...14-foss-2015b.eb => VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/v/VCFtools/{VCFtools-0.1.14-foss-2015b.eb => VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb} (100%) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb similarity index 100% rename from easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b.eb rename to easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb -- GitLab From 9b9f388ef889a0c72a8c0d8fbbaa685e65b85d1d Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sun, 21 Feb 2016 10:53:23 +0100 Subject: [PATCH 0557/2133] added missing ant easyconfig --- .../a/ant/ant-1.9.6-Java-1.7.0_75.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb new file mode 100644 index 0000000000..7da7aa32db --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb @@ -0,0 +1,26 @@ +name = 'ant' +version = '1.9.6' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +java = 'Java' +javaver = '1.7.0_75' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +builddependencies = [('JUnit', '4.11', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 1eae0abdd57fdba61ad9a63ceafa4f005e25e29e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 11:55:35 +0200 Subject: [PATCH 0558/2133] add easyconfig pyringe-1.0.2-intel-2015b-Python-2.7.10.eb --- ...pyringe-1.0.2-intel-2015b-Python-2.7.10.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..ed35150b5b --- /dev/null +++ b/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pyringe' +version = '1.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/pyringe' +description = """Debugger capable of attaching to and injecting code into python processes.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.10'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'tools' -- GitLab From 578aa3da52025de1a0ca1f59a9d188886ed66ddc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 15:06:06 +0200 Subject: [PATCH 0559/2133] add easyconfig pyringe-1.0.2-intel-2016a-Python-2.7.11.eb, add easyconfig GDB-7.10.1-intel-2016a-Python-2.7.11.eb --- .../GDB-7.10.1-intel-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ ...pyringe-1.0.2-intel-2016a-Python-2.7.11.eb | 26 ++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.10.1-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.10.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GDB/GDB-7.10.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..88be8d913f --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.10.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('Python', '2.7.11'), +] + +configopts = '--with-python' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a162402911 --- /dev/null +++ b/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pyringe' +version = '1.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/pyringe' +description = """Debugger capable of attaching to and injecting code into python processes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('GDB', '7.10.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'tools' -- GitLab From f4328f9ee705145ac10740461f8b859adb45a7e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 14:19:28 +0100 Subject: [PATCH 0560/2133] delete intel/2015b pyringe easyconfig --- ...pyringe-1.0.2-intel-2015b-Python-2.7.10.eb | 25 ------------------- 1 file changed, 25 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2015b-Python-2.7.10.eb deleted file mode 100644 index ed35150b5b..0000000000 --- a/easybuild/easyconfigs/p/pyringe/pyringe-1.0.2-intel-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pyringe' -version = '1.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/google/pyringe' -description = """Debugger capable of attaching to and injecting code into python processes.""" - -toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.10'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'tools' -- GitLab From 56bad276998b249044197a0d25081350e84ebfc4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 15:22:35 +0200 Subject: [PATCH 0561/2133] add easyconfig Autotools-20150215-ictce-5.5.0.eb, add easyconfig Automake-1.15-ictce-5.5.0.eb, add easyconfig libtool-2.4.6-ictce-5.5.0.eb --- .../a/Automake/Automake-1.15-ictce-5.5.0.eb | 33 +++++++++++++++++++ .../Autotools-20150215-ictce-5.5.0.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-ictce-5.5.0.eb | 17 ++++++++++ 3 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb new file mode 100644 index 0000000000..25677b6f64 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.5.0.eb new file mode 100644 index 0000000000..72e186977d --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.5.0.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb new file mode 100644 index 0000000000..cbd60cd24a --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.5.0.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.16')] + +moduleclass = 'lib' -- GitLab From 1ee5deb5089f1cdcd20e75d341de349d88e86aa4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 15:04:32 +0100 Subject: [PATCH 0562/2133] sync SQLite/Tcl easyconfigs --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb | 4 ++-- .../{Tcl-8.6.1-ictce-5.5.0.eb => Tcl-8.6.2-ictce-5.5.0.eb} | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/t/Tcl/{Tcl-8.6.1-ictce-5.5.0.eb => Tcl-8.6.2-ictce-5.5.0.eb} (93%) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb index 68d585b3df..d2bc173ef8 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb @@ -25,8 +25,8 @@ source_urls = ['http://www.sqlite.org/2014/'] sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), + ('libreadline', '6.3'), + ('Tcl', '8.6.2'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb similarity index 93% rename from easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb rename to easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb index 335678c031..7f2d451b76 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tcl' -version = '8.6.1' +version = '8.6.2' homepage = 'http://www.tcl.tk/' description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, @@ -13,7 +13,7 @@ source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ - ('zlib', '1.2.7'), + ('zlib', '1.2.8'), ] configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' -- GitLab From 29ea2e21048220d38970dd6256e0a1278fc99e04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 16:22:16 +0200 Subject: [PATCH 0563/2133] add easyconfig libreadline-6.3-ictce-5.5.0.eb, add easyconfig SQLite-3.8.6-ictce-5.5.0.eb, add easyconfig Tcl-8.6.2-ictce-5.5.0.eb --- .../libreadline-6.3-ictce-5.5.0.eb | 32 ++++++++++++++++ .../s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb | 37 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb | 25 +++++++++++++ 3 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..128a4b2314 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """ The GNU Readline library provides a set of functions for use + by applications that allow users to edit command lines as they are typed + in. Both Emacs and vi editing modes are available. The Readline library + includes additional functions to maintain a list of previously-entered + command lines, to recall and perhaps reedit those lines, and perform + csh-like history expansion on previous commands.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb new file mode 100644 index 0000000000..d2bc173ef8 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.6' + +homepage = 'http://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2014/'] +sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.2'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb new file mode 100644 index 0000000000..7f2d451b76 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.2' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From 564274eb22871497463c2e50a55a5e913d455989 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 15:25:45 +0100 Subject: [PATCH 0564/2133] remove custom libreadline/Tcl/SQLite easyconfigs --- .../libreadline-6.3-ictce-5.5.0.eb | 32 ---------------- .../s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb | 37 ------------------- .../t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb | 25 ------------- 3 files changed, 94 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb deleted file mode 100644 index 128a4b2314..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '6.3' - -homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' -description = """ The GNU Readline library provides a set of functions for use - by applications that allow users to edit command lines as they are typed - in. Both Emacs and vi editing modes are available. The Readline library - includes additional functions to maintain a list of previously-entered - command lines, to recall and perhaps reedit those lines, and perform - csh-like history expansion on previous commands.""" - -toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '5.9')] - -# for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" - -sanity_check_paths = { - 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb deleted file mode 100644 index d2bc173ef8..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -easyblock = 'ConfigureMake' - -name = 'SQLite' -version = '3.8.6' - -homepage = 'http://www.sqlite.org/' -description = "SQLite: SQL Database Engine in a C Library" - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz -source_urls = ['http://www.sqlite.org/2014/'] -sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -dependencies = [ - ('libreadline', '6.3'), - ('Tcl', '8.6.2'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb deleted file mode 100644 index 7f2d451b76..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.2' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' -- GitLab From aae0d2d746db75bb197dbeddc32ef35b4d2ea615 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 15:28:49 +0100 Subject: [PATCH 0565/2133] stick with libreadline 6.2 and zlib 1.2.7, for compatibility with existing easyconfigs --- .../libreadline-6.3-ictce-5.5.0.eb | 32 ------------------- .../s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb | 2 +- .../t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb | 2 +- 3 files changed, 2 insertions(+), 34 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb deleted file mode 100644 index 128a4b2314..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-5.5.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '6.3' - -homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' -description = """ The GNU Readline library provides a set of functions for use - by applications that allow users to edit command lines as they are typed - in. Both Emacs and vi editing modes are available. The Readline library - includes additional functions to maintain a list of previously-entered - command lines, to recall and perhaps reedit those lines, and perform - csh-like history expansion on previous commands.""" - -toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '5.9')] - -# for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" - -sanity_check_paths = { - 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb index d2bc173ef8..ac855e7cba 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb @@ -25,7 +25,7 @@ source_urls = ['http://www.sqlite.org/2014/'] sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename dependencies = [ - ('libreadline', '6.3'), + ('libreadline', '6.2'), ('Tcl', '8.6.2'), ] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb index 7f2d451b76..8c3980c54e 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-ictce-5.5.0.eb @@ -13,7 +13,7 @@ source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.7'), ] configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' -- GitLab From b825580bdccf60588f5150a60eab1fbb50d3ef1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 15:56:35 +0100 Subject: [PATCH 0566/2133] stick to libreadline 6.2 --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb index 8fc41ecd35..52574ce4b0 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -33,7 +33,7 @@ patches = ['OCaml-%(version)s_icc-fixes.patch'] builddependencies = [('Autotools', '20150215')] dependencies = [ ('ncurses', '5.9'), - ('libreadline', '6.3'), + ('libreadline', '6.2'), ('GSL', '1.16'), ] -- GitLab From bb8088a795a3739822b1baa6ea5dcbbaefb7d577 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 17:21:29 +0100 Subject: [PATCH 0567/2133] sync up OCaml 4.01.0 easyconfigs --- .../o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 21 ++++++++++++++----- .../o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 3 +-- 2 files changed, 17 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb index 5c4386e5cf..8afea955fc 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -17,21 +17,32 @@ description = """OCaml is a general purpose industrial-strength programming lang toolchain = {'name': 'goolf', 'version': '1.4.10'} -ocaml_sourcedir = name.lower() + '-' + '.'.join(version.split('.')[:-1]) opam_ver = '1.2.2' source_urls = [ - 'http://caml.inria.fr/pub/distrib/%s' % ocaml_sourcedir, + 'http://caml.inria.fr/pub/distrib/ocaml-%(version_major_minor)s', 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, ] sources = [ - SOURCELOWER_TAR_GZ, + 'ocaml-%(version)s.tar.gz', 'opam-full-%s.tar.gz' % opam_ver, ] -builddependencies = [('Autoconf', '2.69')] -dependencies = [('ncurses', '5.9')] +builddependencies = [('Autotools', '20150215', '', ('GCC', '4.7.2'))] +dependencies = [ + ('ncurses', '5.9'), + ('libreadline', '6.3'), + ('GSL', '1.16'), +] # parallel build tends to break parallel = 1 +# handled by OPAM, order matters! +exts_list = [ + ('ocamlfind', '1.5.5'), + ('batteries', '2.3.1'), + ('ocaml+twt', '0.94.0'), + ('gsl', '1.18.5'), +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb index 52574ce4b0..3fb3f65385 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -17,10 +17,9 @@ description = """OCaml is a general purpose industrial-strength programming lang toolchain = {'name': 'ictce', 'version': '5.5.0'} -ocaml_sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) opam_ver = '1.2.2' source_urls = [ - 'http://caml.inria.fr/pub/distrib/%s' % ocaml_sourcedir, + 'http://caml.inria.fr/pub/distrib/ocaml-%(version_major_minor)s', 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, ] sources = [ -- GitLab From 71836c97bf340d96f338f8d4cad9ec9b3b728c37 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 17:29:36 +0100 Subject: [PATCH 0568/2133] fix source URLs for OCaml --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb | 3 +-- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb index 8afea955fc..810207a42e 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} opam_ver = '1.2.2' source_urls = [ - 'http://caml.inria.fr/pub/distrib/ocaml-%(version_major_minor)s', + 'http://caml.inria.fr/pub/distrib/ocaml-%s' % '.'.join(version.split('.')[:2]), 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, ] sources = [ diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb index 3fb3f65385..144def4311 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} opam_ver = '1.2.2' source_urls = [ - 'http://caml.inria.fr/pub/distrib/ocaml-%(version_major_minor)s', + 'http://caml.inria.fr/pub/distrib/ocaml-%s' % '.'.join(version.split('.')[:2]), 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, ] sources = [ diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb index ed1f201357..12dba48bf0 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb @@ -17,10 +17,9 @@ description = """OCaml is a general purpose industrial-strength programming lang toolchain = {'name': 'foss', 'version': '2015a'} -ocaml_sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) opam_ver = '1.2.2' source_urls = [ - 'http://caml.inria.fr/pub/distrib/%s' % ocaml_sourcedir, + 'http://caml.inria.fr/pub/distrib/ocaml-%s' % '.'.join(version.split('.')[:2]), 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, ] sources = [ -- GitLab From 054531f95e602be0d26c0b24a284e02cb197ddae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 17:45:50 +0100 Subject: [PATCH 0569/2133] fix source URL for RAxML 7.2.6 --- .../easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-hybrid-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mpi-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mt-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-seq-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb | 2 +- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb index cbe5be6c23..985c883441 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb @@ -10,7 +10,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb index 884ad84637..e09f71abf5 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb @@ -10,7 +10,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb index 3a380bd6de..0fe0530f3a 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb @@ -9,7 +9,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'goolf', 'version': '1.4.10'} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb index 02608c18da..af08c5c5e5 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb @@ -9,7 +9,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'goolf', 'version': '1.4.10'} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-hybrid-sse3.eb index d138389b54..caa2264650 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-hybrid-sse3.eb @@ -10,7 +10,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'usempi': True} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mpi-sse3.eb index 72d074f334..f75155255a 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mpi-sse3.eb @@ -10,7 +10,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'usempi': True} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mt-sse3.eb index d5270c4549..8d232532fb 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-mt-sse3.eb @@ -9,7 +9,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'ictce', 'version': '4.1.13'} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-seq-sse3.eb index 2cab68e67d..13378694a3 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-4.1.13-seq-sse3.eb @@ -9,7 +9,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'ictce', 'version': '4.1.13'} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb index 58fb5bd173..0868a2b38e 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb @@ -10,7 +10,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb index 2e5e7cabbc..3a1597463c 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb @@ -10,7 +10,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb index e8060e8191..153acb7424 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb @@ -9,7 +9,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'ictce', 'version': '5.3.0'} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb index adabadb76b..e7ee2daf46 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb @@ -9,7 +9,7 @@ description = "RAxML search algorithm for maximum likelihood based inference of toolchain = {'name': 'ictce', 'version': '5.3.0'} -# download from http://sco.h-its.org/exelixis/countSource726.php +source_urls = ['http://sco.h-its.org/exelixis/resource/download/software/'] sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -- GitLab From 2f983996a4c5947813959af930f86d425c9bae2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 17:53:56 +0100 Subject: [PATCH 0570/2133] add easyconfigs for USEARCH --- .../u/USEARCH/USEARCH-5.2.236-i86linux32.eb | 29 +++++++++++++++++++ .../u/USEARCH/USEARCH-6.1.544-i86linux32.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb create mode 100644 easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb diff --git a/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb new file mode 100644 index 0000000000..961153d9b4 --- /dev/null +++ b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb @@ -0,0 +1,29 @@ +easyblock = 'Binary' + +name = 'USEARCH' +version = '5.2.236' +versionsuffix = '-i86linux32' + +homepage = 'http://www.drive5.com/usearch/index.html' +description = """USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are + often orders of magnitude faster than BLAST.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download via http://www.drive5.com/usearch/download.html +usearch_bin = 'usearch%s_%s' % (version, versionsuffix[1:]) +sources = [usearch_bin] + +install_cmd = "mkdir -p %%(installdir)s/bin && mv %s %%(installdir)s/bin/%%(namelower)s && " % usearch_bin +install_cmd += "chmod a+rx %(installdir)s/bin/%(namelower)s" + +modloadmsg = """USEARCH (32-bit) is licensed software but + can be used for free by individuals when registered. A 64-bit version is + also available. For more information see http://www.drive5.com/usearch .""" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb b/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb new file mode 100644 index 0000000000..07e180dab5 --- /dev/null +++ b/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb @@ -0,0 +1,29 @@ +easyblock = 'Binary' + +name = 'USEARCH' +version = '6.1.544' +versionsuffix = '-i86linux32' + +homepage = 'http://www.drive5.com/usearch/index.html' +description = """USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are + often orders of magnitude faster than BLAST.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download via http://www.drive5.com/usearch/download.html +usearch_bin = 'usearch%s_%s' % (version, versionsuffix[1:]) +sources = [usearch_bin] + +install_cmd = "mkdir -p %%(installdir)s/bin && mv %s %%(installdir)s/bin/%%(namelower)s && " % usearch_bin +install_cmd += "chmod a+rx %(installdir)s/bin/%(namelower)s" + +modloadmsg = """USEARCH (32-bit) is licensed software but + can be used for free by individuals when registered. A 64-bit version is + also available. For more information see http://www.drive5.com/usearch .""" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From bdb97bbfc198c2a62a7c2170bd01bf7f9b836c28 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sun, 21 Feb 2016 18:21:45 +0100 Subject: [PATCH 0571/2133] fix readline dependency conflict --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb index 6a41f5863c..7b7e716a53 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb @@ -26,7 +26,7 @@ version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.spl sources = ['sqlite-autoconf-%s.tar.gz' % version_str] dependencies = [ - ('libreadline', '6.3'), + ('libreadline', '6.2'), ('Tcl', '8.6.4'), ] -- GitLab From 7536aa23df9188929e6781e55a05a5988bb943a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 21 Feb 2016 18:57:05 +0100 Subject: [PATCH 0572/2133] add comment in patch file --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch index 1d8950ff29..3b6ab1f097 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0_icc-fixes.patch @@ -1,3 +1,5 @@ +fix for Fatal error: exception Invalid_argument("gettimeofday not implemented") +author: Kenneth Hoste (HPC-UGent) --- configure.orig 2015-10-06 10:19:12.763826416 +0200 +++ configure 2015-10-06 10:19:56.005026703 +0200 @@ -1015,7 +1015,7 @@ -- GitLab From 78b5df7b4437faf94ba8ea6b484e097973e27154 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 22 Feb 2016 12:49:20 +1300 Subject: [PATCH 0573/2133] Removed older version of libspatialite --- .../libspatialite-4.1.1-goolf-1.5.14.eb | 27 ------------------- .../libspatialite-configure.ac.patch | 12 --------- 2 files changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb delete mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb deleted file mode 100644 index 8132d40673..0000000000 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libspatialite' -version = '4.1.1' - -homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" -description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." - -toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'usempi': False, 'pic': True} - -download_suffix = '' -source_urls = ['http://www.gaia-gis.it/gaia-sins/'] -sources = [SOURCE_TAR_GZ] - -patches = ['libspatialite-configure.ac.patch'] - -dependencies = [('FreeXL','1.0.0g'),('GEOS','3.3.5'), ('SQLite', '3.8.4.3'), ('PROJ', '4.8.0')] -configopts = '--disable-geosadvanced' -builddependencies = [('CMake', '2.8.10.2')] - -sanity_check_paths = { - 'files': ["lib/libspatialite.la"], - 'dirs': ["lib","include"] - } - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch deleted file mode 100644 index aacff1481f..0000000000 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -urN libspatialite-4.1.1.orig/configure libspatialite-4.1.1/configure ---- libspatialite-4.1.1.orig/configure 2013-06-29 08:53:15.000000000 +0200 -+++ libspatialite-4.1.1/configure 2014-04-02 11:37:56.484423000 +0200 -@@ -263,7 +263,7 @@ - LIBS="$GEOS_LDFLAGS" - AC_SEARCH_LIBS(GEOSTopologyPreserveSimplify,geos_c,,AC_MSG_ERROR([could not find libgeos_c - you may need to specify the directory of a geos-config file using --with-geosconfig])) - LIBS="$LIBS_SAVE" -- LIBS=$LIBS$GEOS_LDFLAGS' -lgeos_c' -+ LIBS="$LIBS $GEOS_LDFLAGS -lgeos_c" - - #----------------------------------------------------------------------- - # --enable-geosadvanced -- GitLab From 9f4b14efcfb9f49ad9a019c7221341b2cb879bd9 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 22 Feb 2016 12:52:30 +1300 Subject: [PATCH 0574/2133] Removed ec for libspatialite 4.3.0 with the Intel compiler suite --- .../libspatialite-4.3.0-intel-2015a.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb deleted file mode 100644 index 732c224f99..0000000000 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libspatialite' -version = '4.3.0' - -homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" -description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." - -toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'usempi': False, 'pic': True} - -download_suffix = '' -source_urls = ['http://www.gaia-gis.it/gaia-sins/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('FreeXL','1.0.1'), - ('GEOS','3.3.9'), - ('SQLite', '3.8.9'), - ('PROJ', '4.9.1'), -] - -configopts = '--disable-geosadvanced' - -builddependencies = [('CMake', '3.2.2')] - -sanity_check_paths = { - 'files': ["lib/libspatialite.la"], - 'dirs': ["lib","include"] - } - -moduleclass = 'lib' -- GitLab From 5ef79c9ac22b4858d80057fda3c573a826aa1a9a Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 22 Feb 2016 09:35:39 +0100 Subject: [PATCH 0575/2133] added missing dep JUnit-4.11-Java-1.7.0_75.eb --- .../j/JUnit/JUnit-4.11-Java-1.7.0_75.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_75.eb diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_75.eb new file mode 100644 index 0000000000..73ee3252a1 --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_75.eb @@ -0,0 +1,25 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.11' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +java = 'Java' +javaver = '1.7.0_75' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From c389d0a690c7f58d37383c99efb8430c0ad953be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 11:10:20 +0200 Subject: [PATCH 0576/2133] add easyconfig htop-2.0.0.eb --- easybuild/easyconfigs/h/htop/htop-2.0.0.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/htop/htop-2.0.0.eb diff --git a/easybuild/easyconfigs/h/htop/htop-2.0.0.eb b/easybuild/easyconfigs/h/htop/htop-2.0.0.eb new file mode 100644 index 0000000000..cadc02fadc --- /dev/null +++ b/easybuild/easyconfigs/h/htop/htop-2.0.0.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'htop' +version = '2.0.0' + +homepage = 'http://hisham.hm/htop/' +description = """An interactive process viewer for Unix""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://hisham.hm/htop/releases/%(version)s/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['bin/htop'], + 'dirs': ['share'], +} + +moduleclass = 'tools' -- GitLab From 0248c013c5411a7ae5f1e0aaf778088cf1105fd8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 10:41:52 +0100 Subject: [PATCH 0577/2133] fix DB dep in DB_File easyconfigs --- .../easyconfigs/d/DB/DB-2.7.7-ictce-5.5.0.eb | 1 + .../easyconfigs/d/DB/DB-2.7.7-intel-2015b.eb | 26 +++++++++++++++++++ .../DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb | 13 +++------- .../DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb | 13 +++------- .../DB_File-1.831-intel-2015b-Perl-5.20.3.eb | 3 +-- 5 files changed, 36 insertions(+), 20 deletions(-) create mode 100644 easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2015b.eb diff --git a/easybuild/easyconfigs/d/DB/DB-2.7.7-ictce-5.5.0.eb b/easybuild/easyconfigs/d/DB/DB-2.7.7-ictce-5.5.0.eb index e2cb4b55ad..3fd0bf8310 100644 --- a/easybuild/easyconfigs/d/DB/DB-2.7.7-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-2.7.7-ictce-5.5.0.eb @@ -6,6 +6,7 @@ description = """Berkeley DB enables the development of custom data management s without the overhead traditionally associated with such custom projects.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} source_urls = ['http://download.oracle.com/berkeley-db'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2015b.eb b/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2015b.eb new file mode 100644 index 0000000000..14aa5bb4b4 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2015b.eb @@ -0,0 +1,26 @@ +name = 'DB' +version = '2.7.7' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.oracle.com/berkeley-db'] +sources = [SOURCELOWER_TAR_GZ] + +modextrapaths = { + 'PATH': ["BerkeleyDB/bin"], + 'CPATH': ["BerkeleyDB/include"], + 'LD_LIBRARY_PATH': ["BerkeleyDB/lib"], + 'LIBRARY_PATH': ["BerkeleyDB/lib"], +} + +sanity_check_paths = { + 'files': ["BerkeleyDB/include/db.h", "BerkeleyDB/include/db_cxx.h", "BerkeleyDB/lib/libdb.a"], + 'dirs': ["BerkeleyDB/bin"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb index bdcb00e69d..899ca0fe36 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb @@ -2,6 +2,7 @@ easyblock = 'PerlModule' name = 'DB_File' version = '1.831' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://perldoc.perl.org/DB_File.html' description = """Perl5 access to Berkeley DB version 1.x.""" @@ -11,19 +12,13 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] sources = [SOURCE_TAR_GZ] -dependencies = [('DB', '2.7.7')] - -perl = 'Perl' -perlver = '5.18.2' -versionsuffix = '-%s-%s' % (perl, perlver) - dependencies = [ - (perl, perlver), + ('Perl', '5.20.3'), + ('DB', '2.7.7'), ] -perlmajver = perlver.split('.')[0] sanity_check_paths = { - 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DB_File.pm' % (perlmajver, perlver)], + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], } diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb index 831d1e8494..899ca0fe36 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb @@ -2,6 +2,7 @@ easyblock = 'PerlModule' name = 'DB_File' version = '1.831' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://perldoc.perl.org/DB_File.html' description = """Perl5 access to Berkeley DB version 1.x.""" @@ -11,19 +12,13 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] sources = [SOURCE_TAR_GZ] -dependencies = [('DB', '2.7.7')] - -perl = 'Perl' -perlver = '5.20.0' -versionsuffix = '-%s-%s' % (perl, perlver) - dependencies = [ - (perl, perlver), + ('Perl', '5.20.3'), + ('DB', '2.7.7'), ] -perlmajver = perlver.split('.')[0] sanity_check_paths = { - 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DB_File.pm' % (perlmajver, perlver)], + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], } diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb index cfa6ec1084..1d9606650c 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb @@ -12,10 +12,9 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] sources = [SOURCE_TAR_GZ] -dependencies = [('DB', '2.7.7')] - dependencies = [ ('Perl', '5.20.3'), + ('DB', '2.7.7'), ] sanity_check_paths = { -- GitLab From a8db6bf6406186d5c3b505b0437c4f98d0f1452c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 10:45:58 +0100 Subject: [PATCH 0578/2133] fix Perl versions in DB_File easyconfigs --- .../d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb | 2 +- .../d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb index 899ca0fe36..99e1e729bd 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb @@ -13,7 +13,7 @@ source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] sources = [SOURCE_TAR_GZ] dependencies = [ - ('Perl', '5.20.3'), + ('Perl', '5.18.2'), ('DB', '2.7.7'), ] diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb index 899ca0fe36..bbc20f533c 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb @@ -13,7 +13,7 @@ source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] sources = [SOURCE_TAR_GZ] dependencies = [ - ('Perl', '5.20.3'), + ('Perl', '5.20.0'), ('DB', '2.7.7'), ] -- GitLab From 6fc8f1754a8192179e48dc53614c661b2096630e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 11:47:55 +0200 Subject: [PATCH 0579/2133] add easyconfig DB-2.7.7-intel-2016a.eb, add easyconfig DB_File-1.835-intel-2016a-Perl-5.20.3.eb --- .../easyconfigs/d/DB/DB-2.7.7-intel-2016a.eb | 26 +++++++++++++++++++ .../DB_File-1.835-intel-2016a-Perl-5.20.3.eb | 25 ++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2016a.eb create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.835-intel-2016a-Perl-5.20.3.eb diff --git a/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2016a.eb b/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2016a.eb new file mode 100644 index 0000000000..fc6e649d7b --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2016a.eb @@ -0,0 +1,26 @@ +name = 'DB' +version = '2.7.7' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.oracle.com/berkeley-db'] +sources = [SOURCELOWER_TAR_GZ] + +modextrapaths = { + 'PATH': ["BerkeleyDB/bin"], + 'CPATH': ["BerkeleyDB/include"], + 'LD_LIBRARY_PATH': ["BerkeleyDB/lib"], + 'LIBRARY_PATH': ["BerkeleyDB/lib"], +} + +sanity_check_paths = { + 'files': ["BerkeleyDB/include/db.h", "BerkeleyDB/include/db_cxx.h", "BerkeleyDB/lib/libdb.a"], + 'dirs': ["BerkeleyDB/bin"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-intel-2016a-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-intel-2016a-Perl-5.20.3.eb new file mode 100644 index 0000000000..780f3183cd --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-intel-2016a-Perl-5.20.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.835' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.20.3'), + ('DB', '2.7.7'), +] + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 1a3ec6a9434c91a7c0239eb6d93728e051bacb91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 11:12:35 +0100 Subject: [PATCH 0580/2133] add missing configopts --- .../d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb | 2 ++ .../d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb | 2 ++ .../d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb index 99e1e729bd..38bc8c6673 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb @@ -17,6 +17,8 @@ dependencies = [ ('DB', '2.7.7'), ] +configopts = "LIB=$EBROOTDB/lib INCLUDE=$EBROOTDB/include" + sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb index bbc20f533c..0cb2264c0b 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb @@ -17,6 +17,8 @@ dependencies = [ ('DB', '2.7.7'), ] +configopts = "LIB=$EBROOTDB/lib INCLUDE=$EBROOTDB/include" + sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb index 1d9606650c..18e394a447 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb @@ -17,6 +17,8 @@ dependencies = [ ('DB', '2.7.7'), ] +configopts = "LIB=$EBROOTDB/lib INCLUDE=$EBROOTDB/include" + sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], -- GitLab From 06cfa4d1cfc60a1407e7ad551ae91ba2e5146c7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 11:22:46 +0100 Subject: [PATCH 0581/2133] fix configopts --- .../d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb | 2 +- .../d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb | 2 +- .../d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb index 38bc8c6673..ae8fad8810 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '2.7.7'), ] -configopts = "LIB=$EBROOTDB/lib INCLUDE=$EBROOTDB/include" +configopts = "LIB=$EBROOTDB/BerkeleyDB/lib INCLUDE=$EBROOTDB/BerkeleyDB/include" sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb index 0cb2264c0b..d043d18175 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '2.7.7'), ] -configopts = "LIB=$EBROOTDB/lib INCLUDE=$EBROOTDB/include" +configopts = "LIB=$EBROOTDB/BerkeleyDB/lib INCLUDE=$EBROOTDB/BerkeleyDB/include" sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb index 18e394a447..bfb50297a7 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '2.7.7'), ] -configopts = "LIB=$EBROOTDB/lib INCLUDE=$EBROOTDB/include" +configopts = "LIB=$EBROOTDB/BerkeleyDB/lib INCLUDE=$EBROOTDB/BerkeleyDB/include" sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], -- GitLab From bed52ee87acb7282f5e577ca7107cd77a4570a3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 12:05:26 +0100 Subject: [PATCH 0582/2133] fix minor style issues in libspatialite easyconfig --- .../libspatialite-4.3.0a-foss-2015a.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb index 0c50d9148b..9c107ea9d9 100644 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb @@ -4,12 +4,12 @@ name = 'libspatialite' version = '4.3.0a' homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" -description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." +description = """SpatiaLite is an open source library intended to extend the SQLite core to support + fully fledged Spatial SQL capabilities.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'usempi': False, 'pic': True} -download_suffix = '' source_urls = ['http://www.gaia-gis.it/gaia-sins/'] sources = [SOURCE_TAR_GZ] @@ -20,13 +20,13 @@ dependencies = [ ('PROJ', '4.9.1'), ] -configopts = '--disable-geosadvanced' - builddependencies = [('CMake', '3.4.1')] +configopts = '--disable-geosadvanced' + sanity_check_paths = { - 'files': ["lib/libspatialite.la"], - 'dirs': ["lib","include"] - } + 'files': ['include/spatialite.h', 'lib/libspatialite.a', 'lib/libspatialite.%s' % SHLIB_EXT], + 'dirs': ['include/spatialite'], +} moduleclass = 'lib' -- GitLab From 3d06bee341da3eabb296d5135d0e6232c238763f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 14:40:00 +0200 Subject: [PATCH 0583/2133] add easyconfig ncurses-6.0.eb --- .../easyconfigs/n/ncurses/ncurses-6.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb new file mode 100644 index 0000000000..51d2a6f539 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' -- GitLab From deeb8507d99dc04fed2b4c98c6620b27a60844f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 13:57:59 +0100 Subject: [PATCH 0584/2133] bump DB version to 4.8.30 --- .../easyconfigs/d/DB/DB-2.7.7-ictce-5.5.0.eb | 1 - .../easyconfigs/d/DB/DB-2.7.7-intel-2015b.eb | 26 ------------------- .../d/DB/DB-4.8.30-goolf-1.4.10.eb | 4 +-- .../easyconfigs/d/DB/DB-4.8.30-ictce-5.5.0.eb | 18 +++++++++++++ .../easyconfigs/d/DB/DB-4.8.30-intel-2015b.eb | 18 +++++++++++++ .../DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb | 4 +-- .../DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb | 4 +-- .../DB_File-1.831-intel-2015b-Perl-5.20.3.eb | 4 +-- 8 files changed, 41 insertions(+), 38 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2015b.eb create mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2015b.eb diff --git a/easybuild/easyconfigs/d/DB/DB-2.7.7-ictce-5.5.0.eb b/easybuild/easyconfigs/d/DB/DB-2.7.7-ictce-5.5.0.eb index 3fd0bf8310..e2cb4b55ad 100644 --- a/easybuild/easyconfigs/d/DB/DB-2.7.7-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-2.7.7-ictce-5.5.0.eb @@ -6,7 +6,6 @@ description = """Berkeley DB enables the development of custom data management s without the overhead traditionally associated with such custom projects.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'pic': True} source_urls = ['http://download.oracle.com/berkeley-db'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2015b.eb b/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2015b.eb deleted file mode 100644 index 14aa5bb4b4..0000000000 --- a/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2015b.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'DB' -version = '2.7.7' - -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' -description = """Berkeley DB enables the development of custom data management solutions, - without the overhead traditionally associated with such custom projects.""" - -toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'pic': True} - -source_urls = ['http://download.oracle.com/berkeley-db'] -sources = [SOURCELOWER_TAR_GZ] - -modextrapaths = { - 'PATH': ["BerkeleyDB/bin"], - 'CPATH': ["BerkeleyDB/include"], - 'LD_LIBRARY_PATH': ["BerkeleyDB/lib"], - 'LIBRARY_PATH': ["BerkeleyDB/lib"], -} - -sanity_check_paths = { - 'files': ["BerkeleyDB/include/db.h", "BerkeleyDB/include/db_cxx.h", "BerkeleyDB/lib/libdb.a"], - 'dirs': ["BerkeleyDB/bin"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-goolf-1.4.10.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-goolf-1.4.10.eb index bebd111842..bee3a45a5e 100644 --- a/easybuild/easyconfigs/d/DB/DB-4.8.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/DB/DB-4.8.30-goolf-1.4.10.eb @@ -11,8 +11,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ["include/db.h"], - 'dirs': [], + 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['bin'], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-ictce-5.5.0.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-ictce-5.5.0.eb new file mode 100644 index 0000000000..9f4aaab492 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-4.8.30-ictce-5.5.0.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '4.8.30' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2015b.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2015b.eb new file mode 100644 index 0000000000..ba87547173 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2015b.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '4.8.30' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb index ae8fad8810..babf824aa1 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb @@ -14,11 +14,9 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Perl', '5.18.2'), - ('DB', '2.7.7'), + ('DB', '4.8.30'), ] -configopts = "LIB=$EBROOTDB/BerkeleyDB/lib INCLUDE=$EBROOTDB/BerkeleyDB/include" - sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb index d043d18175..2eb7bd63e2 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb @@ -14,11 +14,9 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Perl', '5.20.0'), - ('DB', '2.7.7'), + ('DB', '4.8.30'), ] -configopts = "LIB=$EBROOTDB/BerkeleyDB/lib INCLUDE=$EBROOTDB/BerkeleyDB/include" - sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb index bfb50297a7..7a984ebf4c 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-intel-2015b-Perl-5.20.3.eb @@ -14,11 +14,9 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Perl', '5.20.3'), - ('DB', '2.7.7'), + ('DB', '4.8.30'), ] -configopts = "LIB=$EBROOTDB/BerkeleyDB/lib INCLUDE=$EBROOTDB/BerkeleyDB/include" - sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], -- GitLab From 7b5b30ccc3aec8aeba02be0c6dc49bdef1ce8381 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 14:00:10 +0100 Subject: [PATCH 0585/2133] fix source URL for DB 4.8.30 --- easybuild/easyconfigs/d/DB/DB-4.8.30-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/d/DB/DB-4.8.30-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2015b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-goolf-1.4.10.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-goolf-1.4.10.eb index bee3a45a5e..f567e411fb 100644 --- a/easybuild/easyconfigs/d/DB/DB-4.8.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/DB/DB-4.8.30-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = """Berkeley DB enables the development of custom data management s toolchain = {'name': 'goolf', 'version': '1.4.10'} -# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +source_urls = ['http://download.oracle.com/berkeley-db/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-ictce-5.5.0.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-ictce-5.5.0.eb index 9f4aaab492..42d43b6f8e 100644 --- a/easybuild/easyconfigs/d/DB/DB-4.8.30-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-4.8.30-ictce-5.5.0.eb @@ -7,7 +7,7 @@ description = """Berkeley DB enables the development of custom data management s toolchain = {'name': 'ictce', 'version': '5.5.0'} -# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +source_urls = ['http://download.oracle.com/berkeley-db/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2015b.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2015b.eb index ba87547173..0155873f3f 100644 --- a/easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2015b.eb +++ b/easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2015b.eb @@ -7,7 +7,7 @@ description = """Berkeley DB enables the development of custom data management s toolchain = {'name': 'intel', 'version': '2015b'} -# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +source_urls = ['http://download.oracle.com/berkeley-db/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { -- GitLab From 96a3cb72c685932ecda3566fc8c97146d1633318 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 15:35:50 +0100 Subject: [PATCH 0586/2133] bump DB version to 4.8.30 --- .../easyconfigs/d/DB/DB-2.7.7-intel-2016a.eb | 26 ------------------- .../easyconfigs/d/DB/DB-4.8.30-intel-2016a.eb | 18 +++++++++++++ .../DB_File-1.835-intel-2016a-Perl-5.20.3.eb | 2 +- 3 files changed, 19 insertions(+), 27 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2016a.eb create mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2016a.eb b/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2016a.eb deleted file mode 100644 index fc6e649d7b..0000000000 --- a/easybuild/easyconfigs/d/DB/DB-2.7.7-intel-2016a.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'DB' -version = '2.7.7' - -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' -description = """Berkeley DB enables the development of custom data management solutions, - without the overhead traditionally associated with such custom projects.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True} - -source_urls = ['http://download.oracle.com/berkeley-db'] -sources = [SOURCELOWER_TAR_GZ] - -modextrapaths = { - 'PATH': ["BerkeleyDB/bin"], - 'CPATH': ["BerkeleyDB/include"], - 'LD_LIBRARY_PATH': ["BerkeleyDB/lib"], - 'LIBRARY_PATH': ["BerkeleyDB/lib"], -} - -sanity_check_paths = { - 'files': ["BerkeleyDB/include/db.h", "BerkeleyDB/include/db_cxx.h", "BerkeleyDB/lib/libdb.a"], - 'dirs': ["BerkeleyDB/bin"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2016a.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2016a.eb new file mode 100644 index 0000000000..aec133eedf --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-4.8.30-intel-2016a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '4.8.30' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-intel-2016a-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-intel-2016a-Perl-5.20.3.eb index 780f3183cd..c1d977b9e2 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-intel-2016a-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-intel-2016a-Perl-5.20.3.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Perl', '5.20.3'), - ('DB', '2.7.7'), + ('DB', '4.8.30'), ] sanity_check_paths = { -- GitLab From f01d759d7a83885c7cd546e242c2849723a50b95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 17:32:53 +0200 Subject: [PATCH 0587/2133] add easyconfig BioPerl-1.6.924-intel-2016a-Perl-5.20.3.eb --- ...BioPerl-1.6.924-intel-2016a-Perl-5.20.3.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-intel-2016a-Perl-5.20.3.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-intel-2016a-Perl-5.20.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-intel-2016a-Perl-5.20.3.eb new file mode 100644 index 0000000000..4145ed2b91 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-intel-2016a-Perl-5.20.3.eb @@ -0,0 +1,23 @@ +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.6.924' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.tar.gz' % version.replace('.', '-')] + +dependencies = [ + ('Perl', '5.20.3'), + ('DB_File', '1.835', versionsuffix), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' -- GitLab From db62cbe554a9e0000a51489ac73e335bda616c77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 17:54:42 +0200 Subject: [PATCH 0588/2133] add easyconfig MAST-20160111-intel-2015b-R-3.2.1.eb --- .../MAST/MAST-20160111-intel-2015b-R-3.2.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAST/MAST-20160111-intel-2015b-R-3.2.1.eb diff --git a/easybuild/easyconfigs/m/MAST/MAST-20160111-intel-2015b-R-3.2.1.eb b/easybuild/easyconfigs/m/MAST/MAST-20160111-intel-2015b-R-3.2.1.eb new file mode 100644 index 0000000000..c085da3378 --- /dev/null +++ b/easybuild/easyconfigs/m/MAST/MAST-20160111-intel-2015b-R-3.2.1.eb @@ -0,0 +1,25 @@ +easyblock = 'RPackage' + +name = 'MAST' +version = '20160111' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/RGLab/MAST' +description = """Tools and methods for analysis of single cell assay data in R""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/RGLab/MAST/archive/'] +sources = ['8234b18.tar.gz'] + +dependencies = [ + ('R', '3.2.1'), + ('R-bundle-Bioconductor', '3.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'], +} + +moduleclass = 'lib' -- GitLab From 9976756eff680b58611c1c762960589766047b78 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 17:11:27 +0100 Subject: [PATCH 0589/2133] update list of extensions for R 3.2.1 (req. for ShrinkBayes) --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb index 73337ba428..0b60771f8e 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb @@ -395,6 +395,13 @@ exts_list = [ ('Lmoments', '1.1-6', ext_options), ('distillery', '1.0-2', ext_options), ('extRemes', '2.0-7', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-9', ext_options), + ('ks', '1.10.1', ext_options), + ('logcondens', '2.1.4', ext_options), + ('Iso', '0.0-17', ext_options), ] moduleclass = 'lang' -- GitLab From 94fe4826fb4a4c93f7852e3b7f351d742799a2cb Mon Sep 17 00:00:00 2001 From: John-Paul Robinson Date: Mon, 22 Feb 2016 10:12:08 -0600 Subject: [PATCH 0590/2133] Create texinfo 4.13a easyconfig Create a texinfo 4.13 easyconfig based on the newer 5.2 easyconfig to support builing older GCC (<=4.7.2) on newer systems. The 4.x releases of texinfo tolerated a document parsing error in earlier versions of GCC. In particular, loading the resulting module allows building GCC 4.7.2 on CentOS7. This GCC is the foundation of the goolf-1.4.10 toolchain used by many bioinformatics packages in the current EasyBuild (2.6). The easyconfig's GCC requirement was set to 4.8.4 as a convinience to match the version of GCC likely already built by the goolf-1.7.20 toolchain. --- .../t/texinfo/texinfo-4.13a-GCC-4.8.4.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/t/texinfo/texinfo-4.13a-GCC-4.8.4.eb diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-4.13a-GCC-4.8.4.eb b/easybuild/easyconfigs/t/texinfo/texinfo-4.13a-GCC-4.8.4.eb new file mode 100644 index 0000000000..ab42d5c737 --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-4.13a-GCC-4.8.4.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'texinfo' +version = '4.13a' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +osdependencies = ['texlive'] + +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable \\$TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new \\$TEXMFHOME to your custom directory and reset the value of \\$TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" + +sanity_check_paths = { + 'files': ['bin/info', 'bin/makeinfo', 'bin/texi2pdf', 'texmf/tex/texinfo/texinfo.tex'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 287331b8e9c78e397f19d4b6a5f01f5c149eca66 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 20:24:46 +0100 Subject: [PATCH 0591/2133] fix output of 'pplacer --version' --- .../pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb index b23402e2e0..7d55417f25 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb @@ -39,6 +39,9 @@ prebuildopts = "rm -rf %(installdir)s && export OPAMROOT=%(installdir)s && opam prebuildopts += "opam repo add pplacer-deps %(builddir)s/pplacer-opam-repository*/ && " prebuildopts += "opam update pplacer-deps && eval `opam config env` && " prebuildopts += "export OCAML_BACKEND=gcc && cat opam-requirements.txt | xargs opam install -y && " +prebuildopts += "echo 'let version = \"v%(version)s\"\n' > common_src/version.ml && " + +# parallel build tends to break parallel = 1 files_to_copy = ['bin'] @@ -48,4 +51,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [('pplacer', '--version | grep %(version)s')] + moduleclass = 'bio' -- GitLab From 9dbf17be9966d47aa53cb66632d15ff725c9bf84 Mon Sep 17 00:00:00 2001 From: John-Paul Robinson Date: Mon, 22 Feb 2016 14:00:24 -0600 Subject: [PATCH 0592/2133] Removed GCC version dependency from texinfo-4.13a easyconfig Update the easyconfig for texinfo to build using the dummy toolchain. This removes the version dependency on a particular GCC for the build and allows a cleaner dependency chain. The goal of building GCC 4.7.2 with this easyconfig won't depend on building a later version of GCC first. It will simply depend on the compiler already available in the environment. --- .../t/texinfo/{texinfo-4.13a-GCC-4.8.4.eb => texinfo-4.13a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/t/texinfo/{texinfo-4.13a-GCC-4.8.4.eb => texinfo-4.13a.eb} (95%) diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-4.13a-GCC-4.8.4.eb b/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb similarity index 95% rename from easybuild/easyconfigs/t/texinfo/texinfo-4.13a-GCC-4.8.4.eb rename to easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb index ab42d5c737..1f3105220a 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-4.13a-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb @@ -9,7 +9,7 @@ description = """Texinfo is the official documentation format of the GNU project source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'GCC', 'version': '4.8.4'} +toolchain = {'name': 'dummy', 'version': ''} osdependencies = ['texlive'] -- GitLab From 32da2fef77be402b96b2f0ebc7791d8226879634 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 23 Feb 2016 10:03:29 +1030 Subject: [PATCH 0593/2133] Add picard 1.141 and 2.1.0 with Java 1.8.0_74 --- .../p/picard/picard-1.141-Java-1.8.0_74.eb | 18 +++++++++++++++++ .../p/picard/picard-2.1.0-Java-1.8.0_74.eb | 20 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb create mode 100644 easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb diff --git a/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb new file mode 100644 index 0000000000..3c1e54038f --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb @@ -0,0 +1,18 @@ +name = 'picard' +version = '1.141' + +homepage = 'http://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM + (http://samtools.github.io/hts-specs) format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] +sources = ['%(name)s-tools-%(version)s.zip'] + +java = 'Java' +javaver = '1.8.0_74' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb new file mode 100644 index 0000000000..2c1613a976 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb @@ -0,0 +1,20 @@ +name = 'picard' +version = '2.1.0' + +homepage = 'http://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM + (http://samtools.github.io/hts-specs) format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] +sources = ['%(name)s-tools-%(version)s.zip'] + +java = 'Java' +javaver = '1.8.0_74' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" + +moduleclass = 'bio' -- GitLab From 79893898874cac6df84108d8faa8f2482bf3b0c8 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 23 Feb 2016 10:04:51 +1030 Subject: [PATCH 0594/2133] Added NextClip 1.3.1 using foss-2015b --- .../n/NextClip/NextClip-1.3.1-foss-2015b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/NextClip/NextClip-1.3.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/n/NextClip/NextClip-1.3.1-foss-2015b.eb b/easybuild/easyconfigs/n/NextClip/NextClip-1.3.1-foss-2015b.eb new file mode 100644 index 0000000000..b4ac0527df --- /dev/null +++ b/easybuild/easyconfigs/n/NextClip/NextClip-1.3.1-foss-2015b.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'NextClip' +version = '1.3.1' + +homepage = 'https://github.com/richardmleggett/nextclip' +description = """Nextera Long Mate Pair analysis and processing tool.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/richardmleggett/nextclip/archive'] +sources = ['NextClip_v%(version)s.tar.gz'] + +files_to_copy = ['bin', 'examples', 'scripts', 'nextclipmanual.pdf'] + +sanity_check_paths = { + 'files': ["bin/nextclip"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' -- GitLab From ba11c9863958218fa12ec282f9d15ad2e5a29380 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 23 Feb 2016 12:29:59 +1030 Subject: [PATCH 0595/2133] Made changes according to suggestions by @boegel --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index dfcbaddec1..71dd3c4e06 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -20,13 +20,10 @@ sources = ['%(name)s_%(version)s.tar.gz' ] prebuildopts = 'cd jni && ' -os_type = platform.system() -if os_type == 'Linux': - buildopts = '-f makefile.linux' -elif os_type == 'Darwin': - buildopts = '-f makefile.osx' +suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % suff -files_to_copy = ['./*'] +files_to_copy = ['*'] sanity_check_paths = { 'files': ['bbmap.sh'], -- GitLab From 5ef9ccfb95a4bbc11a2f2c636ec3ea444522d387 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 23 Feb 2016 12:31:01 +1030 Subject: [PATCH 0596/2133] Added easy config for Java 1.8.0_74 --- .../BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb new file mode 100644 index 0000000000..c02118b3a9 --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -0,0 +1,37 @@ +import platform + +easyblock = 'MakeCp' + +name = 'BBMap' +version = '35.82' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +java = 'Java' +javaver = '1.8.0_74' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver, '', True)] + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz' ] + +prebuildopts = 'cd jni && ' + +suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh'], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code." + +moduleclass = 'bio' -- GitLab From c0c654f960fc9865838fa0e1eb87fa608c917529 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 10:46:38 +0200 Subject: [PATCH 0597/2133] add easyconfig Java-1.8.0_74.eb --- easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb new file mode 100644 index 0000000000..c9ef30b97e --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_74' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From fc228cbf1815d938ba8121592264bbc26c525f95 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 23 Feb 2016 10:17:59 +0100 Subject: [PATCH 0598/2133] Remove hard-coded -xSSE4.2 for scipy with intel compiler --- .../p/Python/Python-3.5.1-intel-2016a.eb | 1 + .../p/Python/numpy-1.10.4-sse42.patch | 25 +++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/numpy-1.10.4-sse42.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index 0a2f41e168..d0254354b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -41,6 +41,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'patches': [ 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-%s-sse42.patch' % numpyversion, ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/numpy-1.10.4-sse42.patch b/easybuild/easyconfigs/p/Python/numpy-1.10.4-sse42.patch new file mode 100644 index 0000000000..75ffeaa0d5 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/numpy-1.10.4-sse42.patch @@ -0,0 +1,25 @@ +#Remove hard coded -xSSE4.2 compilation flag for Intel compilers (add the usual -xHOST) +#compilation would fail on non-SSE4.2 CPUs, and for further CPUs/compilers it would restrict the generated code to SSE4.2 +# February 19th, 2016 by B. Hajgato - Free University Brussels (VUB) +--- ./numpy/distutils/intelccompiler.py.orig 2016-01-06 22:07:54.000000000 +0100 ++++ ./numpy/distutils/intelccompiler.py 2016-02-19 15:07:00.438235792 +0100 +@@ -54,7 +54,7 @@ + def __init__(self, verbose=0, dry_run=0, force=0): + UnixCCompiler.__init__(self, verbose, dry_run, force) + self.cc_exe = ('icc -m64 -fPIC -fp-model strict -O3 ' +- '-fomit-frame-pointer -openmp -xSSE4.2') ++ '-fomit-frame-pointer -openmp -xHOST') + compiler = self.cc_exe + if platform.system() == 'Darwin': + shared_flag = '-Wl,-undefined,dynamic_lookup' +--- ./numpy/distutils/fcompiler/intel.py.orig 2016-01-07 03:16:25.000000000 +0100 ++++ ./numpy/distutils/fcompiler/intel.py 2016-02-19 15:07:16.424220745 +0100 +@@ -123,7 +123,7 @@ + return ['-openmp -fp-model strict'] + + def get_flags_arch(self): +- return ['-xSSE4.2'] ++ return ['-xHOST'] + + # Is there no difference in the version string between the above compilers + # and the Visual compilers? -- GitLab From afdf8a54cf71a27b8f4f6824897c26b59dc880c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 11:14:44 +0100 Subject: [PATCH 0599/2133] fix remark --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb index 810207a42e..0a78e38ade 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -23,7 +23,7 @@ source_urls = [ 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, ] sources = [ - 'ocaml-%(version)s.tar.gz', + SOURCELOWER_TAR_GZ, 'opam-full-%s.tar.gz' % opam_ver, ] diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb index 144def4311..eb591f01b3 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -23,7 +23,7 @@ source_urls = [ 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, ] sources = [ - 'ocaml-%(version)s.tar.gz', + SOURCELOWER_TAR_GZ, 'opam-full-%s.tar.gz' % opam_ver, ] -- GitLab From afaa6ff4b4f85865b5ae8ff83ce0a4d9f7d3610b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 23 Feb 2016 11:36:14 +0100 Subject: [PATCH 0600/2133] configfiles with numpy 1.10 included --- .../p/Python/Python-2.7.11-intel-2015b.eb | 5 +++- .../p/Python/Python-2.7.11-intel-2016a.eb | 5 +++- .../p/Python/Python-3.5.1-intel-2016a.eb | 2 +- .../p/Python/numpy-1.10.1-sse42.patch | 25 +++++++++++++++++++ 4 files changed, 34 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/p/Python/numpy-1.10.1-sse42.patch diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index 256977ab08..74d0c82b50 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -43,7 +43,10 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': ['numpy-1.8.0-mkl.patch'], + 'patches': [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%s-sse42.patch' % numpyversion, + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 68dbf9f030..6819a492c9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -43,7 +43,10 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': ['numpy-1.8.0-mkl.patch'], + 'patches': [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%s-sse42.patch' % numpyversion, + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index d0254354b9..e610aff618 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -40,7 +40,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', 'numpy-%s-sse42.patch' % numpyversion, ], }), diff --git a/easybuild/easyconfigs/p/Python/numpy-1.10.1-sse42.patch b/easybuild/easyconfigs/p/Python/numpy-1.10.1-sse42.patch new file mode 100644 index 0000000000..60cdd96731 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/numpy-1.10.1-sse42.patch @@ -0,0 +1,25 @@ +#Remove hard coded -xSSE4.2 compilation flag for Intel compilers (add the usual -xHOST) +#compilation would fail on non-SSE4.2 CPUs, and for further CPUs/compilers it would restrict the generated code to SSE4.2 +# February 19th, 2016 by B. Hajgato - Free University Brussels (VUB) +--- numpy/distutils/intelccompiler.py.orig 2015-10-12 16:29:01.000000000 +0200 ++++ numpy/distutils/intelccompiler.py 2016-02-23 11:31:50.350422787 +0100 +@@ -49,7 +49,7 @@ + def __init__(self, verbose=0, dry_run=0, force=0): + UnixCCompiler.__init__(self, verbose, dry_run, force) + self.cc_exe = ('icc -m64 -fPIC -fp-model strict -O3 ' +- '-fomit-frame-pointer -openmp -xSSE4.2') ++ '-fomit-frame-pointer -openmp -xHOST') + compiler = self.cc_exe + self.set_executables(compiler=compiler, + compiler_so=compiler, +--- numpy/distutils/fcompiler/intel.py.orig 2015-10-12 16:29:01.000000000 +0200 ++++ numpy/distutils/fcompiler/intel.py 2016-02-23 11:31:50.350422787 +0100 +@@ -123,7 +123,7 @@ + return ['-openmp -fp-model strict'] + + def get_flags_arch(self): +- return ['-xSSE4.2'] ++ return ['-xHOST'] + + # Is there no difference in the version string between the above compilers + # and the Visual compilers? -- GitLab From 8cb4757e1083c7f7748737ac153c7c72a2657156 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 11:45:49 +0100 Subject: [PATCH 0601/2133] use pplacer easyblock --- ...cer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb index 7d55417f25..67fa1882a4 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb @@ -1,5 +1,3 @@ -easyblock = 'MakeCp' - name = 'pplacer' version = '1.1.alpha16' @@ -34,23 +32,7 @@ builddependencies = [ ('M4', '1.4.17'), ] -# see http://matsen.github.io/pplacer/compiling.html#opam -prebuildopts = "rm -rf %(installdir)s && export OPAMROOT=%(installdir)s && opam init && " -prebuildopts += "opam repo add pplacer-deps %(builddir)s/pplacer-opam-repository*/ && " -prebuildopts += "opam update pplacer-deps && eval `opam config env` && " -prebuildopts += "export OCAML_BACKEND=gcc && cat opam-requirements.txt | xargs opam install -y && " -prebuildopts += "echo 'let version = \"v%(version)s\"\n' > common_src/version.ml && " - # parallel build tends to break parallel = 1 -files_to_copy = ['bin'] - -sanity_check_paths = { - 'files': ['bin/guppy', 'bin/pplacer', 'bin/rppr'], - 'dirs': [], -} - -sanity_check_commands = [('pplacer', '--version | grep %(version)s')] - moduleclass = 'bio' -- GitLab From 031c4c9f1f87fcccf0248a2f0c73bf1c99e2645a Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 23 Feb 2016 21:16:18 +1030 Subject: [PATCH 0602/2133] removed import statements and wrapped lines longer than 120 chars --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 5 ++--- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 5 ++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 71dd3c4e06..2679eeb7f4 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -1,5 +1,3 @@ -import platform - easyblock = 'MakeCp' name = 'BBMap' @@ -32,6 +30,7 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code." +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the + compiled jni C code." moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index c02118b3a9..e9d0c0554f 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -1,5 +1,3 @@ -import platform - easyblock = 'MakeCp' name = 'BBMap' @@ -32,6 +30,7 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code." +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the + compiled jni C code." moduleclass = 'bio' -- GitLab From fbf8fc17849937fc4749f29ee88bb6d042a73049 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 11:47:46 +0100 Subject: [PATCH 0603/2133] sync up R 3.2.1 and 3.2.3 easyconfigs w.r.t. list of extensions --- .../easyconfigs/r/R/R-3.2.1-foss-2015b.eb | 21 +++++++++++++++++++ .../easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 21 +++++++++++++++++++ .../easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 21 +++++++++++++++++++ 3 files changed, 63 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb index 79832f4acc..23d28da007 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb @@ -383,6 +383,27 @@ exts_list = [ ('EasyABC', '1.5', ext_options), ('shape', '1.4.2', ext_options), ('tidyr', '0.3.1', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.4.0', ext_options), + ('roxygen2', '5.0.1', ext_options), + ('git2r', '0.13.1', ext_options), + ('xml2', '0.1.2', ext_options), + ('rversions', '1.0.2', ext_options), + ('devtools', '1.9.1', ext_options), + ('Rook', '1.1-1', ext_options), + ('rjson', '0.2.15', ext_options), + ('Cairo', '1.5-9', ext_options), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.1-6', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-7', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-9', ext_options), + ('ks', '1.10.1', ext_options), + ('logcondens', '2.1.4', ext_options), + ('Iso', '0.0-17', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 06397a454b..b7ba0004fa 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -383,6 +383,27 @@ exts_list = [ ('EasyABC', '1.5', ext_options), ('shape', '1.4.2', ext_options), ('tidyr', '0.3.1', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.4.0', ext_options), + ('roxygen2', '5.0.1', ext_options), + ('git2r', '0.13.1', ext_options), + ('xml2', '0.1.2', ext_options), + ('rversions', '1.0.2', ext_options), + ('devtools', '1.9.1', ext_options), + ('Rook', '1.1-1', ext_options), + ('rjson', '0.2.15', ext_options), + ('Cairo', '1.5-9', ext_options), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.1-6', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-7', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-9', ext_options), + ('ks', '1.10.1', ext_options), + ('logcondens', '2.1.4', ext_options), + ('Iso', '0.0-17', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index 5a07a10c24..ce43b870fa 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -394,6 +394,27 @@ exts_list = [ ('tensorA', '0.36', ext_options), ('EasyABC', '1.5', ext_options), ('shape', '1.4.2', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.4.0', ext_options), + ('roxygen2', '5.0.1', ext_options), + ('git2r', '0.13.1', ext_options), + ('xml2', '0.1.2', ext_options), + ('rversions', '1.0.2', ext_options), + ('devtools', '1.9.1', ext_options), + ('Rook', '1.1-1', ext_options), + ('rjson', '0.2.15', ext_options), + ('Cairo', '1.5-9', ext_options), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.1-6', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-7', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-9', ext_options), + ('ks', '1.10.1', ext_options), + ('logcondens', '2.1.4', ext_options), + ('Iso', '0.0-17', ext_options), ] moduleclass = 'lang' -- GitLab From 3801590fa7c269c8915ca8bbb7b88e10d2653927 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 23 Feb 2016 11:50:08 +0100 Subject: [PATCH 0604/2133] numpy patches for -xSSE4.2 added --- .../numpy-1.10.1-intel-2015b-Python-2.7.10.eb | 5 +++- .../n/numpy/numpy-1.10.1-sse42.patch | 25 +++++++++++++++++++ .../numpy-1.10.4-intel-2015b-Python-2.7.10.eb | 5 +++- .../numpy-1.10.4-intel-2016a-Python-2.7.11.eb | 5 +++- .../n/numpy/numpy-1.10.4-sse42.patch | 25 +++++++++++++++++++ 5 files changed, 62 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.1-sse42.patch create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.4-sse42.patch diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-intel-2015b-Python-2.7.10.eb index 49bbddc678..8d802d968f 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-intel-2015b-Python-2.7.10.eb @@ -13,7 +13,10 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['numpy-1.8.0-mkl.patch'] +patches = [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%(version)s-sse42.patch', +] python = 'Python' pyver = '2.7.10' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-sse42.patch b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-sse42.patch new file mode 100644 index 0000000000..60cdd96731 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-sse42.patch @@ -0,0 +1,25 @@ +#Remove hard coded -xSSE4.2 compilation flag for Intel compilers (add the usual -xHOST) +#compilation would fail on non-SSE4.2 CPUs, and for further CPUs/compilers it would restrict the generated code to SSE4.2 +# February 19th, 2016 by B. Hajgato - Free University Brussels (VUB) +--- numpy/distutils/intelccompiler.py.orig 2015-10-12 16:29:01.000000000 +0200 ++++ numpy/distutils/intelccompiler.py 2016-02-23 11:31:50.350422787 +0100 +@@ -49,7 +49,7 @@ + def __init__(self, verbose=0, dry_run=0, force=0): + UnixCCompiler.__init__(self, verbose, dry_run, force) + self.cc_exe = ('icc -m64 -fPIC -fp-model strict -O3 ' +- '-fomit-frame-pointer -openmp -xSSE4.2') ++ '-fomit-frame-pointer -openmp -xHOST') + compiler = self.cc_exe + self.set_executables(compiler=compiler, + compiler_so=compiler, +--- numpy/distutils/fcompiler/intel.py.orig 2015-10-12 16:29:01.000000000 +0200 ++++ numpy/distutils/fcompiler/intel.py 2016-02-23 11:31:50.350422787 +0100 +@@ -123,7 +123,7 @@ + return ['-openmp -fp-model strict'] + + def get_flags_arch(self): +- return ['-xSSE4.2'] ++ return ['-xHOST'] + + # Is there no difference in the version string between the above compilers + # and the Visual compilers? diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2015b-Python-2.7.10.eb index db4b5f54bf..a7d1f53ad3 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2015b-Python-2.7.10.eb @@ -13,7 +13,10 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['numpy-1.8.0-mkl.patch'] +patches = [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%(version)s-sse42.patch', +] python = 'Python' pyver = '2.7.10' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2016a-Python-2.7.11.eb index b76b0c1b2e..62945ed938 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2016a-Python-2.7.11.eb @@ -14,7 +14,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['numpy-1.8.0-mkl.patch'] +patches = [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%(version)s-sse42.patch', +] dependencies = [ ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-sse42.patch b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-sse42.patch new file mode 100644 index 0000000000..75ffeaa0d5 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-sse42.patch @@ -0,0 +1,25 @@ +#Remove hard coded -xSSE4.2 compilation flag for Intel compilers (add the usual -xHOST) +#compilation would fail on non-SSE4.2 CPUs, and for further CPUs/compilers it would restrict the generated code to SSE4.2 +# February 19th, 2016 by B. Hajgato - Free University Brussels (VUB) +--- ./numpy/distutils/intelccompiler.py.orig 2016-01-06 22:07:54.000000000 +0100 ++++ ./numpy/distutils/intelccompiler.py 2016-02-19 15:07:00.438235792 +0100 +@@ -54,7 +54,7 @@ + def __init__(self, verbose=0, dry_run=0, force=0): + UnixCCompiler.__init__(self, verbose, dry_run, force) + self.cc_exe = ('icc -m64 -fPIC -fp-model strict -O3 ' +- '-fomit-frame-pointer -openmp -xSSE4.2') ++ '-fomit-frame-pointer -openmp -xHOST') + compiler = self.cc_exe + if platform.system() == 'Darwin': + shared_flag = '-Wl,-undefined,dynamic_lookup' +--- ./numpy/distutils/fcompiler/intel.py.orig 2016-01-07 03:16:25.000000000 +0100 ++++ ./numpy/distutils/fcompiler/intel.py 2016-02-19 15:07:16.424220745 +0100 +@@ -123,7 +123,7 @@ + return ['-openmp -fp-model strict'] + + def get_flags_arch(self): +- return ['-xSSE4.2'] ++ return ['-xHOST'] + + # Is there no difference in the version string between the above compilers + # and the Visual compilers? -- GitLab From 9a32aba82c42a4c8b6b0680b28ddf172aa9c64db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 11:52:05 +0100 Subject: [PATCH 0605/2133] remove duplicate entries in R extensions list --- easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb | 2 -- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb index 23d28da007..b1cc503084 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb @@ -366,8 +366,6 @@ exts_list = [ ('SuperLearner', '2.0-15', ext_options), ('lpSolve', '5.6.13', ext_options), ('mediation', '4.4.5', ext_options), - ('lpSolve', '5.6.13', ext_options), - ('mediation', '4.4.5', ext_options), ('caret', '6.0-57', ext_options), ('adabag', '4.1', ext_options), ('parallelMap', '1.3', ext_options), diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index b7ba0004fa..0e86ace8cb 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -366,8 +366,6 @@ exts_list = [ ('SuperLearner', '2.0-15', ext_options), ('lpSolve', '5.6.13', ext_options), ('mediation', '4.4.5', ext_options), - ('lpSolve', '5.6.13', ext_options), - ('mediation', '4.4.5', ext_options), ('caret', '6.0-57', ext_options), ('adabag', '4.1', ext_options), ('parallelMap', '1.3', ext_options), -- GitLab From d6f0769eac43fe6b190c5deef61b372d41880623 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 14:15:34 +0100 Subject: [PATCH 0606/2133] fix sanity check for xtrans --- easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb | 5 ++--- easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb | 5 ++--- easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb | 5 ++--- .../easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb | 7 ++++--- easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb | 5 ++--- easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb | 5 ++--- 6 files changed, 14 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb index 1d6eb396ed..0edc961a34 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb @@ -15,9 +15,8 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', - 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', - 'Xtranstli.c', 'Xtransutil.c']], + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c']], 'dirs': [], } diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb index 23de4f9f86..1a4f54a0c5 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb @@ -15,9 +15,8 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', - 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', - 'Xtranstli.c', 'Xtransutil.c']], + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], 'dirs': [], } diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb index f7ff52f126..01968fd489 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb @@ -15,9 +15,8 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', - 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', - 'Xtranstli.c', 'Xtransutil.c']], + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], 'dirs': [], } diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb index aba9aa9dae..0f0fef97b7 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb @@ -15,9 +15,10 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', - 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', - 'Xtranstli.c', 'Xtransutil.c']], + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', + 'Xtranssock.c', 'Xtransutil.c']], + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], 'dirs': [], } diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb index 3b75c81b7b..0613532497 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb @@ -15,9 +15,8 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', - 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', - 'Xtranstli.c', 'Xtransutil.c']], + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], 'dirs': [], } diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb index bfcb216ed9..21b74f6cfe 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb @@ -15,9 +15,8 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', - 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', - 'Xtranstli.c', 'Xtransutil.c']], + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], 'dirs': [], } -- GitLab From f6644ed91896d7a7d17000d33204d46d54ebdf6c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 23 Feb 2016 14:23:05 +0100 Subject: [PATCH 0607/2133] {vis}[intel-2016b] libX11 1.6.3 (REVIEW) --- .../inputproto-2.3.1-intel-2016a.eb | 19 ++++++++++ .../k/kbproto/kbproto-1.0.7-intel-2016a.eb | 19 ++++++++++ .../l/libX11/libX11-1.6.3-intel-2016a.eb | 37 +++++++++++++++++++ .../l/libXau/libXau-1.0.8-intel-2016a.eb | 25 +++++++++++++ .../libpthread-stubs-0.3-intel-2016a.eb | 20 ++++++++++ .../l/libxcb/libxcb-1.11.1-intel-2016a.eb | 31 ++++++++++++++++ ...cb-proto-1.11-intel-2016a-Python-2.7.11.eb | 27 ++++++++++++++ .../xextproto/xextproto-7.3.0-intel-2016a.eb | 25 +++++++++++++ .../x/xproto/xproto-7.0.28-intel-2016a.eb | 23 ++++++++++++ .../x/xtrans/xtrans-1.3.5-intel-2016a.eb | 23 ++++++++++++ 10 files changed, 249 insertions(+) create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb new file mode 100644 index 0000000000..323816dd0b --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb new file mode 100644 index 0000000000..29d6a6987a --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb new file mode 100644 index 0000000000..abaa07d7cf --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '-Python-2.7.11'), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb new file mode 100644 index 0000000000..cca4ea1438 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016a.eb new file mode 100644 index 0000000000..afc1225690 --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb new file mode 100644 index 0000000000..0a842ce83c --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('xcb-proto', '1.11', '-Python-2.7.11'), + ('libpthread-stubs', '0.3'), +] +dependencies = [ + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..80c7b50387 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-proto' +version = '1.11' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.11' +versionsuffix = '-%s-%s' % (python, pyver) +builddependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[0:2]) + +sanity_check_paths = { + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb new file mode 100644 index 0000000000..dcc6160700 --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb new file mode 100644 index 0000000000..1d3df458a7 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb new file mode 100644 index 0000000000..217429b1ab --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 4810e815ae6b4bea733def7fae731886979003e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 14:47:40 +0100 Subject: [PATCH 0608/2133] fix double files entry --- easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb index 0f0fef97b7..ed6733fd17 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb @@ -15,8 +15,6 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', - 'Xtranssock.c', 'Xtransutil.c']], 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], 'dirs': [], -- GitLab From 6878b7887ac71609905c68debe4face53a5ed438 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 14:48:31 +0100 Subject: [PATCH 0609/2133] add patch for building multicool with intel/2015a --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- .../r/R/multicool-0.1-9_icpc-wd308.patch | 14 ++++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/multicool-0.1-9_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 0e86ace8cb..81ca43ddff 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -398,7 +398,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-9', ext_options), + ('multicool', '0.1-9', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), ('ks', '1.10.1', ext_options), ('logcondens', '2.1.4', ext_options), ('Iso', '0.0-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/multicool-0.1-9_icpc-wd308.patch b/easybuild/easyconfigs/r/R/multicool-0.1-9_icpc-wd308.patch new file mode 100644 index 0000000000..cb7beebcc6 --- /dev/null +++ b/easybuild/easyconfigs/r/R/multicool-0.1-9_icpc-wd308.patch @@ -0,0 +1,14 @@ +diff -ruN multicool.orig/MD5 multicool/MD5 +--- multicool.orig/MD5 2015-10-28 18:39:18.000000000 +0100 ++++ multicool/MD5 2016-02-23 14:09:09.547773000 +0100 +@@ -20,3 +20,4 @@ + b18b7e9e5912cf1014aa2c2fa8e86047 *src/compositions.cpp + 79239d0d8b59b7533a639d668c3a0857 *src/multicool.cpp + 62c660482671757c5490a422d955cbe1 *src/multinomial.h ++b1d3a4d02405fe08c7983c479bc27f13 *src/Makevars +diff -ruN multicool.orig/src/Makevars multicool/src/Makevars +--- multicool.orig/src/Makevars 1970-01-01 01:00:00.000000000 +0100 ++++ multicool/src/Makevars 2016-02-23 13:24:01.456230240 +0100 +@@ -0,0 +1,2 @@ ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From 752b19dbf1591386f9162513035d783916619b86 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 15:07:19 +0100 Subject: [PATCH 0610/2133] add comment in patch file --- easybuild/easyconfigs/r/R/multicool-0.1-9_icpc-wd308.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R/multicool-0.1-9_icpc-wd308.patch b/easybuild/easyconfigs/r/R/multicool-0.1-9_icpc-wd308.patch index cb7beebcc6..35704c2945 100644 --- a/easybuild/easyconfigs/r/R/multicool-0.1-9_icpc-wd308.patch +++ b/easybuild/easyconfigs/r/R/multicool-0.1-9_icpc-wd308.patch @@ -1,3 +1,5 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +author: Kenneth Hoste (HPC-UGent) diff -ruN multicool.orig/MD5 multicool/MD5 --- multicool.orig/MD5 2015-10-28 18:39:18.000000000 +0100 +++ multicool/MD5 2016-02-23 14:09:09.547773000 +0100 -- GitLab From 48c9941ab0e9a10a48691e432d81dc940cb1fa3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 15:16:02 +0100 Subject: [PATCH 0611/2133] Hercules foundation is now FWO --- setup.py | 2 +- test/__init__.py | 2 +- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/suite.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/setup.py b/setup.py index 73bcfd5c01..52810146f6 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), # the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), -# the Hercules foundation (http://www.herculesstichting.be/in_English) +# FWO (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # # http://github.com/hpcugent/easybuild diff --git a/test/__init__.py b/test/__init__.py index c4b9363e8a..2769d58e65 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -5,7 +5,7 @@ # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), # the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), -# the Hercules foundation (http://www.herculesstichting.be/in_English) +# FWO (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # # http://github.com/hpcugent/easybuild diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index e2e81c58df..5f0914847a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -5,7 +5,7 @@ # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), # the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), -# the Hercules foundation (http://www.herculesstichting.be/in_English) +# FWO (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # # http://github.com/hpcugent/easybuild diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 6afbd6ffb1..bfdd952cee 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -6,7 +6,7 @@ # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), # the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), -# the Hercules foundation (http://www.herculesstichting.be/in_English) +# FWO (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # # http://github.com/hpcugent/easybuild -- GitLab From ed3d5eedf7410555842e2c32df5dba82cfc2a058 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 15:25:05 +0100 Subject: [PATCH 0612/2133] fix remarks --- setup.py | 2 +- test/__init__.py | 2 +- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/suite.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/setup.py b/setup.py index 52810146f6..e1abe096bf 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), # the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), -# FWO (http://www.fwo.be/en) +# Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # # http://github.com/hpcugent/easybuild diff --git a/test/__init__.py b/test/__init__.py index 2769d58e65..856f7e4178 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -5,7 +5,7 @@ # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), # the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), -# FWO (http://www.fwo.be/en) +# Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # # http://github.com/hpcugent/easybuild diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5f0914847a..f3b329c872 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -5,7 +5,7 @@ # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), # the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), -# FWO (http://www.fwo.be/en) +# Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # # http://github.com/hpcugent/easybuild diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index bfdd952cee..79a1fb0d08 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -6,7 +6,7 @@ # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), # the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), -# FWO (http://www.fwo.be/en) +# Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # # http://github.com/hpcugent/easybuild -- GitLab From 9dfe8a7ff4e67d9f2707bbd8dd3a2e4d079a33ca Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 23 Feb 2016 16:06:10 +0100 Subject: [PATCH 0613/2133] added new libxml2 with proper configure options to use zlib provided by easybuild --- .../l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb new file mode 100644 index 0000000000..66513c188b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' -- GitLab From 007e97273afcad25295f6ab2989fb52cde171ef9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 18:05:38 +0200 Subject: [PATCH 0614/2133] add easyconfig ANSYS_CFD-17.0.eb --- .../easyconfigs/a/ANSYS_CFD/ANSYS_CFD-17.0.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-17.0.eb diff --git a/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-17.0.eb b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-17.0.eb new file mode 100644 index 0000000000..0217d1be22 --- /dev/null +++ b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-17.0.eb @@ -0,0 +1,15 @@ +easyblock = 'EB_FLUENT' + +name = 'ANSYS_CFD' +version = '17.0' + +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics' +description = """ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, + the impact of fluid flows on your product throughout design and manufacturing as well as during end use. + ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['FLUIDSTRUCTURES_%s_LINX64.tar' % ''.join(version.split('.'))] + +moduleclass = 'cae' -- GitLab From 1334f50e26a5190c56a8cb49feda8253e36d6cf4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 17:21:56 +0100 Subject: [PATCH 0615/2133] add HCsnip to Bioconductor bundles --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 5 +++++ .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 5 +++++ .../R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb | 4 ++++ 3 files changed, 14 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index b172ff0137..bcc39b48aa 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -133,6 +133,11 @@ exts_list = [ ('derfinder', '1.2.1', bioconductor_options), ('polyester', '1.4.0', bioconductor_options), ('Rsubread', '1.18.0', bioconductor_options), + ('pcaMethods', '1.58.0', bioconductor_options), + ('CGHbase', '1.28.0', bioconductor_options), + ('marray', '1.46.0', bioconductor_options), + ('sigaR', '1.12.0', bioconductor_options), + ('HCsnip', '1.8.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 8c43cb0960..180d089207 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -133,6 +133,11 @@ exts_list = [ ('derfinder', '1.2.1', bioconductor_options), ('polyester', '1.4.0', bioconductor_options), ('Rsubread', '1.18.0', bioconductor_options), + ('pcaMethods', '1.58.0', bioconductor_options), + ('CGHbase', '1.28.0', bioconductor_options), + ('marray', '1.46.0', bioconductor_options), + ('sigaR', '1.12.0', bioconductor_options), + ('HCsnip', '1.8.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb index 1a0beb9ba9..01e62a5a31 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb @@ -134,6 +134,10 @@ exts_list = [ ('polyester', '1.4.0', bioconductor_options), ('Rsubread', '1.18.0', bioconductor_options), ('pcaMethods', '1.58.0', bioconductor_options), + ('CGHbase', '1.28.0', bioconductor_options), + ('marray', '1.46.0', bioconductor_options), + ('sigaR', '1.12.0', bioconductor_options), + ('HCsnip', '1.8.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} -- GitLab From 97c56f72dec2eef45e1cd0379ee51a54b826830e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 17:26:59 +0100 Subject: [PATCH 0616/2133] fix order --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- .../R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index bcc39b48aa..9b319b7e55 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -134,8 +134,8 @@ exts_list = [ ('polyester', '1.4.0', bioconductor_options), ('Rsubread', '1.18.0', bioconductor_options), ('pcaMethods', '1.58.0', bioconductor_options), - ('CGHbase', '1.28.0', bioconductor_options), ('marray', '1.46.0', bioconductor_options), + ('CGHbase', '1.28.0', bioconductor_options), ('sigaR', '1.12.0', bioconductor_options), ('HCsnip', '1.8.0', bioconductor_options), ] diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 180d089207..e7aac6aac1 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -134,8 +134,8 @@ exts_list = [ ('polyester', '1.4.0', bioconductor_options), ('Rsubread', '1.18.0', bioconductor_options), ('pcaMethods', '1.58.0', bioconductor_options), - ('CGHbase', '1.28.0', bioconductor_options), ('marray', '1.46.0', bioconductor_options), + ('CGHbase', '1.28.0', bioconductor_options), ('sigaR', '1.12.0', bioconductor_options), ('HCsnip', '1.8.0', bioconductor_options), ] diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb index 01e62a5a31..e6d844c21e 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb @@ -134,8 +134,8 @@ exts_list = [ ('polyester', '1.4.0', bioconductor_options), ('Rsubread', '1.18.0', bioconductor_options), ('pcaMethods', '1.58.0', bioconductor_options), - ('CGHbase', '1.28.0', bioconductor_options), ('marray', '1.46.0', bioconductor_options), + ('CGHbase', '1.28.0', bioconductor_options), ('sigaR', '1.12.0', bioconductor_options), ('HCsnip', '1.8.0', bioconductor_options), ] -- GitLab From 03f1bcdd659c63cc48230b1fc4e6bbc37bbe637d Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 23 Feb 2016 17:51:03 +0100 Subject: [PATCH 0617/2133] removes craype and fftw from the toolchain --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb | 2 -- easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb | 2 -- easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb | 2 -- easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb | 2 -- easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb | 2 -- easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb | 2 -- 6 files changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb index c35ce0b32e..4fa134a241 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb @@ -11,10 +11,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-cray/5.2.40', EXTERNAL_MODULE), ('cce/8.3.12', EXTERNAL_MODULE), - ('craype/2.4.0', EXTERNAL_MODULE), ('cray-libsci/13.0.4', EXTERNAL_MODULE), ('cray-mpich/7.2.2', EXTERNAL_MODULE), - ('fftw/3.3.4.3', EXTERNAL_MODULE), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb index 3433ca305d..947665d0f0 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb @@ -11,10 +11,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-cray/5.2.82', EXTERNAL_MODULE), ('cce/8.4.1', EXTERNAL_MODULE), - ('craype/2.4.2', EXTERNAL_MODULE), ('cray-libsci/13.2.0', EXTERNAL_MODULE), ('cray-mpich/7.2.6', EXTERNAL_MODULE), - ('fftw/3.3.4.5', EXTERNAL_MODULE), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb index f804d0e859..4f31279f13 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb @@ -11,10 +11,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-gnu/5.2.40', EXTERNAL_MODULE), ('gcc/4.8.2', EXTERNAL_MODULE), - ('craype/2.4.0', EXTERNAL_MODULE), ('cray-libsci/13.0.4', EXTERNAL_MODULE), ('cray-mpich/7.2.2', EXTERNAL_MODULE), - ('fftw/3.3.4.3', EXTERNAL_MODULE), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb index 15eb5087e5..410ddc97f5 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb @@ -11,10 +11,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-gnu/5.2.82', EXTERNAL_MODULE), ('gcc/4.9.3', EXTERNAL_MODULE), - ('craype/2.4.2', EXTERNAL_MODULE), ('cray-libsci/13.2.0', EXTERNAL_MODULE), ('cray-mpich/7.2.6', EXTERNAL_MODULE), - ('fftw/3.3.4.5', EXTERNAL_MODULE), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb index 5ee5f118a3..0c39be9a84 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb @@ -11,10 +11,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-intel/5.2.82', EXTERNAL_MODULE), ('intel/15.0.1.133', EXTERNAL_MODULE), - ('craype/2.4.0', EXTERNAL_MODULE), ('cray-libsci/13.0.4', EXTERNAL_MODULE), ('cray-mpich/7.2.2', EXTERNAL_MODULE), - ('fftw/3.3.4.3', EXTERNAL_MODULE), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb index 7846b2d7c5..d021b8f24e 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb @@ -11,10 +11,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-intel/5.2.82', EXTERNAL_MODULE), ('intel/15.0.1.133', EXTERNAL_MODULE), - ('craype/2.4.2', EXTERNAL_MODULE), ('cray-libsci/13.2.0', EXTERNAL_MODULE), ('cray-mpich/7.2.6', EXTERNAL_MODULE), - ('fftw/3.3.4.5', EXTERNAL_MODULE), ] moduleclass = 'toolchain' -- GitLab From 009ca8514d0d7008cdd3bb986c2ec1eb9cf64095 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 18:23:18 +0100 Subject: [PATCH 0618/2133] add more extensions, use patch file when building multicool with intel toolchain --- easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb | 5 +++++ easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 5 +++++ easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb | 7 ++++++- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 5 +++++ 4 files changed, 21 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb index b1cc503084..de7294123d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb @@ -402,6 +402,11 @@ exts_list = [ ('ks', '1.10.1', ext_options), ('logcondens', '2.1.4', ext_options), ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-45', ext_options), + ('coin', '1.0-24', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.0.7', ext_options), + ('sm', '2.2-5.4', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 81ca43ddff..644dcc259b 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -402,6 +402,11 @@ exts_list = [ ('ks', '1.10.1', ext_options), ('logcondens', '2.1.4', ext_options), ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-45', ext_options), + ('coin', '1.0-24', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.0.7', ext_options), + ('sm', '2.2-5.4', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb index 0b60771f8e..36f8e25856 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb @@ -398,10 +398,15 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-9', ext_options), + ('multicool', '0.1-9', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), ('ks', '1.10.1', ext_options), ('logcondens', '2.1.4', ext_options), ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-45', ext_options), + ('coin', '1.0-24', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.0.7', ext_options), + ('sm', '2.2-5.4', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index ce43b870fa..aae3ac82f6 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -415,6 +415,11 @@ exts_list = [ ('ks', '1.10.1', ext_options), ('logcondens', '2.1.4', ext_options), ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-45', ext_options), + ('coin', '1.1-2', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.0.7', ext_options), + ('sm', '2.2-5.4', ext_options), ] moduleclass = 'lang' -- GitLab From 7ff6b215544bef956a196f30cc7bc67876ffb786 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 18:43:57 +0100 Subject: [PATCH 0619/2133] add --with-zlib configure argument in libxml easyconfigs --- .../l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb | 2 +- .../l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb | 2 +- .../l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb | 2 +- .../l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb | 2 +- .../l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb | 2 +- .../l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb | 2 +- .../l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb | 2 +- .../l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb | 2 +- .../l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb | 2 +- .../l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb | 2 +- .../l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb | 2 +- 46 files changed, 46 insertions(+), 46 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 5fdaa5d70c..e98bac6018 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb index 952422def7..4a4a4816ab 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb index 4a1316692f..e1868be130 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb @@ -13,7 +13,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb index f2fa0134cb..00021cddc9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb @@ -15,7 +15,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb index 33784ddde9..b82e8e6c93 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb index 3117fe0a65..91e1ffbc9c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb index cc27d1b86c..31e824b5ea 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb index 61308782ea..5a92ef8bcb 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb index fd29030590..98b15d6f97 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb index 81d93bf45c..3f185c7e6d 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb index 8a4a61220f..0567c075f0 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb index 0aa0c13986..ee43d716e2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb @@ -15,7 +15,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb index b1af1bc74e..06cdc26c76 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb index 1364db9fd8..3042a3cf37 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb index c35a6e9fc3..f0aa6dee9c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb index 60a6e14404..33b6562e0f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb index b388d01bd8..e44ddd0d64 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb index f80ae7c225..90b9bc8ea5 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb index 6bb7068cf9..487bf333ac 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb index 2382dbbd47..5448805458 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb index 72ae920157..b09000568f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb index 8a60398865..3e1cc77790 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb index a2720d5e9b..5da6298832 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb index 1c1b880f56..aa7e4b1f77 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb index 90f80b2804..e50f08d5e3 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb index 449f38ddfb..9d4e84392a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.6' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb index 118fae1f4c..0cdacffa3a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb index 615b01f264..ca67a911c1 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb index 222bbd19cd..c6335dd8b2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb index 7575c86f51..841eddc11e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb index 01f5647249..8d892b499f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb index 9bdf731db3..3c33fb41da 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb index 541ab91f1b..ae39cc8c24 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb index 8fd891d71a..ad02e51c2e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb index 9d5d34d98e..f232e382c0 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb index aa5618634d..22d8c149d6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb index fe435074c9..acdd85b6e6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb index 7f753229e0..22aefe7d0c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb index e102ff79f5..37724f23f1 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.10' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb index da831a62f3..307b1793d4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.9' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb index f49980dfe3..1a4f4c99c4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb index b18959ba97..b95f92dfd9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb @@ -17,7 +17,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb index 28c3bb06af..6cafc86e4f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.11' pythonshortver = '.'.join(pythonver.split('.')[:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb index 51c493e7e0..34777c9cc6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.10' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb index 61e0b9ca78..b28071061a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pythonver = '2.7.11' pythonshortver = '.'.join(pythonver.split('.')[:2]) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb index 41e4fc099e..41e2af0e98 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb @@ -14,7 +14,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[:2]) -- GitLab From 263c142e3957856e7b302834d5aa74a217b8893a Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 24 Feb 2016 05:29:55 +1030 Subject: [PATCH 0620/2133] triple-quote wrapping string --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 2679eeb7f4..1bf6254658 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -30,7 +30,7 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the - compiled jni C code." +modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the + compiled jni C code.""" moduleclass = 'bio' -- GitLab From 9813d105d5aa2726a0c4ef66f48d6b9495995ade Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 24 Feb 2016 05:30:30 +1030 Subject: [PATCH 0621/2133] triple-quote wrapping string --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index e9d0c0554f..d0f2ef813c 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -30,7 +30,7 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the - compiled jni C code." +modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the + compiled jni C code.""" moduleclass = 'bio' -- GitLab From 2c337996819704e08175c378fc033633ef940ead Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2016 21:11:05 +0100 Subject: [PATCH 0622/2133] add additional deps required for Bioconductor extensions --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 37f178514d..499d383ce4 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -348,6 +348,11 @@ exts_list = [ ('gdalUtils', '0.3.1', ext_options), ('pracma', '1.8.3', ext_options), ('bio3d', '2.2-2', ext_options), + ('penalized', '0.9-45', ext_options), + ('coin', '1.0-24', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.0.7', ext_options), + ('sm', '2.2-5.4', ext_options), ] moduleclass = 'lang' -- GitLab From 3f5d02ad4d2f1206346fca2a7a0ef370c26e5702 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 23 Feb 2016 21:36:38 +0100 Subject: [PATCH 0623/2133] ctffind-4.0.17-intel-2015a.eb --- .../c/ctffind/ctffind-4.0.17-intel-2015a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015a.eb new file mode 100644 index 0000000000..650aea81eb --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015a.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'ctffind' +version = '4.0.17' + +homepage = 'http://grigoriefflab.janelia.org/ctffind4' +description = """program for finding CTFs of electron micrographs""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('GSL', '1.16')] + +# when running ./configure in the root folder it fails. +# application doesn't provide a 'make install' +prebuildopts = 'mkdir build && cd build && ' +prebuildopts += ' ../configure --enable-static --disable-debug --enable-optimisations --enable-openmp FC=${FC} F77=${F77} && ' + +files_to_copy = [(['build/ctffind'], 'bin'), 'doc', 'scripts'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +modloadmsg = """Define OMP_NUM_THREADS or use the command line option --omp-num-threads=N when using this application""" + +moduleclass = 'bio' -- GitLab From 992f0591971ca3c922def68b7ab40e1556b40853 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 24 Feb 2016 14:13:55 +1300 Subject: [PATCH 0624/2133] New EasyConfig for non-Python version of libxml2 2.9.3 with the foss 2015a toolchain --- .../l/libxml2/libxml2-2.9.3-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb new file mode 100644 index 0000000000..7c1a817fb6 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [ + ('zlib', '1.2.8'), +] + +moduleclass = 'lib' -- GitLab From 3021683dd3556e76a3a06e229d4e338153d82764 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 24 Feb 2016 14:22:59 +1300 Subject: [PATCH 0625/2133] No longer require python bindings for libxml2 dependency --- easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb index fdbd875ff2..001e2879da 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('netCDF', '4.3.3.1'), ('HDF5', '1.8.16'), ('expat', '2.1.0'), - ('libxml2', '2.9.3', '-Python-2.7.11'), + ('libxml2', '2.9.3'), ('zlib', '1.2.8'), ] -- GitLab From 5b24009a577a16d5a09779397447cac1a3269c88 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 24 Feb 2016 07:17:15 +0000 Subject: [PATCH 0626/2133] Use Boost 1.60.0 without Python extra ver for BH --- easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb b/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb index 314d4d2d26..16cdd37dda 100644 --- a/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb +++ b/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb @@ -25,7 +25,7 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), - ('Boost', '1.58.0', '-Python-2.7.10'), + ('Boost', '1.60.0'), ] sanity_check_paths = { -- GitLab From 2d163f93442b9a6ba1a2199077229050ae80edff Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 24 Feb 2016 09:03:56 +0100 Subject: [PATCH 0627/2133] switch toolchain from intel-2015a to intel-2015b --- ...find-4.0.17-intel-2015a.eb => ctffind-4.0.17-intel-2015b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/ctffind/{ctffind-4.0.17-intel-2015a.eb => ctffind-4.0.17-intel-2015b.eb} (95%) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb similarity index 95% rename from easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015a.eb rename to easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb index 650aea81eb..c378da306a 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015a.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb @@ -11,7 +11,7 @@ version = '4.0.17' homepage = 'http://grigoriefflab.janelia.org/ctffind4' description = """program for finding CTFs of electron micrographs""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'openmp': True} source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] -- GitLab From 2a35ad1780dabe3004626493e8af25e727e92483 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 24 Feb 2016 09:05:36 +0100 Subject: [PATCH 0628/2133] {compiler}[intel-2016b] LLVM 3.7.1 (REVIEW) --- .../l/LLVM/LLVM-3.7.1-intel-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2016a.eb new file mode 100644 index 0000000000..2605ca36ca --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.7.1' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.4.3'), + ('Python', '2.7.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' -- GitLab From 1c022d289c4f01b916e7e531e83905d8ce590b7d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 24 Feb 2016 09:52:52 +0100 Subject: [PATCH 0629/2133] {system}[intel-2016b] eudev 3.1.5 (REVIEW) --- .../e/eudev/eudev-3.1.5-intel-2016a.eb | 33 +++++++++++++++++++ .../g/gperf/gperf-3.0.4-intel-2016a.eb | 22 +++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.1.5-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-intel-2016a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-intel-2016a.eb new file mode 100644 index 0000000000..8da9fd6afa --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.1.5' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-3.1.2_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016a.eb new file mode 100644 index 0000000000..5938576aa7 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 88d299aab7ad9f435840b3605e00feabfb219c5d Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 24 Feb 2016 10:12:22 +0100 Subject: [PATCH 0630/2133] Removed version from PrgEnv-*, as recommended by Cray (and in order to avoid the swap bugs) --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb | 3 ++- easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb | 3 ++- easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb | 3 ++- easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb | 3 ++- easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb | 3 ++- easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb | 3 ++- 6 files changed, 12 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb index 4fa134a241..c636f35399 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb @@ -9,7 +9,8 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('PrgEnv-cray/5.2.40', EXTERNAL_MODULE), + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-cray', EXTERNAL_MODULE), ('cce/8.3.12', EXTERNAL_MODULE), ('cray-libsci/13.0.4', EXTERNAL_MODULE), ('cray-mpich/7.2.2', EXTERNAL_MODULE), diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb index 947665d0f0..39476d8b11 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb @@ -9,7 +9,8 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('PrgEnv-cray/5.2.82', EXTERNAL_MODULE), + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-cray', EXTERNAL_MODULE), ('cce/8.4.1', EXTERNAL_MODULE), ('cray-libsci/13.2.0', EXTERNAL_MODULE), ('cray-mpich/7.2.6', EXTERNAL_MODULE), diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb index 4f31279f13..0612076d5a 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb @@ -9,7 +9,8 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('PrgEnv-gnu/5.2.40', EXTERNAL_MODULE), + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-gnu', EXTERNAL_MODULE), ('gcc/4.8.2', EXTERNAL_MODULE), ('cray-libsci/13.0.4', EXTERNAL_MODULE), ('cray-mpich/7.2.2', EXTERNAL_MODULE), diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb index 410ddc97f5..370978db76 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb @@ -9,7 +9,8 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('PrgEnv-gnu/5.2.82', EXTERNAL_MODULE), + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-gnu', EXTERNAL_MODULE), ('gcc/4.9.3', EXTERNAL_MODULE), ('cray-libsci/13.2.0', EXTERNAL_MODULE), ('cray-mpich/7.2.6', EXTERNAL_MODULE), diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb index 0c39be9a84..e5197716b4 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb @@ -9,7 +9,8 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('PrgEnv-intel/5.2.82', EXTERNAL_MODULE), + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-intel', EXTERNAL_MODULE), ('intel/15.0.1.133', EXTERNAL_MODULE), ('cray-libsci/13.0.4', EXTERNAL_MODULE), ('cray-mpich/7.2.2', EXTERNAL_MODULE), diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb index d021b8f24e..ead4db02ae 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb @@ -9,7 +9,8 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('PrgEnv-intel/5.2.82', EXTERNAL_MODULE), + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-intel', EXTERNAL_MODULE), ('intel/15.0.1.133', EXTERNAL_MODULE), ('cray-libsci/13.2.0', EXTERNAL_MODULE), ('cray-mpich/7.2.6', EXTERNAL_MODULE), -- GitLab From 986ed755dd319a212e3872e4b0998f2ebf6ae016 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 24 Feb 2016 13:46:34 +0100 Subject: [PATCH 0631/2133] fix pcre config options. Required for future R lang releases --- easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.37-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016a.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb index 4a9ef5925f..497a1cd036 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb @@ -13,6 +13,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb index 5916d698fc..a1e4190b59 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb @@ -13,6 +13,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb index e5f29eb85e..c2c366d78a 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb @@ -13,6 +13,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb index 871d373c07..97cfc3e3dd 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb @@ -13,6 +13,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb index 365ae1e42a..c8297a55fa 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb @@ -13,6 +13,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb index a4df16eaad..4db7f55f63 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb @@ -13,6 +13,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb index 7881c04da4..bb1b441bcd 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb @@ -13,6 +13,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb index f2529df084..968b4462f3 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb @@ -13,6 +13,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.37-foss-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.37-foss-2015a.eb index 58ef584548..2142c1c7b5 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.37-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.37-foss-2015a.eb @@ -13,6 +13,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb index 1218fbc5d1..7e31b8922b 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb @@ -13,6 +13,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015b.eb index ac1733e912..1be2911b8b 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015b.eb @@ -15,6 +15,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016a.eb index 61beae9c6a..12bd040e3c 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016a.eb @@ -15,6 +15,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-pic --disable-cpp --enable-utf8 --enable-unicode-properties" +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" moduleclass = 'devel' -- GitLab From a9eda46e61ffa115f7ff86d5fc1a2b0f20661c5d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 24 Feb 2016 14:19:58 +0100 Subject: [PATCH 0632/2133] {vis}[intel-2016b] libXext 1.3.3 (REVIEW) --- .../l/libXext/libXext-1.3.3-intel-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb new file mode 100644 index 0000000000..5ca8f8bd74 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 135f9f3580f2f147abfbec19015524e2957ae9f3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 24 Feb 2016 14:29:54 +0100 Subject: [PATCH 0633/2133] {vis}[intel-2016b] libXfixes 5.0.1 (REVIEW) --- .../fixesproto/fixesproto-5.0-intel-2016a.eb | 19 +++++++++++++++ .../libXfixes/libXfixes-5.0.1-intel-2016a.eb | 24 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb new file mode 100644 index 0000000000..33951308af --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb new file mode 100644 index 0000000000..3dd084da60 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 89f50747efa7402b7ab8083d77f81e835c8dd3ba Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 24 Feb 2016 14:44:16 +0100 Subject: [PATCH 0634/2133] {vis}[intel-2016b] libXdamage 1.1.4 (REVIEW) --- .../libXdamage-1.1.4-intel-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000..bc72561b6e --- /dev/null +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdamage' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Damage extension library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xdamage.h', 'lib/libXdamage.%s' % SHLIB_EXT, 'lib/libXdamage.a'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From d326521cc5f6abeeaee36467739e71614c9977f3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 24 Feb 2016 15:03:10 +0100 Subject: [PATCH 0635/2133] {vis}[intel-2016b] libXfont 1.5.1 (REVIEW) --- .../fontsproto-2.1.3-intel-2016a.eb | 20 ++++++++++++ .../l/libXfont/libXfont-1.5.1-intel-2016a.eb | 31 +++++++++++++++++++ .../libfontenc-1.1.3-intel-2016a.eb | 23 ++++++++++++++ .../xorg-macros-1.19.0-intel-2016a.eb | 22 +++++++++++++ 4 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb new file mode 100644 index 0000000000..5b1c1517ba --- /dev/null +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'fontsproto' +version = '2.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X11 font extension wire protocol" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a.eb new file mode 100644 index 0000000000..027bd58513 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', '2.6.2'), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb new file mode 100644 index 0000000000..458d0fa78b --- /dev/null +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfontenc' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/xlibs/' +description = """X11 font encoding library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/fonts/fontenc.h', 'lib/libfontenc.%s' % SHLIB_EXT, 'lib/libfontenc.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb new file mode 100644 index 0000000000..0697bb42ab --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From b7a106dd1c2fb81345546e08566979fbcfd9a9ff Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 24 Feb 2016 22:05:45 +0100 Subject: [PATCH 0636/2133] fixed wrong reference to prgenv-gnu --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb | 2 +- easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb | 2 +- easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb | 2 +- easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb index c636f35399..bf91772267 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb @@ -4,7 +4,7 @@ name = 'CrayCCE' version = '2015.06-XC' homepage = 'http://docs.cray.com/books/S-9407-1511' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).\n""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb index 39476d8b11..dbf091ccf3 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb @@ -4,7 +4,7 @@ name = 'CrayCCE' version = '2015.11-XC' homepage = 'http://docs.cray.com/books/S-9407-1511' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).\n""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb index e5197716b4..c80854490a 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb @@ -4,7 +4,7 @@ name = 'CrayIntel' version = '2015.06-XC' homepage = 'http://docs.cray.com/books/S-9407-1511' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: November 2015).\n""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb index ead4db02ae..cc105734db 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb @@ -4,7 +4,7 @@ name = 'CrayIntel' version = '2015.11-XC' homepage = 'http://docs.cray.com/books/S-9407-1511' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: November 2015).\n""" toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From 34f5c330aebf494428f2b9c8dfb9546af34852d9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 25 Feb 2016 06:41:57 +0000 Subject: [PATCH 0637/2133] Update fastqc dummy to 0.11.4 --- .../easyconfigs/f/fastqc/fastqc-0.11.4.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb new file mode 100644 index 0000000000..a4d75eb501 --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Java' + +name = 'fastqc' +version = '0.11.4' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] +sources = ['%(name)s_v%(version)s.zip'] + +dependencies = [('Java', '1.7.0_80')] + +postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' -- GitLab From 6b5d0f1a13edc489f1891040fcef60a7be877098 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 25 Feb 2016 07:50:03 +0100 Subject: [PATCH 0638/2133] added xproto as builddep for libxcb (needed by libXau) --- easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index 0a842ce83c..f95256fd36 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -14,6 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('xcb-proto', '1.11', '-Python-2.7.11'), + ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] dependencies = [ -- GitLab From 6666182f017dd3e4af2fe21f48e4bdc72088f063 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 25 Feb 2016 06:57:03 +0000 Subject: [PATCH 0639/2133] Update cutadapt to 1.9.1 for foss-2015b, update homepage/description and authors --- ...cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..89051e4847 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.9.1' + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads. """ + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt', 'lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From ea900fa9a9db4e81443148e70091e6d1bc29c412 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 25 Feb 2016 07:15:08 +0000 Subject: [PATCH 0640/2133] Port STAR 2.5.1b to foss-2015b --- .../s/STAR/STAR-2.5.1b-foss-2015b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb new file mode 100644 index 0000000000..8c14b0d9a6 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.5.1b' + +homepage = 'https://code.google.com/p/rna-star/' +description = """ STAR aligns RNA-seq reads to a reference genome using + uncompressed suffix arrays. """ + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] + +# a binary is provided with the source files. We delete it +prebuildopts = 'rm -fr bin/ && ' + +parallel = 1 + +files_to_copy = [(["source/STAR"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] + +sanity_check_paths = { + 'files': ["bin/STAR"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 46da2c8bba97084769a33fd6923df165f86bd8de Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 25 Feb 2016 07:29:55 +0000 Subject: [PATCH 0641/2133] Update picard to 2.1.0 including move to GitHub --- .../easyconfigs/p/picard/picard-2.1.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-2.1.0.eb diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0.eb new file mode 100644 index 0000000000..d68d511ad0 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0.eb @@ -0,0 +1,20 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + +name = 'picard' +version = '2.1.0' + +homepage = 'http://broadinstitute.github.io/picard/' +description = """ A set of command line tools (in Java) for manipulating + high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM + and VCF.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/broadinstitute/%(name)s/releases/download/%(version)s'] +sources = ['%(name)s-tools-%(version)s.zip'] + +dependencies = [('Java', '1.8.0_74')] + +moduleclass = 'bio' -- GitLab From 86c85bba0a716af4148bf1f2a945d7e3ea22f031 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 25 Feb 2016 09:56:09 +0100 Subject: [PATCH 0642/2133] {vis}[intel-2016b] Mesa-11.1.2 (WIP) --- .../l/libdrm/libdrm-2.4.67-intel-2016a.eb | 28 +++++++ .../l/libxml2/libxml2-2.9.3-intel-2016a.eb | 29 ++++++++ .../m/Mesa/Mesa-11.1.2-intel-2016a.eb | 74 +++++++++++++++++++ 3 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-intel-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-intel-2016a.eb new file mode 100644 index 0000000000..5a91110f77 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.67' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb new file mode 100644 index 0000000000..b762d96901 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb new file mode 100644 index 0000000000..c0e3c997a1 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -0,0 +1,74 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.1.2' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.67'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1'), + ('LLVM', '3.7.1'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" +configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' + +sanity_check_paths = { + 'files': ['lib/libGL.so', 'lib/libOSMesa.so', + 'lib/libGLESv1_CM.so', 'lib/libGLESv2.so', + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/wglext.h', 'include/GL/gl.h', + 'include/GL/glxext.h', 'include/GL/glx_mangle.h', + 'include/GLES/gl.h', 'include/GLES2/gl2.h', + 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' -- GitLab From 6c0fab2653861c660cede78a50dffa74c84aa6ff Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 25 Feb 2016 09:59:48 +0100 Subject: [PATCH 0643/2133] xorg-macros flrshed out --- .../xorg-macros-1.19.0-intel-2016a.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb deleted file mode 100644 index 0697bb42ab..0000000000 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xorg-macros' -version = '1.19.0' - -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' -description = """X.org macros utilities.""" -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! -sources = ['util-macros-%(version)s.tar.gz'] - -builddependencies = [('Autotools', '20150215')] - -preconfigopts = './autogen.sh && ' - -sanity_check_paths = { - 'files': ['share/pkgconfig/xorg-macros.pc'], - 'dirs': [], -} - -moduleclass = 'devel' -- GitLab From 03e33466685a1ccdbc19f79c0a8e209bda71b667 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 25 Feb 2016 10:01:34 +0100 Subject: [PATCH 0644/2133] {devel}[intel-2016b] xorg-mactos 1.19.0 (REVIEW) --- .../xorg-macros-1.19.0-intel-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb new file mode 100644 index 0000000000..0697bb42ab --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 2271ac6e1a3e0de4a61166fbe3332732fd6182c5 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 25 Feb 2016 10:42:30 +0100 Subject: [PATCH 0645/2133] added libXdmcp as dep for libxcb --- .../l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb | 25 +++++++++++++++++++ .../l/libxcb/libxcb-1.11.1-intel-2016a.eb | 1 + 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb new file mode 100644 index 0000000000..248b0fbfbc --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index f95256fd36..0a6fed4f0e 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -19,6 +19,7 @@ builddependencies = [ ] dependencies = [ ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), ] sanity_check_paths = { -- GitLab From 6f9e153c549f204d30d534593425b076eb44acc2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 25 Feb 2016 11:07:12 +0100 Subject: [PATCH 0646/2133] libXdmcp dep moved to libxcb/libX11 --- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 5ca8f8bd74..3e89327b58 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -19,7 +19,6 @@ builddependencies = [ dependencies = [ ('libX11', '1.6.3'), - ('libXdmcp', '1.1.2'), ] sanity_check_paths = { -- GitLab From 6d8707cc3a58a9174380ca0a92907269e16da346 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 25 Feb 2016 11:17:36 +0000 Subject: [PATCH 0647/2133] Use SHLIB_EXT for Python shared objects --- .../c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb | 2 +- .../c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb | 2 +- .../c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 2 +- .../c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb index 1d7c0f2ab8..141aedc7d3 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], + 'files': ['lib/python%s/site-packages/cutadapt/_align.%s' % (pyshortver, SHLIB_EXT)], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb index 259ebe78db..c50c4a1b5f 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt', 'lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], + 'files': ['bin/cutadapt', 'lib/python%s/site-packages/cutadapt/_align.%s' % (pyshortver, SHLIB_EXT)], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb index 880a7ad08e..8898d1ce85 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -29,7 +29,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt', 'lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], + 'files': ['bin/cutadapt', 'lib/python%s/site-packages/cutadapt/_align.%s' % (pyshortver, SHLIB_EXT)], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb index 89051e4847..6c74a88bb4 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb @@ -30,7 +30,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt', 'lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], + 'files': ['bin/cutadapt', 'lib/python%s/site-packages/cutadapt/_align.%s' % (pyshortver, SHLIB_EXT)], 'dirs': [], } -- GitLab From c98cc913e1018a12ac3b6ba5f01136dc266bc0c0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 25 Feb 2016 12:16:01 +0000 Subject: [PATCH 0648/2133] Port PLINK to foss-2015b --- .../p/PLINK/PLINK-1.07-foss-2015b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb new file mode 100644 index 0000000000..ec21e3a09b --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'PLINK' +version = '1.07' + +homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +description = """ PLINK is a free, open-source whole genome association analysis toolset, + designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for + steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). + Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, + annotation and storage of results. """ + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'openmp': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] + +dependencies = [('zlib', '1.2.8')] + +# plink makefile is a little bit tricky so we pass every options as arguments +# review plink original makefile for details +# if you want "new version check" change to WITH_WEBCHECK="1", but if your compute nodes +# have no internet access better leave it as is +buildopts = ' CXX_UNIX="$CXX $CXXFLAGS" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 ' +buildopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$BLAS_LAPACK_LIB_DIR/libmkl_lapack.a' + +files_to_copy = [ + (["plink", "gPLINK.jar"], 'bin'), + "test.map", + "test.ped", + "COPYING.txt", + "README.txt", +] + +sanity_check_paths = { + 'files': ["bin/plink", "bin/gPLINK.jar", "test.map", "test.ped", "COPYING.txt", "README.txt"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 2b0f12104a46fe2ba2a90cc601dd88e3b1b0c7b8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 25 Feb 2016 14:21:31 +0000 Subject: [PATCH 0649/2133] GROMACS 5.1.2 for foss 2015b --- .../GROMACS-5.1.2-foss-2015b-hybrid.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb new file mode 100644 index 0000000000..8744e777c7 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +# +# Version 5.1.2 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.2' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.60.0')] + +moduleclass = 'bio' -- GitLab From 2377dc54b8e60769418bdf65bd831f68bbd99765 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Fri, 26 Feb 2016 16:46:13 +1030 Subject: [PATCH 0650/2133] move sources and source_urls line above toolchain line --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 6 +++--- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 2679eeb7f4..a0696f7e27 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -6,6 +6,9 @@ version = '35.82' homepage = 'https://sourceforge.net/projects/bbmap/' description = """BBMap short read aligner, and other bioinformatic tools.""" +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz' ] + toolchain = {'name': 'foss', 'version': '2015b'} java = 'Java' @@ -13,9 +16,6 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver, '', True)] -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] - prebuildopts = 'cd jni && ' suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index e9d0c0554f..a8764758d2 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -6,6 +6,9 @@ version = '35.82' homepage = 'https://sourceforge.net/projects/bbmap/' description = """BBMap short read aligner, and other bioinformatic tools.""" +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz' ] + toolchain = {'name': 'foss', 'version': '2015b'} java = 'Java' @@ -13,9 +16,6 @@ javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver, '', True)] -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] - prebuildopts = 'cd jni && ' suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] -- GitLab From a3f61ea62aed39594de22d5f876ccf718a365e9a Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Fri, 26 Feb 2016 17:21:36 +1030 Subject: [PATCH 0651/2133] Added patch to modify shebang lines of supplied scripts --- .../n/NextClip/NextClip-1.3.1-foss-2015b.eb | 2 + .../n/NextClip/NextClip_scripts_shebang.patch | 60 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch diff --git a/easybuild/easyconfigs/n/NextClip/NextClip-1.3.1-foss-2015b.eb b/easybuild/easyconfigs/n/NextClip/NextClip-1.3.1-foss-2015b.eb index b4ac0527df..3b2f0c8e13 100644 --- a/easybuild/easyconfigs/n/NextClip/NextClip-1.3.1-foss-2015b.eb +++ b/easybuild/easyconfigs/n/NextClip/NextClip-1.3.1-foss-2015b.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2015b'} source_urls = ['https://github.com/richardmleggett/nextclip/archive'] sources = ['NextClip_v%(version)s.tar.gz'] +patches = ['NextClip_scripts_shebang.patch'] + files_to_copy = ['bin', 'examples', 'scripts', 'nextclipmanual.pdf'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch b/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch new file mode 100644 index 0000000000..4e078bad33 --- /dev/null +++ b/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch @@ -0,0 +1,60 @@ +diff --git a/scripts/index_bwa.sh b/scripts/index_bwa.sh +index 2862e42..472d7f1 100755 +--- a/scripts/index_bwa.sh ++++ b/scripts/index_bwa.sh +@@ -1,4 +1,4 @@ +-#!/bin/bash ++#!/usr/bin/env bash + + source bwa-0.6.1 + +diff --git a/scripts/nextclip_index_reference.pl b/scripts/nextclip_index_reference.pl +index 03810b3..b7f7649 100755 +--- a/scripts/nextclip_index_reference.pl ++++ b/scripts/nextclip_index_reference.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + + # Script: nextclip_index_reference.pl + # Purpose: Produce simple index file of a reference +diff --git a/scripts/nextclip_lmp_analysis.pl b/scripts/nextclip_lmp_analysis.pl +index 8af0b21..39b0f20 100755 +--- a/scripts/nextclip_lmp_analysis.pl ++++ b/scripts/nextclip_lmp_analysis.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + + # Script: nextclip_lmp_analysis.pl + # Purpose: NextClip Long Mate Pair analysis pipeline +diff --git a/scripts/nextclip_make_report.pl b/scripts/nextclip_make_report.pl +index ed05261..1c80fba 100755 +--- a/scripts/nextclip_make_report.pl ++++ b/scripts/nextclip_make_report.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + + # Script: nextclip_make_report.pl + # Purpose: Produce PDF report of NextClip analysis +diff --git a/scripts/nextclip_plot_graphs.sh b/scripts/nextclip_plot_graphs.sh +index f6a3a2b..d4b809e 100755 +--- a/scripts/nextclip_plot_graphs.sh ++++ b/scripts/nextclip_plot_graphs.sh +@@ -1,4 +1,4 @@ +-#!/bin/bash ++#!/usr/bin/env bash + + # Script: nextclip_plot_graphs.sh + # Purpose: Plot insert length and read length graphs for NextClip +diff --git a/scripts/nextclip_sam_parse.pl b/scripts/nextclip_sam_parse.pl +index cc04193..692326a 100755 +--- a/scripts/nextclip_sam_parse.pl ++++ b/scripts/nextclip_sam_parse.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + + # Script: nextclip_sam_parse.pl + # Purpose: Parse SAM files for NextClip -- GitLab From d10e09de068ed2cfa0e70e8fe7d6e17901803ed3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Feb 2016 09:45:59 +0100 Subject: [PATCH 0652/2133] fix remarks by @ladc --- .../easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb | 2 ++ .../l/libjpeg-turbo/libjpeg-turbo-1.4.2-goolf-1.4.10.eb | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb index 13281d87fa..bea932c18d 100644 --- a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.7-goolf-1.4.10.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] sources = ['lcms2-%(version)s.tar.gz'] +dependencies = [('libjpeg-turbo', '1.4.2')] + sanity_check_paths = { 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-goolf-1.4.10.eb index 548eb81065..c9cc4d2e6f 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-goolf-1.4.10.eb @@ -23,8 +23,8 @@ runtest = "test" sanity_check_paths = { 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', - 'lib/libjpeg.a', 'libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], - 'dirs': ['include', 'man', 'share'], + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share/man'], } moduleclass = 'lib' -- GitLab From f1b8cfbe20d85d6b6286bc08e9b111b30acaa517 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Feb 2016 09:57:28 +0100 Subject: [PATCH 0653/2133] add configopts related to dependencies to ImageMagick easyconfig --- .../i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb index adc09ca30a..160c3c8697 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb @@ -25,6 +25,8 @@ dependencies = [ ('pkg-config', '0.27.1'), ] +configopts = "--with-gslib --with-x" + sanity_check_paths = { 'files': [], 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], -- GitLab From ca253943c24e7b1d039257ae86dac74b9f4b594c Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 26 Feb 2016 10:09:16 +0100 Subject: [PATCH 0654/2133] style fix. builddeps after deps --- .../i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb index e9fe2f9009..8b641aebb3 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.3-3-goolf-1.4.10.eb @@ -11,10 +11,6 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] -builddependencies = [ - ('pkg-config', '0.27.1'), -] - dependencies = [ ('bzip2', '1.0.6'), ('freetype', '2.5.0.1'), @@ -28,6 +24,10 @@ dependencies = [ ('LittleCMS', '2.7'), ] +builddependencies = [ + ('pkg-config', '0.27.1'), +] + configopts = "--with-gslib --with-x" sanity_check_paths = { -- GitLab From a8bfd828e19fecac84950b22b97cb7f8c803490a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Feb 2016 13:58:13 +0200 Subject: [PATCH 0655/2133] add easyconfig MLC-3.0.eb --- easybuild/easyconfigs/m/MLC/MLC-3.0.eb | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/MLC/MLC-3.0.eb diff --git a/easybuild/easyconfigs/m/MLC/MLC-3.0.eb b/easybuild/easyconfigs/m/MLC/MLC-3.0.eb new file mode 100644 index 0000000000..6f9d7320ea --- /dev/null +++ b/easybuild/easyconfigs/m/MLC/MLC-3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'Tarball' + +name = 'MLC' +version = '3.0' + +homepage = 'https://software.intel.com/en-us/articles/intelr-memory-latency-checker' +description = """Intel Memory Latency Checker (Intel MLC) is a tool used to measure memory latencies and b/w, + and how they change with increasing load on the system.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download requires agreeing to license +# https://software.intel.com/en-us/articles/intelr-memory-latency-checker#download +sources = ['mlcv3.0.tgz'] + +sanity_check_paths = { + 'files': ['Linux/mlc', 'Linux/mlc_avx512', 'mlc_license.txt', 'readme.pdf'], + 'dirs': [], +} + +modextrapaths = {'PATH': 'Linux'} + +moduleclass = 'tools' -- GitLab From 8c0dab16657a63779f5f1ab23d30528a131fe803 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 26 Feb 2016 13:37:19 +0100 Subject: [PATCH 0656/2133] Python added as dep instead of builddep for xcb-proto --- .../x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb index 80c7b50387..ab4aaa83ac 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.11' versionsuffix = '-%s-%s' % (python, pyver) -builddependencies = [(python, pyver)] +dependencies = [(python, pyver)] pyshortver = '.'.join(pyver.split('.')[0:2]) -- GitLab From 37064bb76ce2e9c22f0ee04b5d5c570e7efed68c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Feb 2016 15:21:28 +0100 Subject: [PATCH 0657/2133] add metagenomeSeq in Bioconductor bundle --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 1 + .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + .../R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 9b319b7e55..1fcada1694 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -138,6 +138,7 @@ exts_list = [ ('CGHbase', '1.28.0', bioconductor_options), ('sigaR', '1.12.0', bioconductor_options), ('HCsnip', '1.8.0', bioconductor_options), + ('metagenomeSeq', '1.10.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index e7aac6aac1..21cd4399f4 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -138,6 +138,7 @@ exts_list = [ ('CGHbase', '1.28.0', bioconductor_options), ('sigaR', '1.12.0', bioconductor_options), ('HCsnip', '1.8.0', bioconductor_options), + ('metagenomeSeq', '1.10.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb index e6d844c21e..c3940a9034 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015b-R-3.2.1.eb @@ -138,6 +138,7 @@ exts_list = [ ('CGHbase', '1.28.0', bioconductor_options), ('sigaR', '1.12.0', bioconductor_options), ('HCsnip', '1.8.0', bioconductor_options), + ('metagenomeSeq', '1.10.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} -- GitLab From b31fab3acd0c8a686836236940bdf97239e5fede Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 26 Feb 2016 15:32:15 +0100 Subject: [PATCH 0658/2133] add xcb-proto with system python dep (toolchainless) --- .../l/libxcb/libxcb-1.11.1-intel-2016a.eb | 2 ++ .../easyconfigs/x/xcb-proto/xcb-proto-1.11.eb | 24 +++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index 0a6fed4f0e..faa9778d64 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -14,6 +14,8 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('xcb-proto', '1.11', '-Python-2.7.11'), + # Alternatively, you can use xcb-proto using system Python: + #('xcb-proto', 1.11', '', ('dummy', 'dummy')) ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb new file mode 100644 index 0000000000..27a89ed005 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-proto' +version = '1.11' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +sanity_check_paths = { + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} + +moduleclass = 'devel' -- GitLab From d24df53180230f32708ac4364cedcf6d63710433 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 26 Feb 2016 15:37:36 +0100 Subject: [PATCH 0659/2133] use of 'pyver' template --- .../xcb-proto-1.11-intel-2016a-Python-2.7.11.eb | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb index ab4aaa83ac..97ddefed62 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb @@ -12,16 +12,12 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] -python = 'Python' -pyver = '2.7.11' -versionsuffix = '-%s-%s' % (python, pyver) -dependencies = [(python, pyver)] - -pyshortver = '.'.join(pyver.split('.')[0:2]) +versionsuffix = '-Python-%(pyver)s' +dependencies = [('Python', '2.7.11')] sanity_check_paths = { 'files': ['lib/pkgconfig/xcb-proto.pc'], - 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] + 'dirs': ['lib/python%(pyshortver)s/site-packages/xcbgen' % pyshortver] } moduleclass = 'devel' -- GitLab From 28295bfcdf710044b12df5ce0b42839aaf3c0e51 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Sat, 27 Feb 2016 07:32:32 +1030 Subject: [PATCH 0660/2133] Cleaned up patch file. 1) Added comment and author. 2) Strip superfluous `-w` from perl shebang line. - the scripts already use the `use warnings;` pragma. --- .../n/NextClip/NextClip_scripts_shebang.patch | 23 ++++++------------- 1 file changed, 7 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch b/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch index 4e078bad33..35d7d7811b 100644 --- a/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch +++ b/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch @@ -1,5 +1,6 @@ -diff --git a/scripts/index_bwa.sh b/scripts/index_bwa.sh -index 2862e42..472d7f1 100755 +Fix hardcoding of /usr/bin/perl, use perl available through $PATH +Fix hardcoding of /bin/bash, use bash available through $PATH +author: Nathan S. Watson-Haigh (ACPFG) --- a/scripts/index_bwa.sh +++ b/scripts/index_bwa.sh @@ -1,4 +1,4 @@ @@ -8,38 +9,30 @@ index 2862e42..472d7f1 100755 source bwa-0.6.1 -diff --git a/scripts/nextclip_index_reference.pl b/scripts/nextclip_index_reference.pl -index 03810b3..b7f7649 100755 --- a/scripts/nextclip_index_reference.pl +++ b/scripts/nextclip_index_reference.pl @@ -1,4 +1,4 @@ -#!/usr/bin/perl -w -+#!/usr/bin/env perl -w ++#!/usr/bin/env perl # Script: nextclip_index_reference.pl # Purpose: Produce simple index file of a reference -diff --git a/scripts/nextclip_lmp_analysis.pl b/scripts/nextclip_lmp_analysis.pl -index 8af0b21..39b0f20 100755 --- a/scripts/nextclip_lmp_analysis.pl +++ b/scripts/nextclip_lmp_analysis.pl @@ -1,4 +1,4 @@ -#!/usr/bin/perl -w -+#!/usr/bin/env perl -w ++#!/usr/bin/env perl # Script: nextclip_lmp_analysis.pl # Purpose: NextClip Long Mate Pair analysis pipeline -diff --git a/scripts/nextclip_make_report.pl b/scripts/nextclip_make_report.pl -index ed05261..1c80fba 100755 --- a/scripts/nextclip_make_report.pl +++ b/scripts/nextclip_make_report.pl @@ -1,4 +1,4 @@ -#!/usr/bin/perl -w -+#!/usr/bin/env perl -w ++#!/usr/bin/env perl # Script: nextclip_make_report.pl # Purpose: Produce PDF report of NextClip analysis -diff --git a/scripts/nextclip_plot_graphs.sh b/scripts/nextclip_plot_graphs.sh -index f6a3a2b..d4b809e 100755 --- a/scripts/nextclip_plot_graphs.sh +++ b/scripts/nextclip_plot_graphs.sh @@ -1,4 +1,4 @@ @@ -48,13 +41,11 @@ index f6a3a2b..d4b809e 100755 # Script: nextclip_plot_graphs.sh # Purpose: Plot insert length and read length graphs for NextClip -diff --git a/scripts/nextclip_sam_parse.pl b/scripts/nextclip_sam_parse.pl -index cc04193..692326a 100755 --- a/scripts/nextclip_sam_parse.pl +++ b/scripts/nextclip_sam_parse.pl @@ -1,4 +1,4 @@ -#!/usr/bin/perl -w -+#!/usr/bin/env perl -w ++#!/usr/bin/env perl # Script: nextclip_sam_parse.pl # Purpose: Parse SAM files for NextClip -- GitLab From 1c72713e304c89211af163e7b5198c679f7efd12 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Sat, 27 Feb 2016 00:02:38 +0100 Subject: [PATCH 0661/2133] syntax corrected --- .../x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb index 97ddefed62..67fb1d84ea 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb @@ -17,7 +17,7 @@ dependencies = [('Python', '2.7.11')] sanity_check_paths = { 'files': ['lib/pkgconfig/xcb-proto.pc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/xcbgen' % pyshortver] + 'dirs': ['lib/python%(pyshortver)s/site-packages/xcbgen'] } moduleclass = 'devel' -- GitLab From c20c697fea73326d6717032c50feb178c94eb0ee Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 26 Feb 2016 23:31:01 +0000 Subject: [PATCH 0662/2133] Update GROMACS to 5.1.2 for foss 2015b --- .../easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb index 8744e777c7..db2a991381 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb @@ -30,7 +30,7 @@ source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('CMake', '3.2.2'), + ('CMake', '3.4.1'), ('libxml2', '2.9.2') ] -- GitLab From efbe383c0a9c022f859c2f59f6be6d4199aa199d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 27 Feb 2016 08:32:37 +0000 Subject: [PATCH 0663/2133] Add fixes for building with modern GCC --- .../p/PLINK/PLINK-1.07-foss-2015b.eb | 4 +- .../p/PLINK/PLINK-1.07_redeclaration.patch | 68 +++++++++++++++++++ 2 files changed, 71 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.07_redeclaration.patch diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb index ec21e3a09b..8218ead1ea 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb @@ -24,6 +24,8 @@ toolchainopts = {'openmp': True} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] +patches = ['PLINK-1.07_redeclaration.patch'] + dependencies = [('zlib', '1.2.8')] # plink makefile is a little bit tricky so we pass every options as arguments @@ -31,7 +33,7 @@ dependencies = [('zlib', '1.2.8')] # if you want "new version check" change to WITH_WEBCHECK="1", but if your compute nodes # have no internet access better leave it as is buildopts = ' CXX_UNIX="$CXX $CXXFLAGS" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 ' -buildopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$BLAS_LAPACK_LIB_DIR/libmkl_lapack.a' +buildopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$EBROOTOPENBLAS/lib/libopenblas.so' files_to_copy = [ (["plink", "gPLINK.jar"], 'bin'), diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07_redeclaration.patch b/easybuild/easyconfigs/p/PLINK/PLINK-1.07_redeclaration.patch new file mode 100644 index 0000000000..20e3f284a8 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07_redeclaration.patch @@ -0,0 +1,68 @@ +diff --git a/sets.cpp b/sets.cpp +index 3a8f92f..adef60f 100644 +--- a/sets.cpp ++++ b/sets.cpp +@@ -768,11 +768,11 @@ vector_t Set::profileTestScore() + ////////////////////////////////////////////// + // Reset original missing status + +- vector::iterator i = PP->sample.begin(); +- while ( i != PP->sample.end() ) ++ vector::iterator i_iter = PP->sample.begin(); ++ while ( i_iter != PP->sample.end() ) + { +- (*i)->missing = (*i)->flag; +- ++i; ++ (*i_iter)->missing = (*i_iter)->flag; ++ ++i_iter; + } + + //////////////////////////////////////////////// +diff --git a/elf.cpp b/elf.cpp +index ec2ed3d..49bda44 100644 +--- a/elf.cpp ++++ b/elf.cpp +@@ -1175,10 +1175,10 @@ void Plink::elfBaseline() + << setw(8) << gcnt << " " + << setw(8) << (double)cnt / (double)gcnt << "\n"; + +- map::iterator i = chr_cnt.begin(); +- while ( i != chr_cnt.end() ) ++ map::iterator i_iter = chr_cnt.begin(); ++ while ( i_iter != chr_cnt.end() ) + { +- int c = i->first; ++ int c = i_iter->first; + int x = chr_cnt.find( c )->second; + int y = chr_gcnt.find( c )->second; + +@@ -1189,7 +1189,7 @@ void Plink::elfBaseline() + << setw(8) << y << " " + << setw(8) << (double)x / (double)y << "\n"; + +- ++i; ++ ++i_iter; + } + + } +diff --git a/idhelp.cpp b/idhelp.cpp +index a9244fa..8353c9e 100644 +--- a/idhelp.cpp ++++ b/idhelp.cpp +@@ -772,12 +772,12 @@ void IDHelper::idHelp() + for (int j = 0 ; j < jointField.size(); j++ ) + { + set & jf = jointField[j]; +- set::iterator j = jf.begin(); ++ set::iterator j_iter = jf.begin(); + PP->printLOG(" { "); +- while ( j != jf.end() ) ++ while ( j_iter != jf.end() ) + { +- PP->printLOG( (*j)->name + " " ); +- ++j; ++ PP->printLOG( (*j_iter)->name + " " ); ++ ++j_iter; + } + PP->printLOG(" }"); + } -- GitLab From 36ed24d791b618dc064b589abc3f5829f3373e8a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 27 Feb 2016 08:58:37 +0000 Subject: [PATCH 0664/2133] Update BWA to 0.7.13, including move to GitHub --- .../b/BWA/BWA-0.7.13-foss-2015b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb new file mode 100644 index 0000000000..2d42585347 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.13 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'BWA' +version = '0.7.13' + +homepage = 'https://github.com/lh3/bwa' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +#Sanity check included in custom easyblock + +moduleclass = 'bio' -- GitLab From 2537e3c0735b05034ae291b72fc65aa946e0960e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 27 Feb 2016 09:08:57 +0000 Subject: [PATCH 0665/2133] Update Bowtie2 to 2.2.7 --- .../b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb new file mode 100644 index 0000000000..2b67034216 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman >adam.huffman@crick.ac.uk> +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.7' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' -- GitLab From 9938fc7b765ad8f868236c6a5d0be506158f59ea Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 27 Feb 2016 09:10:41 +0000 Subject: [PATCH 0666/2133] Fix typo --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb index 2b67034216..f74362241f 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb @@ -4,7 +4,7 @@ # Biozentrum - University of Basel # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -# Modified by: Adam Huffman >adam.huffman@crick.ac.uk> +# Modified by: Adam Huffman # The Francis Crick Institute easyblock = 'MakeCp' -- GitLab From a17dc36d1ae356e5982d0beacbd21b68222670d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2016 10:30:57 +0100 Subject: [PATCH 0667/2133] fix FFTW lib/include path in configopts for GROMACS w/ CrayGNU --- .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb index 94600c2c59..7d022ac778 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb @@ -31,8 +31,8 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW} && " -preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/../include && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " dependencies = [ ('fftw/3.3.4.5', EXTERNAL_MODULE), -- GitLab From e1f2153568e1e11ac44c07ebcbb0ddda5f34ea89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2016 10:31:23 +0100 Subject: [PATCH 0668/2133] fix FFTW lib/include path in configopts for GROMACS w/ CrayGNU --- .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb index 8fe8110183..eb693a5ca3 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb @@ -31,8 +31,8 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW} && " -preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/../include && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/include && " dependencies = [ ('fftw/3.3.4.3', EXTERNAL_MODULE), -- GitLab From 9922ff5412d8eaa7cb477e2fb31de862bb9988a1 Mon Sep 17 00:00:00 2001 From: perettig Date: Sat, 27 Feb 2016 12:04:23 +0100 Subject: [PATCH 0669/2133] deleted deprecated .eb versions 5.x --- .../b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb | 22 ---- .../b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb | 22 ---- .../b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb | 22 ---- .../b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb | 15 --- .../b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb | 15 --- .../b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb | 15 --- .../c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb | 23 ---- .../c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb | 23 ---- .../c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb | 23 ---- .../c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb | 38 ------ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb | 38 ------ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb | 38 ------ .../easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 16 --- .../easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 16 --- 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a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.0.2' - -homepage = 'http://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [('M4', '1.4.17')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb deleted file mode 100644 index 79f11b47fe..0000000000 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.0.2' - -homepage = 'http://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [('M4', '1.4.17')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb deleted file mode 100644 index 67832ccafa..0000000000 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.0.2' - -homepage = 'http://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [('M4', '1.4.17')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb deleted file mode 100644 index a04591dede..0000000000 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,15 +0,0 @@ -name = 'bzip2' -version = '1.0.6' - -homepage = 'http://www.bzip.org/' -description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically - compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical - compressors), whilst being around twice as fast at compression and six times faster at decompression.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.bzip.org/%(version)s'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb deleted file mode 100644 index 3f96190606..0000000000 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,15 +0,0 @@ -name = 'bzip2' -version = '1.0.6' - -homepage = 'http://www.bzip.org/' -description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically - compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical - compressors), whilst being around twice as fast at compression and six times faster at decompression.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.bzip.org/%(version)s'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb deleted file mode 100644 index 58489cb68f..0000000000 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,15 +0,0 @@ -name = 'bzip2' -version = '1.0.6' - -homepage = 'http://www.bzip.org/' -description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically - compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical - compressors), whilst being around twice as fast at compression and six times faster at decompression.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.bzip.org/%(version)s'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb deleted file mode 100644 index 68df962efa..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.2.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'dynamic': True} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb deleted file mode 100644 index 75190be28b..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.2.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'dynamic': True} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb deleted file mode 100644 index 275dc8cada..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.2.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'dynamic': True} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb deleted file mode 100644 index e1f9bdb729..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'CP2K' -version = '2.6.0' - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.1'), -] - -builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test reports failures -ignore_regtest_fails = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb deleted file mode 100644 index 43baa97a11..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'CP2K' -version = '2.6.0' - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.1'), -] - -builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test reports failures -ignore_regtest_fails = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb deleted file mode 100644 index eea0ba5f73..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'CP2K' -version = '2.6.0' - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.1'), -] - -builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test reports failures -ignore_regtest_fails = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb deleted file mode 100644 index 766d96d756..0000000000 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb +++ /dev/null @@ -1,16 +0,0 @@ -easyblock = 'Toolchain' - -name = 'CrayCCE' -version = '5.1.29' - -homepage = '(none)' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -dependencies = [ - ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci - ('fftw/3.3.4.0', EXTERNAL_MODULE), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb deleted file mode 100644 index 7a2e621e24..0000000000 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb +++ /dev/null @@ -1,16 +0,0 @@ -easyblock = 'Toolchain' - -name = 'CrayCCE' -version = '5.2.25' - -homepage = '(none)' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -dependencies = [ - ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci - ('fftw/3.3.4.2', EXTERNAL_MODULE), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb deleted file mode 100644 index b31f4b3a23..0000000000 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb +++ /dev/null @@ -1,16 +0,0 @@ -easyblock = 'Toolchain' - -name = 'CrayCCE' -version = '5.2.40' - -homepage = '(none)' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -dependencies = [ - ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci - ('fftw/3.3.4.2', EXTERNAL_MODULE), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb deleted file mode 100644 index b3e7499933..0000000000 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ /dev/null @@ -1,16 +0,0 @@ -easyblock = 'Toolchain' - -name = 'CrayGNU' -version = '5.1.29' - -homepage = '(none)' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -dependencies = [ - ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci - ('fftw/3.3.4.0', EXTERNAL_MODULE), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb deleted file mode 100644 index 4015746894..0000000000 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ /dev/null @@ -1,16 +0,0 @@ -easyblock = 'Toolchain' - -name = 'CrayGNU' -version = '5.2.25' - -homepage = '(none)' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -dependencies = [ - ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci - ('fftw/3.3.4.2', EXTERNAL_MODULE), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb deleted file mode 100644 index dbbbbbd303..0000000000 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb +++ /dev/null @@ -1,16 +0,0 @@ -easyblock = 'Toolchain' - -name = 'CrayGNU' -version = '5.2.40' - -homepage = '(none)' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -dependencies = [ - ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci - ('fftw/3.3.4.2', EXTERNAL_MODULE), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb deleted file mode 100644 index 7c17b80f7e..0000000000 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb +++ /dev/null @@ -1,16 +0,0 @@ -easyblock = 'Toolchain' - -name = 'CrayIntel' -version = '5.1.29' - -homepage = '(none)' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -dependencies = [ - ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci - ('fftw/3.3.4.0', EXTERNAL_MODULE), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb deleted file mode 100644 index edaac85f54..0000000000 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb +++ /dev/null @@ -1,16 +0,0 @@ -easyblock = 'Toolchain' - -name = 'CrayIntel' -version = '5.2.25' - -homepage = '(none)' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -dependencies = [ - ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci - ('fftw/3.3.4.2', EXTERNAL_MODULE), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb deleted file mode 100644 index 5937accfe4..0000000000 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb +++ /dev/null @@ -1,16 +0,0 @@ -easyblock = 'Toolchain' - -name = 'CrayIntel' -version = '5.2.40' - -homepage = '(none)' -description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -dependencies = [ - ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci - ('fftw/3.3.4.2', EXTERNAL_MODULE), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb deleted file mode 100644 index a6d2ced89c..0000000000 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,14 +0,0 @@ -name = 'flex' -version = '2.5.39' - -homepage = 'http://flex.sourceforge.net/' -description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb deleted file mode 100644 index e9455b96ac..0000000000 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,14 +0,0 @@ -name = 'flex' -version = '2.5.39' - -homepage = 'http://flex.sourceforge.net/' -description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb deleted file mode 100644 index 470ec059e0..0000000000 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,14 +0,0 @@ -name = 'flex' -version = '2.5.39' - -homepage = 'http://flex.sourceforge.net/' -description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb deleted file mode 100644 index 1aa3886405..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.7' -versionsuffix = '-mpi' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'usempi': True} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -builddependencies = [('CMake', '3.2.2')] - -runtest = False - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb deleted file mode 100644 index 4a945e2af8..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.7' -versionsuffix = '-mpi' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'usempi': True} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -builddependencies = [('CMake', '3.2.2')] - -runtest = False - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb deleted file mode 100644 index 239ea564c8..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.7' -versionsuffix = '-mpi' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'usempi': True} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -builddependencies = [('CMake', '3.2.2')] - -runtest = False - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb deleted file mode 100644 index a7abc8534e..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayCCE', 'version': '5.1.29'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -patches = [ - # fix Make dependencies, so parallel build also works - 'HPL_parallel-make.patch', - 'HPL-2.1_LINKER-ld.patch', -] - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb deleted file mode 100644 index 109c7ddafc..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayCCE', 'version': '5.2.25'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -patches = [ - # fix Make dependencies, so parallel build also works - 'HPL_parallel-make.patch', - 'HPL-2.1_LINKER-ld.patch', -] - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb deleted file mode 100644 index b91a1eb499..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayCCE', 'version': '5.2.40'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -patches = [ - # fix Make dependencies, so parallel build also works - 'HPL_parallel-make.patch', - 'HPL-2.1_LINKER-ld.patch', -] - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb deleted file mode 100644 index 806d976659..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb deleted file mode 100644 index b4acf0c1bc..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb deleted file mode 100644 index dcfcc5ca6e..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb deleted file mode 100644 index c8cac688c8..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayIntel', 'version': '5.1.29'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb deleted file mode 100644 index 0344d227a5..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayIntel', 'version': '5.2.25'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb deleted file mode 100644 index 8a33b68ad9..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayIntel', 'version': '5.2.40'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb deleted file mode 100644 index feca7c584a..0000000000 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'JasPer' -version = '1.900.1' - -homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' -description = """The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_ZIP] -source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] - -sanity_check_paths = { - 'files': ["bin/jasper", "lib/libjasper.a"], - 'dirs': ["include"], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb deleted file mode 100644 index 606c94876c..0000000000 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'JasPer' -version = '1.900.1' - -homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' -description = """The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_ZIP] -source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] - -sanity_check_paths = { - 'files': ["bin/jasper", "lib/libjasper.a"], - 'dirs': ["include"], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb deleted file mode 100644 index 7d4d9128c9..0000000000 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'Libint' -version = '1.1.4' - -homepage = 'https://sourceforge.net/p/libint/' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'opt': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') - -configopts = "--enable-deriv --enable-r12" - -sanity_check_paths = { - 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + - ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + - ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb deleted file mode 100644 index e7bca79f1d..0000000000 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'Libint' -version = '1.1.4' - -homepage = 'https://sourceforge.net/p/libint/' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'opt': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') - -configopts = "--enable-deriv --enable-r12" - -sanity_check_paths = { - 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + - ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + - ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb deleted file mode 100644 index 1069375589..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '6.3' - -homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' -description = """The GNU Readline library provides a set of functions for use by applications that - allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. - The Readline library includes additional functions to maintain a list of previously-entered command lines, - to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '5.9')] - -# for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" - -sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb deleted file mode 100644 index 33f071a9b3..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '6.3' - -homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' -description = """The GNU Readline library provides a set of functions for use by applications that - allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. - The Readline library includes additional functions to maintain a list of previously-entered command lines, - to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '5.9')] - -# for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" - -sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb deleted file mode 100644 index 548d650cde..0000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '2.2.1' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'opt': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] - -configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' - -# From the libxc mailing list -# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -# a fully working testsuite soon (unless someone wants to volunteer to do -# it, of course ) In the meantime, unless the majority of the tests -# fail, your build should be fine. -#runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc.a'], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb deleted file mode 100644 index 79002b6ce4..0000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '2.2.1' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'opt': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] - -configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' - -# From the libxc mailing list -# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -# a fully working testsuite soon (unless someone wants to volunteer to do -# it, of course ) In the meantime, unless the majority of the tests -# fail, your build should be fine. -#runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc.a'], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb deleted file mode 100644 index de4b325756..0000000000 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'M4' -version = '1.4.17' - -homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -configopts = "--enable-cxx" - -sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb deleted file mode 100644 index 06f80557f1..0000000000 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'M4' -version = '1.4.17' - -homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -configopts = "--enable-cxx" - -sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb deleted file mode 100644 index 6b7bb1c347..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'optarch': True, 'shared': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['ncurses-%(version)s_configure_darwin.patch'] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb deleted file mode 100644 index 01680ab5b7..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'optarch': True, 'shared': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['ncurses-%(version)s_configure_darwin.patch'] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb deleted file mode 100644 index 49b27458ee..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'numpy' -version = '1.9.2' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['numpy-1.8.0-mkl.patch'] - -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb deleted file mode 100644 index fa04b42299..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'numpy' -version = '1.9.2' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['numpy-1.8.0-mkl.patch'] - -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb deleted file mode 100644 index 5c84059a20..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'Python' -version = '2.7.9' -versionsuffix = '-bare' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'opt': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -# bare installation: no extensions included -exts_list = [] - -buildopts = 'LINKCC="$CC -dynamic"' - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb deleted file mode 100644 index 2e085966c7..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,115 +0,0 @@ -name = 'Python' -version = '2.7.9' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.9.1' -scipyversion = '0.14.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -buildopts = 'LINKCC="$CC -dynamic"' - -# order is important! -# package versions updated Jan 19th 2015 -exts_list = [ - ('setuptools', '11.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.4.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.13', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), -] - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb deleted file mode 100644 index 1e9572eb83..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'Python' -version = '2.7.9' -versionsuffix = '-bare' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True, 'opt': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -# bare installation: no extensions included -exts_list = [] - -buildopts = 'LINKCC="$CC -dynamic"' - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb deleted file mode 100644 index 0c1b139dda..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,115 +0,0 @@ -name = 'Python' -version = '2.7.9' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.9.1' -scipyversion = '0.14.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -buildopts = 'LINKCC="$CC -dynamic"' - -# order is important! -# package versions updated Jan 19th 2015 -exts_list = [ - ('setuptools', '11.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.4.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.13', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), -] - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb deleted file mode 100644 index 04ccb9df33..0000000000 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1' - -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' -description = "Szip compression software, providing lossless compression of scientific data" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'dynamic': True} - -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb deleted file mode 100644 index ce6dcbcc3d..0000000000 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1' - -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' -description = "Szip compression software, providing lossless compression of scientific data" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True, 'dynamic': True} - -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb deleted file mode 100644 index d6c03f828c..0000000000 --- a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'scipy' -version = '0.15.1' -versionsuffix = '-Python-2.7.9' - -homepage = 'http://www.scipy.org' -description = """SciPy is a collection of mathematical algorithms and convenience - functions built on the Numpy extension for Python.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True} - -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('numpy', '1.9.2', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb deleted file mode 100644 index be06b3e907..0000000000 --- a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'scipy' -version = '0.15.1' -versionsuffix = '-Python-2.7.9' - -homepage = 'http://www.scipy.org' -description = """SciPy is a collection of mathematical algorithms and convenience - functions built on the Numpy extension for Python.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True} - -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('numpy', '1.9.2', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb deleted file mode 100644 index b62190e55f..0000000000 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,39 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -# Authors:: Valentin Plugaru -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html -## -easyblock = 'ConfigureMake' - -name = 'tcsh' -version = '6.18.01' - -homepage = 'http://www.tcsh.org' -description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). - It is a command language interpreter usable both as an interactive login shell and a shell script command - processor. It includes a command-line editor, programmable word completion, spelling correction, a history - mechanism, job control and a C-like syntax.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'dynamic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.astron.com/pub/%(namelower)s', - 'ftp://ftp.astron.com/pub/%(namelower)s/old', -] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/tcsh"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb deleted file mode 100644 index c678adaf68..0000000000 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,39 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -# Authors:: Valentin Plugaru -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html -## -easyblock = 'ConfigureMake' - -name = 'tcsh' -version = '6.18.01' - -homepage = 'http://www.tcsh.org' -description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). - It is a command language interpreter usable both as an interactive login shell and a shell script command - processor. It includes a command-line editor, programmable word completion, spelling correction, a history - mechanism, job control and a C-like syntax.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'dynamic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.astron.com/pub/%(namelower)s', - 'ftp://ftp.astron.com/pub/%(namelower)s/old', -] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/tcsh"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb deleted file mode 100644 index cfdc17ab69..0000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb +++ /dev/null @@ -1,42 +0,0 @@ -name = 'WRF' -version = '3.6.1' - -homepage = 'http://www.wrf-model.org' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -sources = ['%(name)sV%(version)s.TAR.gz'] -source_urls = [ - 'http://www2.mmm.ucar.edu/wrf/src/', - 'http://www.mmm.ucar.edu/wrf/src/', -] - -# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems -osdependencies = ['tcsh'] -#builddependencies = [('tcsh', '6.18.01')] - -dependencies = [ - ('JasPer', '1.900.1'), - ('cray-netcdf/4.3.2', EXTERNAL_MODULE), - ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), -] - -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-3.6.1_known_problems.patch', - 'WRF_tests_limit-runtimes.patch', -] - -# limit parallel build to 20 -maxparallel = 20 - -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -runtest = False - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb deleted file mode 100644 index b4103d924f..0000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb +++ /dev/null @@ -1,42 +0,0 @@ -name = 'WRF' -version = '3.6.1' - -homepage = 'http://www.wrf-model.org' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -sources = ['%(name)sV%(version)s.TAR.gz'] -source_urls = [ - 'http://www2.mmm.ucar.edu/wrf/src/', - 'http://www.mmm.ucar.edu/wrf/src/', -] - -# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems -osdependencies = ['tcsh'] -#builddependencies = [('tcsh', '6.18.01')] - -dependencies = [ - ('JasPer', '1.900.1'), - ('cray-netcdf/4.3.2', EXTERNAL_MODULE), - ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), -] - -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-3.6.1_known_problems.patch', - 'WRF_tests_limit-runtimes.patch', -] - -# limit parallel build to 20 -maxparallel = 20 - -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -runtest = False - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb deleted file mode 100644 index e23fdc62cb..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.8' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'dynamic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb deleted file mode 100644 index 196dc1e3be..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.8' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True, 'dynamic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' -- GitLab From 732df2686676167f531b7e4de3268b978f878747 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2016 14:31:03 +0100 Subject: [PATCH 0670/2133] update with R 3.2.3 easyconfig in current develop --- .../easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 1 - .../easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 26 +++++++++++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index aae3ac82f6..229ad73a8c 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -56,7 +56,6 @@ exts_list = [ 'utils', # non-standard libraries, should be specified with fixed versions! ('Rmpi', '0.6-5', ext_options), - ('Rmpi', '0.6-5', ext_options), ('abind', '1.4-3', ext_options), ('magic', '1.5-6', ext_options), ('geometry', '0.3-6', ext_options), diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 2f1c082832..46ed150b7a 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -393,6 +393,32 @@ exts_list = [ ('tensorA', '0.36', ext_options), ('EasyABC', '1.5', ext_options), ('shape', '1.4.2', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.4.0', ext_options), + ('roxygen2', '5.0.1', ext_options), + ('git2r', '0.13.1', ext_options), + ('xml2', '0.1.2', ext_options), + ('rversions', '1.0.2', ext_options), + ('devtools', '1.9.1', ext_options), + ('Rook', '1.1-1', ext_options), + ('rjson', '0.2.15', ext_options), + ('Cairo', '1.5-9', ext_options), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.1-6', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-7', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-9', ext_options), + ('ks', '1.10.1', ext_options), + ('logcondens', '2.1.4', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-45', ext_options), + ('coin', '1.1-2', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.0.7', ext_options), + ('sm', '2.2-5.4', ext_options), ] moduleclass = 'lang' -- GitLab From b0d06e61a6bb264589f31d972212e831480b7c76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2016 17:56:10 +0100 Subject: [PATCH 0671/2133] add binutils as dependency in flex easyconfig --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index 0c9f4d80a4..e1a9437774 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -13,6 +13,9 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] dependencies = [('Bison', '3.0.4')] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + parallel = 1 moduleclass = 'lang' -- GitLab From b28601235af520ecfd1a97b6375802e123717d2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2016 21:04:26 +0100 Subject: [PATCH 0672/2133] add icc/ifort/impi/imkl easyconfigs for intel/2016.02 + HPL as testcase --- .../h/HPL/HPL-2.1-intel-2016.02.eb | 18 +++++++++ .../i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 34 +++++++++++++++++ .../iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 18 +++++++++ .../ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 34 +++++++++++++++++ .../i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb | 22 +++++++++++ ...11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 38 +++++++++++++++++++ ....181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 34 +++++++++++++++++ 7 files changed, 198 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb new file mode 100644 index 0000000000..f4c0fccb16 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.02'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..f4abc8bef2 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['d6f8529a44231e427219c8e025dec3b2'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..e07e4371a2 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.2.181' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..916145cd26 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..9e93414ff1 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -0,0 +1,22 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.02' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '2.181' +compver = '2016.%s' % suff + +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..74cc4cff3a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.2.181' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-5.3.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..ef29e9af70 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-5.3.0-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' -- GitLab From ce8f1d793d00f67a5dce1baaa21ffec30ccc7471 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 27 Feb 2016 20:09:20 +0000 Subject: [PATCH 0673/2133] Add details about purpose and provenance of the patch --- .../easyconfigs/p/PLINK/PLINK-1.07_redeclaration.patch | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07_redeclaration.patch b/easybuild/easyconfigs/p/PLINK/PLINK-1.07_redeclaration.patch index 20e3f284a8..9ba80c7478 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07_redeclaration.patch +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07_redeclaration.patch @@ -1,3 +1,10 @@ +Taken from https://github.com/Homebrew/homebrew-science/pull/958 + +This fixes code in PLINK that causes errors when building with +GCC >= 4.8. + +The patch is itself derived from Debian originally. + diff --git a/sets.cpp b/sets.cpp index 3a8f92f..adef60f 100644 --- a/sets.cpp -- GitLab From fec82c4c000dd1f46ab3e57f95f3ec7479092339 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 27 Feb 2016 20:12:03 +0000 Subject: [PATCH 0674/2133] Use platform-agnostic dynamic library extension --- easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb index 8218ead1ea..3dbf1f6dcc 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb @@ -33,7 +33,7 @@ dependencies = [('zlib', '1.2.8')] # if you want "new version check" change to WITH_WEBCHECK="1", but if your compute nodes # have no internet access better leave it as is buildopts = ' CXX_UNIX="$CXX $CXXFLAGS" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 ' -buildopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$EBROOTOPENBLAS/lib/libopenblas.so' +buildopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$EBROOTOPENBLAS/lib/libopenblas.%s' % SHLIB_EXT files_to_copy = [ (["plink", "gPLINK.jar"], 'bin'), -- GitLab From 3ab3bd7a72ddaf4c7aa4ca42b3d283b3e68c63e9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 27 Feb 2016 20:16:27 +0000 Subject: [PATCH 0675/2133] Remove superfluous comment --- easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb index 2d42585347..c4baaa942f 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb @@ -27,6 +27,4 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['https://github.com/lh3/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] -#Sanity check included in custom easyblock - moduleclass = 'bio' -- GitLab From 881a1af7508fe81b6716e69ca4cf91469764b885 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 08:24:29 +0000 Subject: [PATCH 0676/2133] Port HTSeq and matplotlib dep to foss-2015b --- .../HTSeq-0.6.1p1-foss-2015b-Python-2.7.10.eb | 32 +++++++++++++ ...tplotlib-1.5.1-foss-2015b-Python-2.7.10.eb | 45 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..59b6c70412 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.6.1p1' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.10' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) +eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver + +dependencies = [ + (python, pythonver), + ('matplotlib', '1.5.1', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%s/site-packages/%s" % (pyshortver, eggname)], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..207a23ff90 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c "import %(ext_name)s"', '') + +dependencies = [ + ('Python', '2.7.10'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From 23f91104b705ad48bb482f5e9dd34e22c11e1b10 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 08:27:08 +0000 Subject: [PATCH 0677/2133] Change moduleclass to bio --- .../h/HTSeq/HTSeq-0.6.1p1-foss-2015b-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2015b-Python-2.7.10.eb index 59b6c70412..84e43a6849 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2015b-Python-2.7.10.eb @@ -29,4 +29,4 @@ sanity_check_paths = { options = {'modulename': '%(name)s'} -moduleclass = 'data' +moduleclass = 'bio' -- GitLab From 345cfaa10d12af8d373e52420b02c22ef47226c8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 10:32:34 +0000 Subject: [PATCH 0678/2133] Add missing deps freetype and libpng --- .../f/freetype/freetype-2.6.2-foss-2015b.eb | 21 +++++++++++++++++++ .../l/libpng/libpng-1.6.21-foss-2015b.eb | 19 +++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2015b.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb new file mode 100644 index 0000000000..54449d2405 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2015b.eb new file mode 100644 index 0000000000..eb62c5487c --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' -- GitLab From 2ee94c2ec31992f07aeca2aa10ed443b97b87235 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 28 Feb 2016 14:08:46 +0100 Subject: [PATCH 0679/2133] add missing easyconfigs to resolve deps for R 3.2.3 w/ intel/2016a --- .../c/cURL/cURL-7.47.0-intel-2016a.eb | 31 +++++++++++++++++ .../d/Doxygen/Doxygen-1.8.11-intel-2016a.eb | 19 +++++++++++ .../g/GDAL/GDAL-2.0.2-intel-2016a.eb | 29 ++++++++++++++++ .../l/libxml2/libxml2-2.9.3-intel-2016a.eb | 29 ++++++++++++++++ .../n/netCDF/netCDF-4.3.3.1-intel-2016a.eb | 34 +++++++++++++++++++ 5 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb new file mode 100644 index 0000000000..d47702643f --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.47.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1r')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb new file mode 100644 index 0000000000..dd1ad80d3a --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.11' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.1'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a.eb new file mode 100644 index 0000000000..203a2ae454 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.2' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.3.3.1'), + ('expat', '2.1.0'), + ('libxml2', '2.9.3'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb new file mode 100644 index 0000000000..b762d96901 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016a.eb new file mode 100644 index 0000000000..40796ae26b --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.3.3.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.47.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.11'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From 8dd7e4c9c70387654f7b9e18936ad94767d668fc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 20:59:47 +0000 Subject: [PATCH 0680/2133] Add sanity checks from intel version --- easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2015b.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2015b.eb index eb62c5487c..03fb87f59f 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2015b.eb @@ -16,4 +16,11 @@ dependencies = [('zlib', '1.2.8')] configopts = "--with-pic" +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + moduleclass = 'lib' -- GitLab From 9ccd759202411cc04a8a5c4c20dfe5f0601cf9f4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 21:08:20 +0000 Subject: [PATCH 0681/2133] Revert homepage to SourceForge, keep source url as GitHub --- easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb index c4baaa942f..2018ca59b4 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb @@ -12,12 +12,14 @@ # Version >= 0.7.13 # Author: Adam Huffman # The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa ## name = 'BWA' version = '0.7.13' -homepage = 'https://github.com/lh3/bwa' +homepage = 'http://bio-bwa.sourceforge.net/' description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.""" -- GitLab From 4c85cfcbcaf4214827916aa863bfb6425503d90b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 21:21:01 +0000 Subject: [PATCH 0682/2133] Port to foss-2015b with Perl 5.22.0 --- .../PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb | 118 ++++++++++++++++++ 1 file changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb new file mode 100644 index 0000000000..c5cac8c87f --- /dev/null +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb @@ -0,0 +1,118 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'PRINSEQ' +version = '0.20.4' + +homepage = 'http://prinseq.sourceforge.net' +description = """A bioinformatics tool to PRe-process and show INformation of SEQuence data.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] +sources = ['%(namelower)s-lite-%(version)s.tar.gz'] + +perl = 'Perl' +perlver = '5.22.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::Depends', '0.405', { + 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('ExtUtils::PkgConfig', '1.15', { + 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], + }), + ('Pod::Usage', '1.68', { + 'source_tmpl': 'Pod-Usage-1.68.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + }), + ('File::Temp', '0.2304', { + 'source_tmpl': 'File-Temp-0.2304.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Digest::MD5', '2.54', { + 'source_tmpl': 'Digest-MD5-2.54.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/'], + }), + ('Cairo', '1.106', { + 'source_tmpl': 'Cairo-1.106.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('Statistics::PCA', '0.0.1', { + 'source_tmpl': 'Statistics-PCA-0.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSTH/'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-3.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Math::Cephes::Matrix', '0.5304', { + 'source_tmpl': 'Math-Cephes-0.5304.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + }), + ('Math::MatrixReal', '2.12', { + 'source_tmpl': 'Math-MatrixReal-2.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LETO/'], + }), + ('Text::SimpleTable', '2.03', { + 'source_tmpl': 'Text-SimpleTable-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRAMBERG/'], + }), + ('Contextual::Return', '0.004008', { + 'source_tmpl': 'Contextual-Return-0.004008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], + }), +] + +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = [('perl', '%(installdir)s/prinseq-graphs.pl')] + +modextrapaths = { + 'PATH': "", # add installation dir to PATH + 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) +} + +postinstallcmds = [ + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + "chmod +x %(installdir)s/*.pl" # add execution permission +] + +sanity_check_paths = { + 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From e3b608a17ab7d1d29ad29f1585ca97e9048ae9c6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 21:23:08 +0000 Subject: [PATCH 0683/2133] Use bare Perl --- .../p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb index c5cac8c87f..9d69ec6346 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb @@ -23,7 +23,7 @@ perlver = '5.22.0' versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ - (perl, perlver), + (perl, perlver, '-bare'), ] # these are the perl libraries dependencies -- GitLab From 1fd2f757002f308e9a18d8da6607d72be91112fb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 21:55:51 +0000 Subject: [PATCH 0684/2133] Port TopHat2 to foss-2015b --- .../t/TopHat/TopHat-2.1.1-foss-2015b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb new file mode 100644 index 0000000000..31db65ea57 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.1' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = [ + 'tophat_ictce.patch', + 'tophat-2.0.13-zlib.patch', +] + +dependencies = [ + ('Boost', '1.60.0'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 78dc6d965f6ee331912f3d693fbb044ce7e713db Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 22:03:45 +0000 Subject: [PATCH 0685/2133] Disable obsolete bundled SeqAn patch for ictce --- easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb index 31db65ea57..dfc3160664 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb @@ -20,7 +20,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] patches = [ - 'tophat_ictce.patch', + #'tophat_ictce.patch', 'tophat-2.0.13-zlib.patch', ] -- GitLab From 2a49fc45bee7a42924637dc5db55c101d5081b91 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 22:06:27 +0000 Subject: [PATCH 0686/2133] Remove reference to obsolete patch --- easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb index dfc3160664..3bdcb05552 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb @@ -20,7 +20,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] patches = [ - #'tophat_ictce.patch', 'tophat-2.0.13-zlib.patch', ] -- GitLab From c57b21df6e316880f727115ae54e8018ba22e9bd Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 22:34:55 +0000 Subject: [PATCH 0687/2133] Update ATSAS PR to 2.7.1 for EL7 --- .../a/ATSAS/ATSAS-2.7.1-1.el7.x86_64.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATSAS/ATSAS-2.7.1-1.el7.x86_64.eb diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.7.1-1.el7.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.7.1-1.el7.x86_64.eb new file mode 100644 index 0000000000..d2e1adc5f0 --- /dev/null +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.7.1-1.el7.x86_64.eb @@ -0,0 +1,24 @@ +easyblock = 'Tarball' + +name = 'ATSAS' +version = '2.7.1-1' +versionsuffix = '.el7.x86_64' + +homepage = 'http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html' +description = """ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download via http://www.embl-hamburg.de/biosaxs/download.html +sources = ['%(name)s-%(version)s%(versionsuffix)s.tar.gz'] + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/atsas'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib64/atsas', 'share/atsas'], +} + +moduleclass = 'bio' -- GitLab From 706d522e108ed3af7d674ac1bb113b427cca4a18 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 22:58:56 +0000 Subject: [PATCH 0688/2133] Port Exonerate to foss-2015b --- .../e/Exonerate/Exonerate-2.2.0-foss-2015b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb new file mode 100644 index 0000000000..56718e16b7 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.2.0' + +homepage = 'http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('GLib', '2.34.3')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' -- GitLab From 27e6de9cdc5b54a3fbe4949e34e2cf94aefcb414 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Mon, 29 Feb 2016 14:19:59 +1030 Subject: [PATCH 0689/2133] Do not patch standard /bin/bash shebang --- .../n/NextClip/NextClip_scripts_shebang.patch | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch b/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch index 35d7d7811b..41d0a5aee9 100644 --- a/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch +++ b/easybuild/easyconfigs/n/NextClip/NextClip_scripts_shebang.patch @@ -1,14 +1,5 @@ Fix hardcoding of /usr/bin/perl, use perl available through $PATH -Fix hardcoding of /bin/bash, use bash available through $PATH author: Nathan S. Watson-Haigh (ACPFG) ---- a/scripts/index_bwa.sh -+++ b/scripts/index_bwa.sh -@@ -1,4 +1,4 @@ --#!/bin/bash -+#!/usr/bin/env bash - - source bwa-0.6.1 - --- a/scripts/nextclip_index_reference.pl +++ b/scripts/nextclip_index_reference.pl @@ -1,4 +1,4 @@ @@ -33,14 +24,6 @@ author: Nathan S. Watson-Haigh (ACPFG) # Script: nextclip_make_report.pl # Purpose: Produce PDF report of NextClip analysis ---- a/scripts/nextclip_plot_graphs.sh -+++ b/scripts/nextclip_plot_graphs.sh -@@ -1,4 +1,4 @@ --#!/bin/bash -+#!/usr/bin/env bash - - # Script: nextclip_plot_graphs.sh - # Purpose: Plot insert length and read length graphs for NextClip --- a/scripts/nextclip_sam_parse.pl +++ b/scripts/nextclip_sam_parse.pl @@ -1,4 +1,4 @@ -- GitLab From f3d74231e0f1cb067f670ada15b04c1b3bc167ee Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Feb 2016 08:14:15 +0000 Subject: [PATCH 0690/2133] Add GLib-2.34.3 for foss-2015b, dep of Exonerate --- .../g/GLib/GLib-2.34.3-foss-2015b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb new file mode 100644 index 0000000000..7b323a630d --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.34.3' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.0.13'), + ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), +] +builddependencies = [('Python', '2.7.3')] + +moduleclass = 'vis' -- GitLab From 5696614ee4628512d461fd548e76d172f013c2fc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Feb 2016 08:21:31 +0000 Subject: [PATCH 0691/2133] Add gettext 0.18.2 for foss-2015b, required by Exonerate --- .../g/gettext/gettext-0.18.2-foss-2015b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb new file mode 100644 index 0000000000..e7d30bfac7 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.18.2' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' -- GitLab From 16dff43802386b1e30413b192c45ba9ad28c6da9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Feb 2016 08:27:30 +0000 Subject: [PATCH 0692/2133] Add libxml2 2.9.1 for foss-2015b, required by Exonerate --- .../l/libxml2/libxml2-2.9.1-foss-2015b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb new file mode 100644 index 0000000000..03c075bd1a --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' -- GitLab From 39cce5364c3d11f2fe5beb6d4df0b7b9a217156e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Feb 2016 08:31:24 +0000 Subject: [PATCH 0693/2133] Add libreadline-6.2 & Python-2.7.3 for foss-2015b, required by Exonerate --- .../libreadline/libreadline-6.2-foss-2015b.eb | 30 ++++++ .../p/Python/Python-2.7.3-foss-2015b.eb | 91 +++++++++++++++++++ 2 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb new file mode 100644 index 0000000000..6589e3ba7c --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.2' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb new file mode 100644 index 0000000000..7bff359058 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb @@ -0,0 +1,91 @@ +name = 'Python' +version = '2.7.3' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.6.1' +scipyversion = '0.10.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +exts_list = [ + ('setuptools', '0.6c11', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('mpi4py', '1.3', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.17.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.1', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '1.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.12.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), +] + +moduleclass = 'lang' -- GitLab From 9d482c5f629fd622429a12205cc78e75481f2823 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Feb 2016 09:12:02 +0000 Subject: [PATCH 0694/2133] Fix source location for Exonerate --- easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb index 56718e16b7..6a9d4b5398 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb @@ -17,7 +17,7 @@ description = """ Exonerate is a generic tool for pairwise sequence comparison. toolchain = {'name': 'foss', 'version': '2015b'} -source_urls = [homepage] +source_urls = ['http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [('GLib', '2.34.3')] -- GitLab From 25fc417f23ed3aace68b32d6940139fa6ce109a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 11:09:45 +0100 Subject: [PATCH 0695/2133] minor update in sanity_check_paths in ATSAS easyconfigs --- easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb | 2 +- easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb index 60a094505c..3806f502e6 100644 --- a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb @@ -18,7 +18,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['bin', 'lib64/atsas'], + 'dirs': ['bin', 'lib64/atsas', 'share/atsas'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb index 5dc5ca2151..53cffee901 100644 --- a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb @@ -18,7 +18,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['bin', 'lib64/atsas'], + 'dirs': ['bin', 'lib64/atsas', 'share/atsas'], } moduleclass = 'bio' -- GitLab From eeeeb1d63b5aa30279312e603ab101ca0b9b801d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 11:14:21 +0100 Subject: [PATCH 0696/2133] no 'atsas' subdir in 'share' for older ATSAS versions --- easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb | 2 +- easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb index 3806f502e6..72a18e6d64 100644 --- a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb @@ -18,7 +18,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['bin', 'lib64/atsas', 'share/atsas'], + 'dirs': ['bin', 'lib64/atsas', 'share'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb index 53cffee901..8f8ca911d7 100644 --- a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb @@ -18,7 +18,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['bin', 'lib64/atsas', 'share/atsas'], + 'dirs': ['bin', 'lib64/atsas', 'share'], } moduleclass = 'bio' -- GitLab From 9615ed7316f14d2de87e1c4eb2be54a01236071a Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Mon, 29 Feb 2016 14:44:13 +0100 Subject: [PATCH 0697/2133] Add easyconfig for latest MVAPICH2 2.1 and 2.2b --- .../m/MVAPICH2/MVAPICH2-2.1-GCC-4.9.3-2.25.eb | 17 +++++++++++++++++ .../m/MVAPICH2/MVAPICH2-2.2b-GCC-4.9.3-2.25.eb | 17 +++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.1-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.2b-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.1-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.1-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..13f9a5a43d --- /dev/null +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.1-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +name = 'MVAPICH2' +version = '2.1' + +homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' +description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH." + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/'] +sources = [SOURCELOWER_TAR_GZ] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['0095ceecb19bbb7fb262131cb9c2cdd6'] + +builddependencies = [('Bison', '3.0.4')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.2b-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.2b-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..7f35d9ebdf --- /dev/null +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.2b-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +name = 'MVAPICH2' +version = '2.2b' + +homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' +description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH." + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/'] +sources = [SOURCELOWER_TAR_GZ] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['5651e8b7a72d7c77ca68da48f3a5d108'] + +builddependencies = [('Bison', '3.0.4')] + +moduleclass = 'mpi' -- GitLab From 59b3ad2fd4b84df9d337f8ec5e1b94dcb7dbaf40 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Mon, 29 Feb 2016 14:57:59 +0100 Subject: [PATCH 0698/2133] Add new toolchain foos_mv2 2016a Same as foss 2016a except that OpenMPI is replaced by MVAPICH2. --- .../b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb | 22 ++++++++++++ .../f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb | 34 ++++++++++++++++++ .../easyconfigs/f/foss_mv2/foss_mv2-2016a.eb | 35 +++++++++++++++++++ .../g/gmvapich2/gmvapich2-2016a.eb | 25 +++++++++++++ ...ich2-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb | 25 +++++++++++++ 5 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb create mode 100644 easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb create mode 100644 easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..570b1b1c8b --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb new file mode 100644 index 0000000000..757b5eba91 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gmvapich2', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb b/easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb new file mode 100644 index 0000000000..868fa56f62 --- /dev/null +++ b/easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss_mv2' +version = '2016a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + MVAPICH2 for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.3-2.25' + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gmvapich2' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('MVAPICH2', '2.2b', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb new file mode 100644 index 0000000000..efd6351300 --- /dev/null +++ b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb @@ -0,0 +1,25 @@ +easyblock = "Toolchain" + +name = 'gmvapich2' +version = '2016a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including MVAPICH2 for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.9.3-2.25' +comp = (compname, compver) + +mpilib = 'MVAPICH2' +mpiver = '2.2b' + +# compiler toolchain dependencies +dependencies = [ + comp, + (mpilib, mpiver, '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..ea5206c7ec --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gmvapich2', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blassuff = '-LAPACK-3.6.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.3-2.25'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From cf8af929948aab0e69ac63c4a69a2ca95d097779 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 18:31:30 +0100 Subject: [PATCH 0699/2133] {numlib}[intel/2016a] CGAL 4.7 (WIP) --- .../CGAL-4.7-intel-2016a-Python-2.7.11.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1e7bf4a653 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['623d91fb2ab0a35049dc6098a0f235cc'] + + +mesaver = '11.1.2' +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('MPFR', '3.1.3', '-GMP-6.1.0'), + ('Qt5', '5.5.1', '-Mesa-%s' % mesaver), + ('Mesa', mesaver, versionsuffix), + ('libGLU', '9.0.0', '-Mesa-%s' % mesaver), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.4.1'), +] + +moduleclass = 'numlib' -- GitLab From 5568d14ced220871b5303bd34e8cf295dfb338c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 20:05:44 +0200 Subject: [PATCH 0700/2133] add easyconfig Boost-1.60.0-intel-2016a-Python-2.7.11.eb --- .../Boost-1.60.0-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..5a42251165 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.60.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From a13cd4a58ec6afa53a1a94456cde5b0132321982 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 19:56:21 +0100 Subject: [PATCH 0701/2133] fix binutils version in M4 easyconfig --- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb index 0a925c97ef..434b6f02ff 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.26', '', True)] configopts = "--enable-cxx" -- GitLab From 56f9e64c25579bf780f1673462c44839ef9b62ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 19:57:44 +0100 Subject: [PATCH 0702/2133] fix source URL for GCC tarball in GCCcore easyconfig --- easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index e7aac86863..1f2fc04edb 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.3' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official -- GitLab From adbae798a1cb89db32c3a047537bb6f2318ae7c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 20:17:02 +0100 Subject: [PATCH 0703/2133] add clarifying comment --- easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/icc/icc-2016.0.109.eb | 1 + easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 1 + 8 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 7354472c7e..17d0ffe45a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index c6144a5afd..e56edba4db 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -12,6 +12,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] checksums = ['f57a892fb494db3c80f20a88aa3e901f'] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index 0748e2d400..d80f4b798c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index f4abc8bef2..080cfccc9a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index c188753ac5..b41f57ab66 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index b01714a6f5..c64470205a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -12,6 +12,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tg checksums = ['bce7f6a71f7e44f67956197501d00b7c'] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index f961cef224..4e5be0a9bb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 916145cd26..3ee926155e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -- GitLab From 99911e51a62b180a0e56cb2e817e54ad28acbd71 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 1 Mar 2016 06:21:44 +1030 Subject: [PATCH 0704/2133] Moved sources and source_urls to below toolchain --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 4 ++-- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 543fdf8204..cd21d99d6d 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -6,11 +6,11 @@ version = '35.82' homepage = 'https://sourceforge.net/projects/bbmap/' description = """BBMap short read aligner, and other bioinformatic tools.""" +toolchain = {'name': 'foss', 'version': '2015b'} + source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz' ] -toolchain = {'name': 'foss', 'version': '2015b'} - java = 'Java' javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index 5ec7a87ccc..dff5ba78e2 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -6,11 +6,11 @@ version = '35.82' homepage = 'https://sourceforge.net/projects/bbmap/' description = """BBMap short read aligner, and other bioinformatic tools.""" +toolchain = {'name': 'foss', 'version': '2015b'} + source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz' ] -toolchain = {'name': 'foss', 'version': '2015b'} - java = 'Java' javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) -- GitLab From 2396154e2efec2abc991051f89c4bbfdd954969c Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 1 Mar 2016 09:12:29 +1030 Subject: [PATCH 0705/2133] rm empty line and moved sources above dependencies. --- .../g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb index 01cd80052a..db19b2803a 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb @@ -14,6 +14,9 @@ description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST toolchain = {'name': 'foss', 'version': '2015b'} +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] + # with these deps you can use standard compressed files # to support files in gobby format take a look at README for extra dependencies # http://research-pub.gene.com/gmap/src/README @@ -22,9 +25,6 @@ dependencies = [ ('zlib', '1.2.8'), ] -source_urls = ['http://research-pub.gene.com/gmap/src/'] -sources = [SOURCELOWER_TAR_GZ] - # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README #configopts = 'MAX_READLENGTH=250' @@ -35,4 +35,3 @@ sanity_check_paths = { } moduleclass = 'bio' - -- GitLab From 59c143639c705d0790db523ba85984b9ebe2c9db Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 1 Mar 2016 11:02:34 +1030 Subject: [PATCH 0706/2133] Patch fastqc shebang --- .../f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb | 2 ++ .../f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb | 2 ++ .../f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb | 2 ++ .../f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb | 2 ++ easybuild/easyconfigs/f/FastQC/FastQC_shebang.patch | 11 +++++++++++ 5 files changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastQC/FastQC_shebang.patch diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb index 505f4f2807..02def8d267 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb @@ -22,6 +22,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%(namelower)s_v%(version)s.zip'] source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +patches = ['FastQC_shebang.patch'] + java = 'Java' javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb index c8f4df417f..77e77bc53c 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] +patches = ['FastQC_shebang.patch'] + java = 'Java' javaver = '1.7.0_60' versionsuffix = '-%s-%s' % (java, javaver) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb index 5b66419773..cda11898cd 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] +patches = ['FastQC_shebang.patch'] + java = 'Java' javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb index 301434b905..811ae1b2f1 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] +patches = ['FastQC_shebang.patch'] + java = 'Java' javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC_shebang.patch b/easybuild/easyconfigs/f/FastQC/FastQC_shebang.patch new file mode 100644 index 0000000000..8e9733bfce --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC_shebang.patch @@ -0,0 +1,11 @@ +Fix hardcoding of /usr/bin/perl, use perl available through $PATH +author: Nathan S. Watson-Haigh (ACPFG) +--- fastqc.orig 2016-03-01 10:53:17.433849105 +1030 ++++ fastqc 2016-03-01 10:53:44.850579745 +1030 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + use warnings; + use strict; + use FindBin qw($RealBin); + -- GitLab From e235142f01298e92a3ba422e3ae49c75f8b40b00 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 1 Mar 2016 11:03:20 +1030 Subject: [PATCH 0707/2133] Added FastQC easyconfig for Java 1.8.0_74 --- .../f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb new file mode 100644 index 0000000000..1ade195661 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb @@ -0,0 +1,33 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.4' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] + +patches = ['FastQC_shebang.patch'] + +java = 'Java' +javaver = '1.8.0_74' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +postinstallcmds = ['chmod +x %(installdir)s/fastqc'] + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' -- GitLab From 3fb3472a3993017be1dbe49d2dd4384d9b3d8674 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 1 Mar 2016 13:03:14 +1030 Subject: [PATCH 0708/2133] Added additional dependencies for foss-2015b --- .../s/SQLite/SQLite-3.8.8.1-foss-2015b.eb | 38 +++++++++++++++++++ .../t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb | 24 ++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015b.eb new file mode 100644 index 0000000000..b3cfb08afd --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015b.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015b'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb new file mode 100644 index 0000000000..31e024fb43 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 422795e79def0a88f53e09422dbb906e261a1080 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 1 Mar 2016 13:12:08 +1030 Subject: [PATCH 0709/2133] Ignore EasyBuild log files generated when using gc3pie --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 8179a745b4..ed706988e3 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ dist/ *egg-info/ *.swp *.ropeproject/ +eb-*.log -- GitLab From c54e5589cbcb366b1b2b76a4ed2348722307d723 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 1 Mar 2016 09:08:09 +0100 Subject: [PATCH 0710/2133] use system python xcb-proto (with dummy toolchain) --- .../l/libxcb/libxcb-1.11.1-intel-2016a.eb | 4 +--- ...cb-proto-1.11-intel-2016a-Python-2.7.11.eb | 23 ------------------- 2 files changed, 1 insertion(+), 26 deletions(-) delete mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index faa9778d64..fb5897b62d 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -13,9 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '-Python-2.7.11'), - # Alternatively, you can use xcb-proto using system Python: - #('xcb-proto', 1.11', '', ('dummy', 'dummy')) + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb deleted file mode 100644 index 67fb1d84ea..0000000000 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xcb-proto' -version = '1.11' - -homepage = 'http://xcb.freedesktop.org/' -description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, -latency hiding, direct access to the protocol, improved threading support, and extensibility.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://xcb.freedesktop.org/dist/'] -sources = [SOURCELOWER_TAR_GZ] - -versionsuffix = '-Python-%(pyver)s' -dependencies = [('Python', '2.7.11')] - -sanity_check_paths = { - 'files': ['lib/pkgconfig/xcb-proto.pc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/xcbgen'] -} - -moduleclass = 'devel' -- GitLab From 1bc43aa964c4c9b1bbf2248d5179def7f2e3a3eb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 1 Mar 2016 09:13:04 +0100 Subject: [PATCH 0711/2133] added comment for xcb-proto --- easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb index 27a89ed005..6a306d862e 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb @@ -7,6 +7,8 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" +# even though xcb-proto is installed with configure-make-make install, nothing is actually built; +# only .py files are installed using Python, and some .xlm flies copied, so OK to use dummy toolchain toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://xcb.freedesktop.org/dist/'] -- GitLab From 178df22db68499259f8f0b9039d6679e7d0707e7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 1 Mar 2016 09:16:14 +0100 Subject: [PATCH 0712/2133] libX11 using system python dependent xcb-proto --- easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb index abaa07d7cf..5df5e13e43 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '-Python-2.7.11'), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), -- GitLab From dabd9c350d7c563b0afcfd5ba24418d6e90b2394 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Mar 2016 09:49:09 +0100 Subject: [PATCH 0713/2133] minor style fixes in X lib easyconfigs --- .../easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb | 2 +- .../easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb | 2 +- .../easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb | 8 ++++---- .../x/xextproto/xextproto-7.3.0-intel-2016a.eb | 1 - .../easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb | 1 - 5 files changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb index cca4ea1438..243dbd6f22 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb index 248b0fbfbc..24fc239d5e 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.28'), ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index fb5897b62d..098e8569bb 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -23,10 +23,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb index dcc6160700..af65fa2a9d 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb index 217429b1ab..bb8657a96c 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb @@ -9,7 +9,6 @@ description = """xtrans includes a number of routines to make X implementations """ toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] -- GitLab From 13e0fd850081d09820f7b98047e2b220018c26cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Mar 2016 10:03:03 +0100 Subject: [PATCH 0714/2133] don't hardcode optarch=True in xextproto/xtrans easyconfigs --- .../easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb | 1 - .../easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb | 1 - .../easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb | 1 - easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb | 1 - easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb | 1 - easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb | 1 - .../easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb | 1 - easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb | 1 - easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb | 1 - easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb | 1 - easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb | 1 - easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb | 1 - easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb | 1 - easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb | 1 - easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb | 1 - easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb | 1 - easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb | 1 - easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb | 1 - easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb | 1 - 20 files changed, 20 deletions(-) diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb index d4118dc48c..222c1cb8a9 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb index 6e6a5a03b2..f8d28a6517 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb index 054bc51cbe..7e5dd65346 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb index 4f5a5e2a0d..e73a8f9515 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb index 829a1e95f8..0f74426405 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb index 0c9b21f3fb..bceed61321 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb index 18ab59d5ae..eb7322e162 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb index 673a0e5e21..6156597f8b 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb index 494a482b64..96189817b0 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb index 6c19b3821e..d2b93b5852 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb index 6694ef584a..247e613160 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb @@ -9,7 +9,6 @@ description = """xtrans includes a number of routines to make X implementations """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb index 7ac7af4a53..33279f3ceb 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.5.14.eb @@ -9,7 +9,6 @@ description = """xtrans includes a number of routines to make X implementations """ toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb index ec378cd83c..7b02bd54ca 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb @@ -8,7 +8,6 @@ description = """xtrans includes a number of routines to make X implementations at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. """ toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb index 98cc20e543..2b8c6ebbdd 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb @@ -9,7 +9,6 @@ description = """xtrans includes a number of routines to make X implementations """ toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb index 0edc961a34..6edc4ce87f 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2.6-foss-2014b.eb @@ -9,7 +9,6 @@ description = """xtrans includes a number of routines to make X implementations """ toolchain = {'name': 'foss', 'version': '2014b'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb index 1a4f54a0c5..eac6d863c0 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2014b.eb @@ -9,7 +9,6 @@ description = """xtrans includes a number of routines to make X implementations """ toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb index 01968fd489..788f0681d1 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb @@ -9,7 +9,6 @@ description = """xtrans includes a number of routines to make X implementations """ toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb index ed6733fd17..573dd33276 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb @@ -9,7 +9,6 @@ description = """xtrans includes a number of routines to make X implementations """ toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb index 0613532497..a2e3133d2a 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb @@ -9,7 +9,6 @@ description = """xtrans includes a number of routines to make X implementations """ toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb index 21b74f6cfe..e36d13a40f 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015b.eb @@ -9,7 +9,6 @@ description = """xtrans includes a number of routines to make X implementations """ toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] -- GitLab From 09f7bcf1f365506804290e641cc0d42e32528357 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Mar 2016 10:10:13 +0100 Subject: [PATCH 0715/2133] minor style fixes in libXau/libXdmcp/libxcb easyconfigs --- easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2014b.eb | 2 +- .../easyconfigs/l/libXau/libXau-1.0.8-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb | 2 +- .../easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb | 2 +- .../easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb | 2 +- .../easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb | 2 +- .../easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb | 2 +- .../easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb | 2 +- .../easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb | 2 +- .../easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb | 2 +- .../easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb | 2 +- .../l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb | 8 ++++---- .../l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb | 8 ++++---- .../l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb | 8 ++++---- .../l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb | 8 ++++---- .../l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb | 8 ++++---- .../l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb | 8 ++++---- .../l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb | 8 ++++---- .../libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 8 ++++---- .../l/libxcb/libxcb-1.8-goolf-1.4.10-Python-2.7.3.eb | 8 ++++---- .../l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.3.eb | 8 ++++---- .../l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb | 8 ++++---- .../l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb | 8 ++++---- .../l/libxcb/libxcb-1.8-ictce-5.3.0-Python-2.7.3.eb | 8 ++++---- .../l/libxcb/libxcb-1.8-intel-2014b-Python-2.7.8.eb | 8 ++++---- 26 files changed, 68 insertions(+), 68 deletions(-) diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2014b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2014b.eb index fb7fa9047c..7a01f9c781 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2014b.eb @@ -18,7 +18,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.4.10.eb index bb9632f8a7..12dd6869a6 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.4.10.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb index 658d67c165..f1bc2bfb36 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb @@ -18,7 +18,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb index 20b6db8b12..2131263c1d 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb index 7fec589824..6493f4c619 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb index 4d40c3b428..22bf8016cf 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb @@ -18,7 +18,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb index 724c920249..408dc4aede 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb index 9cfc777f9e..9304d0fc79 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.%s' % SHLIB_EXT]], + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb index a15cb924db..735a0391ab 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.26'), ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb index dfac851674..cc513f2315 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.27'), ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb index 0bcd783d04..79416debdd 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.27'), ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb index e4f8395c43..93de3908f0 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.28'), ] sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb index 104ccdae65..6921c06b50 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb @@ -26,10 +26,10 @@ dependencies = [ #preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb index 72ed48fe99..ce3fc060e8 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-intel-2014b-Python-2.7.8.eb @@ -24,10 +24,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb index 26de0f9322..5ba8e74d17 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb @@ -21,10 +21,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb index 4f2074c3fb..24ebce544e 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb @@ -24,10 +24,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb index d72a9273ac..5da025a420 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb @@ -24,10 +24,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb index 6621cf1702..89cf21ee1e 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.10.eb @@ -24,10 +24,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb index cc7392bf9e..59081eb776 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2015b-Python-2.7.11.eb @@ -24,10 +24,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 2a52455403..3b3682ba69 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.4.10-Python-2.7.3.eb index a52d5bb05d..ed4684b89c 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.4.10-Python-2.7.3.eb @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.3.eb index 056448ccd2..768ffc0072 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.3.eb @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb index 1368050899..228e1f7aaf 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb index 68e4849e58..4733d7980f 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-5.3.0-Python-2.7.3.eb index 16f804c17d..e27e71a1c5 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-5.3.0-Python-2.7.3.eb @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2014b-Python-2.7.8.eb index 8c055b9572..008c8f05f6 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2014b-Python-2.7.8.eb @@ -25,10 +25,10 @@ dependencies = [ preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], 'dirs': ['include/xcb', 'lib/pkgconfig'], } -- GitLab From f5dc75d383fdf09e64c446e1ab94694f2e84d493 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 1 Mar 2016 10:55:10 +0100 Subject: [PATCH 0716/2133] GAMESS-US for intel/2016a --- .../GAMESS-US-20141205-R1-intel-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20141205-R1-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20141205-R1-intel-2016a.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20141205-R1-intel-2016a.eb new file mode 100644 index 0000000000..b9f96d96e3 --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20141205-R1-intel-2016a.eb @@ -0,0 +1,23 @@ +name = 'GAMESS-US' +version = '20141205-R1' + +homepage = 'http://www.msg.chem.iastate.edu/gamess/index.html' +description = """ The General Atomic and Molecular Electronic Structure System (GAMESS) + is a general ab initio quantum chemistry package. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +# manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) +# rename gamess-current.tar.gz by changing 'current' to the proper version +sources = ['gamess-%(version)s.tar.gz'] +checksums = ['6403592eaa885cb3691505964d684516'] + +patches = ['GAMESS-US_rungms-slurm.patch'] + +# increase these numbers if your system is bigger in terms of cores-per-node or number of nodes +# it's OK if these values are larger than what your system provides +maxcpus = '1000' +maxnodes = '100000' + +moduleclass = 'chem' -- GitLab From 1f99e880ce30ff3e36228c2f81e7ff171519586e Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 1 Mar 2016 11:51:14 +0100 Subject: [PATCH 0717/2133] Bring xtrans sanity check in line with new 2015 check. --- easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb index 8366af681c..983b4ae968 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb @@ -15,9 +15,8 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', - 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', 'Xtranssock.c', - 'Xtranstli.c', 'Xtransutil.c']], + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], 'dirs': [], } -- GitLab From f1ea4e405247379130399eecb2ea64b88ad2ef1a Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 1 Mar 2016 14:39:31 +0100 Subject: [PATCH 0718/2133] Rename foss_mv2/2016a to gmvolf/2016a --- .../{f/foss_mv2/foss_mv2-2016a.eb => g/gmvolf/gmvolf-2016a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/{f/foss_mv2/foss_mv2-2016a.eb => g/gmvolf/gmvolf-2016a.eb} (98%) diff --git a/easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb b/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb similarity index 98% rename from easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb rename to easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb index 868fa56f62..b9a63b2c7c 100644 --- a/easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb +++ b/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'Toolchain' -name = 'foss_mv2' +name = 'gmvolf' version = '2016a' homepage = '(none)' -- GitLab From 41d4edb4448ceed6054e0ec90e1f016dcbc6257a Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 1 Mar 2016 14:52:20 +0100 Subject: [PATCH 0719/2133] Add new toolchain gmpolf/2016a (same as foss/2016a but with MPICH 3.2) --- .../f/FFTW/FFTW-3.3.4-gmpich-2016a.eb | 34 ++++++++++++++++++ .../easyconfigs/g/gmpich/gmpich-2016a.eb | 25 +++++++++++++ .../easyconfigs/g/gmpolf/gmpolf-2016a.eb | 35 +++++++++++++++++++ .../m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb | 16 +++++++++ ...pich-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb | 25 +++++++++++++ 5 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmpich-2016a.eb create mode 100644 easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb create mode 100644 easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb create mode 100644 easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmpich-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmpich-2016a.eb new file mode 100644 index 0000000000..71efac9c7e --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmpich-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gmpich', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb new file mode 100644 index 0000000000..d495830401 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb @@ -0,0 +1,25 @@ +easyblock = "Toolchain" + +name = 'gmpich' +version = '2016a' + +homepage = '(none)' +description = """gcc and GFortran based compiler toolchain, + including MPICH for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.9.3-2.25' +comp = (compname, compver) + +mpilib = 'MPICH' +mpiver = '3.2' + +# compiler toolchain dependencies +dependencies = [ + comp, + (mpilib, mpiver, '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb new file mode 100644 index 0000000000..391d1f7f0c --- /dev/null +++ b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb @@ -0,0 +1,35 @@ +easyblock = "Toolchain" + +name = 'gmpolf' +version = '2016a' + +homepage = '(none)' +description = """gcc and GFortran based compiler toolchain, + MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.3-2.25' + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gmpich' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('MVAPICH2', '2.2b', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..06251f71e8 --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,16 @@ +name = 'MPICH' +version = '3.2' + +homepage = 'http://www.mpich.org/' +description = """MPICH v3.x is an open source high-performance MPI 3.0 implementation. +It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.mpich.org/static/tarballs/%(version)s'] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['f414cfa77099cd1fa1a5ae4e22db508a'] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..9cf751a2ad --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gmpich', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blassuff = '-LAPACK-3.6.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.3-2.25'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 53522dffe1b16b4875262a28d04e656704bbd150 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Tue, 1 Mar 2016 15:59:25 +0100 Subject: [PATCH 0720/2133] New horton easyconfig --- ...Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 59 +++++++++++++++++++ .../l/Libint/Libint-2.0.3-intel-2015b.eb | 14 +++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/h/horton/horton-2.0.0-intel2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2015b.eb diff --git a/easybuild/easyconfigs/h/horton/horton-2.0.0-intel2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/h/horton/horton-2.0.0-intel2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb new file mode 100644 index 0000000000..b7da1e5b9b --- /dev/null +++ b/easybuild/easyconfigs/h/horton/horton-2.0.0-intel2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -0,0 +1,59 @@ +easyblock = "PythonPackage" +name = 'horton' +version = '2.0.0' + +homepage = 'http://theochem.github.io/horton' +description = """\ +HORTON is a Helpful Open-source Research TOol for N-fermion systems, written +primarily in the Python programming language. (HORTON is named after the helpful +pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON +is to provide a platform for testing new ideas on the quantum many-body problem +at a reasonable computational cost. Although HORTON is primarily designed to be +a quantum-chemistry program, it can perform computations involving model +Hamiltonians, and could be extended for computations in nuclear physics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +pythonversionsuffix = "-%s-%s" % (python, pythonversion) + +hdf5version = '1.8.15-patch1' +hdf5versionsuffix = '-HDF5-%s-serial' % hdf5version + +versionsuffix = pythonversionsuffix + hdf5versionsuffix + +dependencies = [ + (python, pythonversion), + ('h5py', '2.5.0', versionsuffix), + ('matplotlib', '1.4.3', pythonversionsuffix), + ('sympy', '0.7.6.1', pythonversionsuffix), + ('Libint', '2.0.3'), + ('libxc', '2.2.2'), +] + + +prebuildopts = ' '.join([ + 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', + 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', + 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', +]) + +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +runtest = ' '.join([ + 'export MATPLOTLIBRC=$PWD;', + 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', + '%s python setup.py build_ext -i; ' % prebuildopts, + 'nosetests -v', +]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/horton' % pythonshortversion] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2015b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2015b.eb new file mode 100644 index 0000000000..114eb8bcef --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2015b.eb @@ -0,0 +1,14 @@ +name = 'Libint' +version = '2.0.3' + +homepage = 'https://sourceforge.net/p/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = ['libint-%(version)s-stable.tgz'] +source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] + +moduleclass = 'chem' -- GitLab From 8a11bb1ce7d28aef4ba678bb2d5f8d040a98eb4e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Mar 2016 17:23:04 +0100 Subject: [PATCH 0721/2133] fix syntax & style issues in horton easyconfig file --- ...Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 53 +++++++++++++++++ ...Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 59 ------------------- 2 files changed, 53 insertions(+), 59 deletions(-) create mode 100644 easybuild/easyconfigs/h/horton/horton-2.0.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb delete mode 100644 easybuild/easyconfigs/h/horton/horton-2.0.0-intel2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb diff --git a/easybuild/easyconfigs/h/horton/horton-2.0.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/h/horton/horton-2.0.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb new file mode 100644 index 0000000000..ab045435b2 --- /dev/null +++ b/easybuild/easyconfigs/h/horton/horton-2.0.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonPackage' + +name = 'horton' +version = '2.0.0' + +homepage = 'http://theochem.github.io/horton' +description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written + primarily in the Python programming language. (HORTON is named after the helpful + pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON + is to provide a platform for testing new ideas on the quantum many-body problem + at a reasonable computational cost. Although HORTON is primarily designed to be + a quantum-chemistry program, it can perform computations involving model + Hamiltonians, and could be extended for computations in nuclear physics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.10' +hdf5ver = '1.8.15-patch1' +versionsuffix = '-Python-%s-HDF5-%s-serial' % (pyver, hdf5ver) + +dependencies = [ + ('Python', pyver), + ('h5py', '2.5.0', versionsuffix), + ('matplotlib', '1.4.3', '-Python-%s' % pyver), + ('sympy', '0.7.6.1', '-Python-%s' % pyver), + ('Libint', '2.0.3'), + ('libxc', '2.2.2'), +] + +prebuildopts = ' '.join([ + 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', + 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', + 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', +]) + +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +runtest = ' '.join([ + 'export MATPLOTLIBRC=$PWD;', + 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', + '%s python setup.py build_ext -i; ' % prebuildopts, + 'nosetests -v', +]) + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/horton' % pyshortver], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/h/horton/horton-2.0.0-intel2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/h/horton/horton-2.0.0-intel2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb deleted file mode 100644 index b7da1e5b9b..0000000000 --- a/easybuild/easyconfigs/h/horton/horton-2.0.0-intel2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb +++ /dev/null @@ -1,59 +0,0 @@ -easyblock = "PythonPackage" -name = 'horton' -version = '2.0.0' - -homepage = 'http://theochem.github.io/horton' -description = """\ -HORTON is a Helpful Open-source Research TOol for N-fermion systems, written -primarily in the Python programming language. (HORTON is named after the helpful -pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON -is to provide a platform for testing new ideas on the quantum many-body problem -at a reasonable computational cost. Although HORTON is primarily designed to be -a quantum-chemistry program, it can perform computations involving model -Hamiltonians, and could be extended for computations in nuclear physics.""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] -sources = [SOURCE_TAR_GZ] - -python = 'Python' -pythonversion = '2.7.10' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) -pythonversionsuffix = "-%s-%s" % (python, pythonversion) - -hdf5version = '1.8.15-patch1' -hdf5versionsuffix = '-HDF5-%s-serial' % hdf5version - -versionsuffix = pythonversionsuffix + hdf5versionsuffix - -dependencies = [ - (python, pythonversion), - ('h5py', '2.5.0', versionsuffix), - ('matplotlib', '1.4.3', pythonversionsuffix), - ('sympy', '0.7.6.1', pythonversionsuffix), - ('Libint', '2.0.3'), - ('libxc', '2.2.2'), -] - - -prebuildopts = ' '.join([ - 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', - 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', - 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', -]) - -# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc -runtest = ' '.join([ - 'export MATPLOTLIBRC=$PWD;', - 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', - '%s python setup.py build_ext -i; ' % prebuildopts, - 'nosetests -v', -]) - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/horton' % pythonshortversion] -} - -moduleclass = 'chem' -- GitLab From 85f5c7e0dab202958c57ad7cb10fb67f786c8aa0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 1 Mar 2016 17:13:24 +0000 Subject: [PATCH 0722/2133] Bump Python dep of GLib to 2.7.11 --- easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb index 7b323a630d..9226838fbe 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb @@ -17,6 +17,6 @@ dependencies = [ ('gettext', '0.18.2'), ('libxml2', '2.9.1'), ] -builddependencies = [('Python', '2.7.3')] +builddependencies = [('Python', '2.7.11')] moduleclass = 'vis' -- GitLab From d7d10195adce9a593aa947a3fd4a0ba24c63f910 Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 1 Mar 2016 18:31:13 +0100 Subject: [PATCH 0723/2133] Adding Gromacs for CrayIntel --- .../CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb | 22 +++++++++ .../GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb | 45 +++++++++++++++++++ .../ncurses-5.9-CrayIntel-2015.11-XC.eb | 36 +++++++++++++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb new file mode 100644 index 0000000000..8fe0d6e4d8 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb new file mode 100644 index 0000000000..492e226263 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " + +dependencies = [ + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb new file mode 100644 index 0000000000..c7ee77bd84 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' -- GitLab From 1f685ceb9d80a2941679fe46507deaaf3ae549e8 Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 1 Mar 2016 18:34:22 +0100 Subject: [PATCH 0724/2133] adding wrf CrayIntel --- .../JasPer-1.900.1-CrayIntel-2015.11-XC.eb | 21 ++++++++++ .../ncurses-5.9-CrayIntel-2015.11-XC.eb | 36 ++++++++++++++++++ .../tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb | 38 +++++++++++++++++++ 3 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb new file mode 100644 index 0000000000..45bc1007dd --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb new file mode 100644 index 0000000000..c7ee77bd84 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb new file mode 100644 index 0000000000..df83e70f3b --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 43be742f7950497b92e6004429e1505b6e7b7ab3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 1 Mar 2016 17:39:51 +0000 Subject: [PATCH 0725/2133] Fix GLib Python dep to 2.7.10 --- easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb index 9226838fbe..04873f8e5c 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb @@ -17,6 +17,6 @@ dependencies = [ ('gettext', '0.18.2'), ('libxml2', '2.9.1'), ] -builddependencies = [('Python', '2.7.11')] +builddependencies = [('Python', '2.7.10')] moduleclass = 'vis' -- GitLab From 7e675b855e2101b45b32327fca4557549dc15d3a Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 1 Mar 2016 18:40:50 +0100 Subject: [PATCH 0726/2133] add wrf --- .../WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb new file mode 100644 index 0000000000..dc552a3235 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' -- GitLab From 6d09160f4ab0a0189093278d00998be5eeb280dc Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 1 Mar 2016 18:41:10 +0100 Subject: [PATCH 0727/2133] Remove explicit ConfigureMake in MPICH easyconfig because it now has its own easyblock --- easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb | 2 -- easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb index ecc1ac4836..971d6adf6f 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'MPICH' version = '3.0.3' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb index f81230a16b..1b8044cecf 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'MPICH' version = '3.0.4' -- GitLab From 03e8089e885b5067fd74b9e361bc7ce43a1ae062 Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 1 Mar 2016 20:21:03 +0100 Subject: [PATCH 0728/2133] adding python 2.7.11 craygnu as used by CSCS --- .../freetype-2.5.5-CrayGNU-2015.11-XC.eb | 22 ++++++ .../libpng-1.6.16-CrayGNU-2015.11-XC.eb | 19 +++++ .../ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb | 20 +++++ .../Python-2.7.11-CrayGNU-2015.11-XC.eb | 75 +++++++++++++++++++ 4 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..5231cd9418 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.5.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'dynamic': True} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.16')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..6191aef3b9 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.16' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'dynamic': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--disable-static" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..ac14395c2f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb @@ -0,0 +1,20 @@ +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files' : ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses6-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + ['lib/lib%s.a' % x for x in ["form", "form", "menu", "menu_g", "ncurses", "ncurses++", "ncurses_g", "panel", "panel_g"]], + 'dirs' : ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..73a8ef05b0 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -0,0 +1,75 @@ +# contributed by Luca MArsella and GPPezzi (CSCS) + +name = 'Python' +version = "2.7.11" + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'dynamic': True, 'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.4' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +patches = ['unixccompiler-Python-2.7.9.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +osdependencies = [('libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Mar 1st 2016 +exts_list = [ + ('setuptools', '20.2.2', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.0.3', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), + ('matplotlib', '1.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + }), +] + +moduleclass = 'lang' -- GitLab From c0ab8886803c3276ff804174ef73fcaae9a8c56e Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 1 Mar 2016 20:25:25 +0100 Subject: [PATCH 0729/2133] adding patch --- .../p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 2 +- .../p/Python/unixccompiler-Python-2.7.11.patch | 11 +++++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Python/unixccompiler-Python-2.7.11.patch diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 73a8ef05b0..58773af2db 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -15,7 +15,7 @@ scipyversion = '0.16.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['unixccompiler-Python-2.7.9.patch'] +patches = ['unixccompiler-Python-2.7.11.patch'] # python needs bzip2 to build the bz2 package dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/unixccompiler-Python-2.7.11.patch b/easybuild/easyconfigs/p/Python/unixccompiler-Python-2.7.11.patch new file mode 100644 index 0000000000..b0b4febb27 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/unixccompiler-Python-2.7.11.patch @@ -0,0 +1,11 @@ +--- EasyBuildTesting/Python-2.7.9/Lib/distutils.orig/unixccompiler.py 2014-12-10 16:59:34.000000000 +0100 ++++ EasyBuildTesting/Python-2.7.9/Lib/distutils/unixccompiler.py 2015-06-12 16:02:06.000000000 +0200 +@@ -237,7 +237,7 @@ + elif self._is_gcc(compiler): + return "-Wl,-R" + dir + else: +- return "-R" + dir ++ return "-Wl,-R " + dir + + def library_option(self, lib): + return "-l" + lib -- GitLab From daa3272710f05a34d76e94a6b3941c1215a1422a Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 1 Mar 2016 20:26:02 +0100 Subject: [PATCH 0730/2133] Update MPICH easyconfig files --- .../m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb | 16 +++------------- .../m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb | 17 +++-------------- 2 files changed, 6 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb index 971d6adf6f..e96f02635c 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb @@ -8,19 +8,9 @@ It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).""" toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.mpich.org/static/tarballs/%s' % version] +source_urls = ['http://www.mpich.org/static/tarballs/%(version)s'] -# MPICH configure wants F90/F90FLAGS to be renamed to FC/FCFLAGS. -preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset F90FLAGS; ' - -# Build shared libraries -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', - 'bin/mpiexec', 'bin/mpirun', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h'], - 'dirs': [], -} +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['ee2b8a8b88e3915804df0efcc747c48b'] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb index 1b8044cecf..cf4928e564 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb @@ -7,21 +7,10 @@ It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).""" toolchain = {'name': 'GCC', 'version': '4.8.1'} -sources = ['mpich-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.mpich.org/static/tarballs/%(version)s'] -# MPICH configure wants F90/F90FLAGS to be renamed to FC/FCFLAGS. -preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset F90FLAGS; ' - -# Build shared libraries -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', 'bin/mpiexec', 'bin/mpirun', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', 'lib/libfmpich.a', 'lib/libfmpich.%s' % SHLIB_EXT, - 'lib/libmpich.a', 'lib/libmpich.%s' % SHLIB_EXT, 'lib/libmpichcxx.a', 'lib/libmpichcxx.%s' % SHLIB_EXT, 'lib/libmpichf90.a', - 'lib/libmpichf90.%s' % SHLIB_EXT], - 'dirs': [], -} +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['9c5d5d4fe1e17dd12153f40bc5b6dbc0'] moduleclass = 'mpi' -- GitLab From ee240ae136ccae9728c02f9ea66c4efd1f51715e Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 1 Mar 2016 22:18:41 +0100 Subject: [PATCH 0731/2133] ncurses 5.9 --- .../easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 58773af2db..e7139b7c31 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -22,7 +22,7 @@ dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), ('libreadline', '6.3'), - ('ncurses', '6.0'), + ('ncurses', '5.9'), ('freetype', '2.5.5'), ('libpng', '1.6.16'), ] -- GitLab From 6705f22d89a2e38e66fa5f7a2a65c4a518ed0979 Mon Sep 17 00:00:00 2001 From: Guilherme Date: Tue, 1 Mar 2016 22:25:20 +0100 Subject: [PATCH 0732/2133] Delete ncurses-6.0-CrayGNU-2015.11-XC.eb --- .../ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb | 20 ------------------- 1 file changed, 20 deletions(-) delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb deleted file mode 100644 index ac14395c2f..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,20 +0,0 @@ -name = 'ncurses' -version = '6.0' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files' : ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses6-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + ['lib/lib%s.a' % x for x in ["form", "form", "menu", "menu_g", "ncurses", "ncurses++", "ncurses_g", "panel", "panel_g"]], - 'dirs' : ['include'] -} - -moduleclass = 'devel' -- GitLab From fc76451b18136caaa9a9cc19f0454d1b7da9e238 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 2 Mar 2016 15:20:59 +1030 Subject: [PATCH 0733/2133] More foss-2015b dependencies --- .../easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015b.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015b.eb new file mode 100644 index 0000000000..ec3f168cb0 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From 7cf577650c3dcd1123711d9c309bffb0b7911724 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 2 Mar 2016 10:57:57 +0100 Subject: [PATCH 0734/2133] 2 --- .../g/glproto/glproto-1.4.17-intel-2016a.eb | 20 ++++++++++++++ .../libpciaccess-0.13.4-intel-2016a.eb | 26 ++++++++++++++++++ .../m/Mesa/Mesa-11.1.2-intel-2016a.eb | 7 ++--- .../easyconfigs/m/Mesa/libdrm-2.4.67.tar.gz | Bin 0 -> 957783 bytes .../makedepend-1.0.5-intel-2016a.eb | 20 ++++++++++++++ 5 files changed, 68 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/libdrm-2.4.67.tar.gz create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb new file mode 100644 index 0000000000..c26a1ac08a --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'glproto' +version = '1.4.17' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb new file mode 100644 index 0000000000..2ac72299c5 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.4' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +builddependencies = [ + ('Autotools', '20150215'), + ('xorg-macros', '1.19.0'), +] + +preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index c0e3c997a1..9f80ae7c43 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -16,17 +16,14 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] -pythonver = '2.7.11' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - builddependencies = [ - ('flex', '2.5.39'), + ('flex', '2.6.0'), ('Bison', '3.0.4'), ('Autotools', '20150215'), ('pkg-config', '0.29'), ('glproto', '1.4.17'), ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), ('xextproto', '7.3.0'), ('xproto', '7.0.28'), ('makedepend', '1.0.5'), diff --git a/easybuild/easyconfigs/m/Mesa/libdrm-2.4.67.tar.gz b/easybuild/easyconfigs/m/Mesa/libdrm-2.4.67.tar.gz new file mode 100644 index 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zyNP(Mssr3;P0M_a#!5#im?Bv%#^d2=)u=f2Z>;2oWdmTV8yg#~Pdp6oH?V9arO(zm z6#tDiG=7zo&fKPB_&S#hVv#O5RI!#v(?E;Bs*MB@X|3Up(iOxaK9&30hE^r4NFD+y_zB9C z6Dd>n1ajaB%VY!0R!q zbR&U^jJ38NE}~Zk##w;RhzwN@YYlJOOpWlS$;($q$0urW?I!=F&%eFeJMN|lbp7=& zJFmLCDZ-Fjt>q!WM?S|N{=Bod-`$k~@#@KE4+P44zsSddz$h)hY0a{F9L}$9d%M$s zAb-6e$hY5N7k&3u0^09Z%>uuQf? literal 0 HcmV?d00001 diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb new file mode 100644 index 0000000000..1158bd68be --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 8d57ec45291dca774dba2830b599f50bed341ee8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 2 Mar 2016 11:05:03 +0100 Subject: [PATCH 0735/2133] LLVM llvm-config needs ncurses --- .../easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a-Python-2.7.9.eb | 4 ++++ easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb | 4 ++++ easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015b.eb | 4 ++++ easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb | 4 ++++ easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015b.eb | 4 ++++ easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb | 4 ++++ easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2015b.eb | 4 ++++ easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2016a.eb | 4 ++++ 8 files changed, 32 insertions(+) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a-Python-2.7.9.eb index 3c0e36d72c..222230619c 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a-Python-2.7.9.eb @@ -26,6 +26,10 @@ builddependencies = [ (python, pyver), ] +dependencies = [ + ('ncurses', '5.9'), +] + configopts = '-DBUILD_SHARED_LIBS=ON ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb index bb160486fd..7c0771c083 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb @@ -23,6 +23,10 @@ builddependencies = [ ('Python', '2.7.10'), ] +dependencies = [ + ('ncurses', '5.9'), +] + configopts = '-DBUILD_SHARED_LIBS=ON ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015b.eb index 435d7783c6..ab41e5094e 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015b.eb @@ -23,6 +23,10 @@ builddependencies = [ ('Python', '2.7.11'), ] +dependencies = [ + ('ncurses', '5.9'), +] + configopts = '-DBUILD_SHARED_LIBS=ON ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb index 88dcd90478..40c74c411b 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb @@ -23,6 +23,10 @@ builddependencies = [ ('Python', '2.7.10'), ] +dependencies = [ + ('ncurses', '5.9'), +] + configopts = '-DBUILD_SHARED_LIBS=ON ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015b.eb index 28f4906cec..b307f91c10 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015b.eb @@ -23,6 +23,10 @@ builddependencies = [ ('Python', '2.7.10'), ] +dependencies = [ + ('ncurses', '5.9'), +] + configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb index eca1371a7b..1594ed4eb1 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb @@ -22,6 +22,10 @@ builddependencies = [ ('Python', '2.7.11'), ] +dependencies = [ + ('ncurses', '5.9'), +] + configopts = '-DBUILD_SHARED_LIBS=ON' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2015b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2015b.eb index 4bf8e3225f..79c6af9120 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2015b.eb @@ -23,6 +23,10 @@ builddependencies = [ ('Python', '2.7.11'), ] +dependencies = [ + ('ncurses', '5.9'), +] + configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2016a.eb index 2605ca36ca..24445c47fb 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-intel-2016a.eb @@ -23,6 +23,10 @@ builddependencies = [ ('Python', '2.7.11'), ] +dependencies = [ + ('ncurses', '6.0'), +] + configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' sanity_check_paths = { -- GitLab From b76dfdf632cdb87cc12faff269a944e24263ad75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 11:18:06 +0100 Subject: [PATCH 0736/2133] add patch to build bigmemory w/ icc --- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 46ed150b7a..8e876a2b37 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -277,7 +277,7 @@ exts_list = [ ('adephylo', '1.1-6', ext_options), ('animation', '2.4', ext_options), ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.5.8', ext_options), + ('bigmemory', '4.5.8', dict(ext_options.items() + [('patches', ['bigmemory-0.3-4-icc.patch'])])), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), ('raster', '2.5-2', ext_options), -- GitLab From 1d39971546133b43cacb60b26d6b12ea6c248aba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 11:33:45 +0100 Subject: [PATCH 0737/2133] add missing patch --- .../r/R/bigmemory-4.5.8_icpc-wd308.patch | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch b/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch new file mode 100644 index 0000000000..36618acdb7 --- /dev/null +++ b/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch @@ -0,0 +1,17 @@ +diff -ruN bigmemory.orig/MD5 bigmemory/MD5 +--- bigmemory.orig/MD5 2015-10-20 08:17:15.000000000 +0200 ++++ bigmemory/MD5 2016-03-02 11:15:44.341327000 +0100 +@@ -45,6 +45,7 @@ + ab68983ecd8292d8986b54fd4cbcac25 *man/typeof-big.matrix-method.Rd + 1bdc8e05fa99285561a41b8cb46287a2 *man/write.big.matrix.Rd + dc93a6dce890660533e7fd18dc1ce2d2 *src/BigMatrix.cpp ++b1d3a4d02405fe08c7983c479bc27f13 *src/Makevars + a55f990cdca7b9de45640aa60febaecd *src/RcppExports.cpp + 81e6f49c7f623fb97376bd4b7132b176 *src/SharedCounter.cpp + 33e9321c8b0fc07df926fcc2f80a41d6 *src/bigmemory.cpp +diff -ruN bigmemory.orig/src/Makevars bigmemory/src/Makevars +--- bigmemory.orig/src/Makevars 1970-01-01 01:00:00.000000000 +0100 ++++ bigmemory/src/Makevars 2016-03-02 11:15:00.997797000 +0100 +@@ -0,0 +1,2 @@ ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From af2655aae036d77c0aded05120bcdee447f70a32 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Wed, 2 Mar 2016 11:35:27 +0100 Subject: [PATCH 0738/2133] Update LLVM-3.7.1-foss-2016a.eb --- easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb index 1594ed4eb1..4228c8e824 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('ncurses', '5.9'), + ('ncurses', '6.0'), ] configopts = '-DBUILD_SHARED_LIBS=ON' -- GitLab From f5900df6c659bc407fd34d1babf69a7589b85b48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 11:48:30 +0100 Subject: [PATCH 0739/2133] fix name for bigmemory patch file --- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 8e876a2b37..1ca3e7f554 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -277,7 +277,7 @@ exts_list = [ ('adephylo', '1.1-6', ext_options), ('animation', '2.4', ext_options), ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.5.8', dict(ext_options.items() + [('patches', ['bigmemory-0.3-4-icc.patch'])])), + ('bigmemory', '4.5.8', dict(ext_options.items() + [('patches', ['bigmemory-4.5.8-icc.patch'])])), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), ('raster', '2.5-2', ext_options), -- GitLab From 4bbe0fdd78daab5df64565e4995954774d21987c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 2 Mar 2016 11:49:01 +0100 Subject: [PATCH 0740/2133] not needed file deleted --- .../easyconfigs/m/Mesa/libdrm-2.4.67.tar.gz | Bin 957783 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Mesa/libdrm-2.4.67.tar.gz diff --git a/easybuild/easyconfigs/m/Mesa/libdrm-2.4.67.tar.gz b/easybuild/easyconfigs/m/Mesa/libdrm-2.4.67.tar.gz deleted file mode 100644 index 220679b472741c37e8fbfb6655cbd0687f87b9fd..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 957783 zcmV(tK@@Ke%N{P@PT;n 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zyNP(Mssr3;P0M_a#!5#im?Bv%#^d2=)u=f2Z>;2oWdmTV8yg#~Pdp6oH?V9arO(zm z6#tDiG=7zo&fKPB_&S#hVv#O5RI!#v(?E;Bs*MB@X|3Up(iOxaK9&30hE^r4NFD+y_zB9C z6Dd>n1ajaB%VY!0R!q zbR&U^jJ38NE}~Zk##w;RhzwN@YYlJOOpWlS$;($q$0urW?I!=F&%eFeJMN|lbp7=& zJFmLCDZ-Fjt>q!WM?S|N{=Bod-`$k~@#@KE4+P44zsSddz$h)hY0a{F9L}$9d%M$s zAb-6e$hY5N7k&3u0^09Z%>uuQf? -- GitLab From e5189e93371e21b791605baaa60992fb30cc61b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 11:55:06 +0100 Subject: [PATCH 0741/2133] really fix name for bigmemory patch file --- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 1ca3e7f554..a34a11bc6c 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -277,7 +277,7 @@ exts_list = [ ('adephylo', '1.1-6', ext_options), ('animation', '2.4', ext_options), ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.5.8', dict(ext_options.items() + [('patches', ['bigmemory-4.5.8-icc.patch'])])), + ('bigmemory', '4.5.8', dict(ext_options.items() + [('patches', ['bigmemory-4.5.8_icpc-wd308.patch'])])), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), ('raster', '2.5-2', ext_options), -- GitLab From 919686dd4342204f7de48059ab0542448d1fe3b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 12:06:59 +0100 Subject: [PATCH 0742/2133] fix patch for bigmemory --- .../r/R/bigmemory-4.5.8_icpc-wd308.patch | 36 ++++++++++--------- 1 file changed, 20 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch b/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch index 36618acdb7..965affb5c9 100644 --- a/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch +++ b/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch @@ -1,17 +1,21 @@ -diff -ruN bigmemory.orig/MD5 bigmemory/MD5 +diff -ru bigmemory.orig/configure bigmemory/configure +--- bigmemory.orig/configure 2015-10-16 18:44:28.000000000 +0200 ++++ bigmemory/configure 2016-03-02 12:05:54.465799000 +0100 +@@ -37,3 +37,5 @@ + + echo "${FLAGS}" > src/Makevars + echo "${LIBS}" >> src/Makevars ++echo "# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member \"std::complex::_M_value\" is inaccessible'" >> src/Makevars ++echo "PKG_CXXFLAGS = -wd308" >> src/Makevars +diff -ru bigmemory.orig/MD5 bigmemory/MD5 --- bigmemory.orig/MD5 2015-10-20 08:17:15.000000000 +0200 -+++ bigmemory/MD5 2016-03-02 11:15:44.341327000 +0100 -@@ -45,6 +45,7 @@ - ab68983ecd8292d8986b54fd4cbcac25 *man/typeof-big.matrix-method.Rd - 1bdc8e05fa99285561a41b8cb46287a2 *man/write.big.matrix.Rd - dc93a6dce890660533e7fd18dc1ce2d2 *src/BigMatrix.cpp -+b1d3a4d02405fe08c7983c479bc27f13 *src/Makevars - a55f990cdca7b9de45640aa60febaecd *src/RcppExports.cpp - 81e6f49c7f623fb97376bd4b7132b176 *src/SharedCounter.cpp - 33e9321c8b0fc07df926fcc2f80a41d6 *src/bigmemory.cpp -diff -ruN bigmemory.orig/src/Makevars bigmemory/src/Makevars ---- bigmemory.orig/src/Makevars 1970-01-01 01:00:00.000000000 +0100 -+++ bigmemory/src/Makevars 2016-03-02 11:15:00.997797000 +0100 -@@ -0,0 +1,2 @@ -+# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' -+PKG_CXXFLAGS = -wd308 ++++ bigmemory/MD5 2016-03-02 12:06:21.181928000 +0100 +@@ -7,7 +7,7 @@ + 08d8ac748bb99e6cd73cbc851ba24e6f *R/zzz.R + ba12d9a9f21ff33b7f0e51d5645eeb67 *build/vignette.rds + da4cdd259fd09ece34aad718a9a11207 *cleanup +-3c21afb0f744e005b69e519259d85021 *configure ++f7c1fffb1d14974537e82237574eb11e *configure + fc5c8f75e424213609b3e3cd9b57f5bf *configure.win + 0cd9765e8adee62083d32a17a6b9aa07 *inst/CITATION + f883e7fbbec7e35f5142805cd80548cf *inst/doc/Overview.R -- GitLab From 632135c92ddbb7aa60981c3261db3f0dcaf9cfbf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 12:16:59 +0100 Subject: [PATCH 0743/2133] add diveRsity + deps to R 3.2.3 easyconfig --- .../easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index aae3ac82f6..ed1d008211 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -420,6 +420,24 @@ exts_list = [ ('clusterRepro', '0.5-1.1', ext_options), ('randomForestSRC', '2.0.7', ext_options), ('sm', '2.2-5.4', ext_options), + ('psych', '1.5.8', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-20', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.8-6', ext_options), + ('mi', '1.0', ext_options), + ('htmlwidgets', '0.6', ext_options), + ('visNetwork', '0.2.1', ext_options), + ('DiagrammeR', '0.8.2', ext_options), + ('sem', '3.1-6', ext_options), + ('jpeg', '0.1-8', ext_options), + ('sna', '2.3-2', ext_options), + ('glasso', '1.8', ext_options), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.3.2', ext_options), + ('diveRsity', '1.9.89', ext_options), ] moduleclass = 'lang' -- GitLab From 3f20edc2d26a5ba156a57c62e964fe2d190f174b Mon Sep 17 00:00:00 2001 From: Alan Date: Wed, 2 Mar 2016 12:38:46 +0100 Subject: [PATCH 0744/2133] Update files that have dummy as toolchain, are not a toolchain themselves and have dependencies. Without an empty version the dependencies do not get loaded at build time --- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb | 2 +- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb | 2 +- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb | 2 +- easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb | 2 +- easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb | 2 +- easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb | 2 +- .../easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb | 2 +- easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb | 2 +- easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb | 2 +- easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb | 2 +- easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb | 2 +- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb | 2 +- .../easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb | 2 +- .../easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb | 2 +- easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb | 2 +- easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb | 2 +- easybuild/easyconfigs/m/MCR/MCR-R2014a.eb | 2 +- easybuild/easyconfigs/m/MCR/MCR-R2015a.eb | 2 +- easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb | 2 +- .../easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb | 2 +- .../easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb | 2 +- .../easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb | 2 +- .../easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb | 2 +- easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0.eb | 2 +- easybuild/easyconfigs/p/picard/picard-1.100.eb | 2 +- easybuild/easyconfigs/p/picard/picard-1.109.eb | 2 +- easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/p/picard/picard-1.119.eb | 2 +- easybuild/easyconfigs/p/picard/picard-1.39.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.1.0.eb | 2 +- easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb | 2 +- 80 files changed, 80 insertions(+), 80 deletions(-) diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb index b75c3fcda9..094f648512 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb @@ -5,7 +5,7 @@ versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TGZ] diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb index 5f10d53c00..f899ce8f01 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb @@ -5,7 +5,7 @@ versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TGZ] diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb index db92841b05..2063066a88 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb @@ -5,7 +5,7 @@ versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TGZ] diff --git a/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb index 6395f17b38..107e9cc668 100755 --- a/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb @@ -6,7 +6,7 @@ version = '2009.01a.pc64_linux.intelmpi' homepage = 'http://www.scm.com/' description = "ADF is a premium-quality quantum chemistry software package based on Density Functional Theory (DFT)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s%(version)s.bin.tgz'] diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb b/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb index 16f5b548ac..f28387fbee 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb @@ -16,7 +16,7 @@ description = """ BEAST is a cross-platform program for Bayesian MCMC analysis o tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://github.com/CompEvol/beast2/releases/download/v%(version)s/'] sources = ['BEAST.v%(version)s.tgz'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb index d2b515088f..873f4f2f72 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb index 3107e6dbdf..fea9079c88 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb b/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb index 5e9ad2796e..d050aae52b 100644 --- a/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb +++ b/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb @@ -12,7 +12,7 @@ description = """ UCSF Chimera is a highly extensible program for interactive vi and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # no public download URL. Go to https://www.cgl.ucsf.edu/chimera/download.html sources = ['%(namelower)s-%(version)s%(versionsuffix)s.bin'] diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb index 928b078aac..d2027312f5 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb @@ -9,7 +9,7 @@ read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/enasequence/%(name)s/archive/'] diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb index a1ceee68c9..f79371e678 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb @@ -9,7 +9,7 @@ description = """ Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download .sh from https://bintray.com/nist-fire-research/releases/FDS-SMV/6.0.1/view/files to create tarball sources = ['FDS_6.0.1-SMV_6.1.5_linux64.tar.gz'] diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb index 9ff730ebed..e49f289165 100644 --- a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb @@ -6,7 +6,7 @@ version = '0.11.2' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] sources = ['%(name)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb index c5f20b9165..72e66f0b0c 100644 --- a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb @@ -6,7 +6,7 @@ version = '0.11.3' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] sources = ['%(name)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb index a4d75eb501..7665c9edda 100644 --- a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.4.eb @@ -6,7 +6,7 @@ version = '0.11.4' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] sources = ['%(name)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb index ddd5712d6f..dd2c25a627 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb @@ -9,7 +9,7 @@ description = """The GATK is a structured software library that makes writing ef medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb index daf5220902..ee70681358 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb index 0c9ece0c95..dde93eb10a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb index 12fe8dadb4..a45cb4ec3b 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb index 98e7df7db8..1bdef83c68 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb @@ -9,7 +9,7 @@ description = """The GATK is a structured software library that makes writing ef medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb index aa6e7fe232..21448792b2 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb index 13de380c1b..a6fc22eedf 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb index 065919e6f3..38e7ae6db1 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb index f53b54862b..689accfbd9 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb index 00459becfc..520cb6b37a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb index 2dc9a277e2..adf96fa7cf 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index df30b5f05b..935c3f665f 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} java = 'Java' javaver = '1.7.0_80' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb index 23b5d632b0..446396ee03 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb @@ -4,7 +4,7 @@ version = '2013.5.192' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb index 1c9509e4ed..d02dca7d22 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.0.090' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb index b547268098..368b594177 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.1.133' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb index 6ae91f49df..8439c044f4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.2.164' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb index 5d89d21731..37331a1488 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '2015.3.187' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb index 3a9d4088ae..1ca6568cb7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '2015.5.223' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 7354472c7e..4ec5788f7f 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index 0748e2d400..2a840e4a5b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.1.150' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb index cba97b45a2..901fc019cc 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb @@ -4,7 +4,7 @@ version = '2013.5.192' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb index 6f1139a94c..a94df9884b 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.0.090' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb index b653c4f858..419e0257c0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.1.133' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb index 4f376249d8..5767d1400f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '2015.2.164' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb index f944202e89..0f54df3a82 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '2015.3.187' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb index faee88adb1..2fd9b5a946 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '2015.5.223' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index c188753ac5..930a3dc326 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index f961cef224..dd3cee42fa 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.1.150' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb index 4619863d5f..2312f4b388 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_p_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb index a693a15b86..b1eb6ee6e3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_p_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb index b3d47b810d..91c64cfa0d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s_intel64.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb index 078c8848d8..4d5ef42fcf 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb @@ -6,7 +6,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, ext for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb index 725bb2b396..2bd88ac625 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb @@ -6,7 +6,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, ext for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index 0db4c8f64f..b8769ef805 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb index c3fb0d1e8e..b5b58cc188 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s_intel64.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb index 209f8143d8..8adf971a63 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb index 94a66c877f..ccd95b2a7a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb index 14cee49479..8b97b3ff26 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb index 339abe07e2..98e5ffd25f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb index 5b2f5de9a8..0fe1b14e46 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb index ca26f636cc..7b7f159547 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb index 6c2f677c6c..cc9f1d89b5 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb index 716cd4b3dd..3b9cb14613 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb index d1128e7799..4843fd2442 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb index 7c293cda0a..3ad520461a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb @@ -6,7 +6,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, ext for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb index 03e70ed442..47e59ba9fc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb index 3f03a3bd36..bd599cfe0d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb index ba3d36b9c7..b0b8036c47 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb @@ -6,7 +6,7 @@ description = """MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb index acdae43db5..65e39e1872 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb @@ -6,7 +6,7 @@ description = """MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb index 1c593f7430..67a1f39096 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb index f459048eeb..ccbd003e89 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index ae7ad64f4d..d28d21b593 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -10,7 +10,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb index 1944afede8..81bfa462d1 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb @@ -11,7 +11,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb index 7c21787b12..3d3c83269c 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb @@ -13,7 +13,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb index 4c7272b6aa..b51b51028c 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb @@ -13,7 +13,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb index 30c44ae3d4..1c8c6b0daf 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb @@ -13,7 +13,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb index e722b3a3d5..49864adcd3 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '15.10' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] checksums = ['cae307f7ad467a1811a5d5da758048ab'] diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0.eb index f7408c2984..e0b6cd1a17 100644 --- a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0.eb +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0.eb @@ -9,7 +9,7 @@ description = """The pbs_python package is a wrapper class for the Torque C libr an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ...""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://ftp.sara.nl/pub/outgoing/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/p/picard/picard-1.100.eb b/easybuild/easyconfigs/p/picard/picard-1.100.eb index d852bf4290..aa4b9cb85c 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.100.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.100.eb @@ -4,7 +4,7 @@ version = '1.100' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.109.eb b/easybuild/easyconfigs/p/picard/picard-1.109.eb index b02c4dfde3..054ac53148 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.109.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.109.eb @@ -4,7 +4,7 @@ version = '1.109' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb index a097dca76d..0d8e511c3f 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb @@ -4,7 +4,7 @@ version = '1.119' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.119.eb b/easybuild/easyconfigs/p/picard/picard-1.119.eb index b6b8db08ef..b8822ebb22 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.119.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.119.eb @@ -4,7 +4,7 @@ version = '1.119' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.39.eb b/easybuild/easyconfigs/p/picard/picard-1.39.eb index 47c911c385..3f179ac9b7 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.39.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.39.eb @@ -4,7 +4,7 @@ version = '1.39' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0.eb index d68d511ad0..702287f8f6 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.0.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0.eb @@ -10,7 +10,7 @@ description = """ A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/broadinstitute/%(name)s/releases/download/%(version)s'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb index eb194cd37c..429f565ab3 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb @@ -7,7 +7,7 @@ homepage = 'http://sourceforge.net/projects/snpeff/' description = """SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} java = 'Java' javaver = '1.7.0_80' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb index 8b1570a181..ba982d8d09 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb @@ -7,7 +7,7 @@ homepage = 'http://sourceforge.net/projects/snpeff/' description = """SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} java = 'Java' javaver = '1.7.0_80' diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb index 5f66c5f283..36d97df090 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb @@ -10,7 +10,7 @@ version = '2.4.1' homepage = 'https://github.com/dkoboldt/varscan' description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['%(name)s.v%(version)s.jar'] source_urls = ['https://github.com/dkoboldt/varscan/releases/download/v%(version)s'] -- GitLab From e906c927130051e6a538f19f81f6589adc685602 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 13:11:46 +0100 Subject: [PATCH 0745/2133] use patch for multicool in R 3.2.3 easyconfig w/ intel/2016a --- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index a34a11bc6c..13de8b1f35 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -410,7 +410,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-9', ext_options), + ('multicool', '0.1-9', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), ('ks', '1.10.1', ext_options), ('logcondens', '2.1.4', ext_options), ('Iso', '0.0-17', ext_options), -- GitLab From 0c844364bc8a006a58e600a5a6528f88dbcfa363 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 13:30:21 +0100 Subject: [PATCH 0746/2133] add diveRsity + deps to R 3.2.3 intel/2016a easyconfig --- .../easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 13de8b1f35..9d75c8323c 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -419,6 +419,24 @@ exts_list = [ ('clusterRepro', '0.5-1.1', ext_options), ('randomForestSRC', '2.0.7', ext_options), ('sm', '2.2-5.4', ext_options), + ('psych', '1.5.8', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-20', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.8-6', ext_options), + ('mi', '1.0', ext_options), + ('htmlwidgets', '0.6', ext_options), + ('visNetwork', '0.2.1', ext_options), + ('DiagrammeR', '0.8.2', ext_options), + ('sem', '3.1-6', ext_options), + ('jpeg', '0.1-8', ext_options), + ('sna', '2.3-2', ext_options), + ('glasso', '1.8', ext_options), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.3.2', ext_options), + ('diveRsity', '1.9.89', ext_options), ] moduleclass = 'lang' -- GitLab From 11da7eb4ab05c2ed1fbf262aa75131b8cd5adc21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 13:56:39 +0100 Subject: [PATCH 0747/2133] add patch file to build glasso with recent ifort --- .../easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- .../r/R/glasso-1.8-ifort-no-fixed.patch | 24 +++++++++++++++++++ 2 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/glasso-1.8-ifort-no-fixed.patch diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 9d75c8323c..eb2673295f 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -431,7 +431,7 @@ exts_list = [ ('sem', '3.1-6', ext_options), ('jpeg', '0.1-8', ext_options), ('sna', '2.3-2', ext_options), - ('glasso', '1.8', ext_options), + ('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), ('huge', '1.2.7', ext_options), ('d3Network', '0.5.2.1', ext_options), ('ggm', '2.3', ext_options), diff --git a/easybuild/easyconfigs/r/R/glasso-1.8-ifort-no-fixed.patch b/easybuild/easyconfigs/r/R/glasso-1.8-ifort-no-fixed.patch new file mode 100644 index 0000000000..aaa1fda26e --- /dev/null +++ b/easybuild/easyconfigs/r/R/glasso-1.8-ifort-no-fixed.patch @@ -0,0 +1,24 @@ +diff -ru glasso.orig/configure glasso/configure +--- glasso.orig/configure 2014-07-22 00:12:05.000000000 +0200 ++++ glasso/configure 2016-03-02 14:01:48.276280000 +0100 +@@ -2194,7 +2194,7 @@ + ;; + ifort) + echo " R configured for Intel fortran..." +- OUR_FCFLAGS="-O3 -axsse4.2 -r8 -fpp -fixed" ++ OUR_FCFLAGS="-O3 -axsse4.2 -r8 -fpp" + + ;; + *) +diff -ru glasso.orig/MD5 glasso/MD5 +--- glasso.orig/MD5 2014-07-22 10:29:36.000000000 +0200 ++++ glasso/MD5 2016-03-02 14:02:05.854342000 +0100 +@@ -3,7 +3,7 @@ + 9b2f2da42cd1d66c4e3cd38427a0bf7a *R/glasso.R + c1a3c7a42d3c130ba02f4827f056ac9a *R/glassopath.R + d5b44b59f23b953d6c2f8835e3fb180d *cleanup +-07f1fbe29f410cac4048f7dd0f838efb *configure ++cefcd7f95dc125a297700cb21bab535d *configure + 57edafaaa2abcf7a51526b81c0bae33f *configure.in + a92a091ed68d9cf0d5ee056b4ead20fb *man/glasso.Rd + e624eb3357a4d5c9dd0f2c5c734c7116 *man/glassopath.Rd -- GitLab From 59b581d6a86960e43ca10b7c796d7fe5fad76d16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 14:12:37 +0100 Subject: [PATCH 0748/2133] add comments in patch files for R extensions --- easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch | 2 ++ easybuild/easyconfigs/r/R/glasso-1.8-ifort-no-fixed.patch | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch b/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch index 965affb5c9..11064f05f7 100644 --- a/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch +++ b/easybuild/easyconfigs/r/R/bigmemory-4.5.8_icpc-wd308.patch @@ -1,3 +1,5 @@ +add -wd308 compiler option to dance around harmless compiler warning being treated as en error +author: Kenneth Hoste (HPC-UGent) diff -ru bigmemory.orig/configure bigmemory/configure --- bigmemory.orig/configure 2015-10-16 18:44:28.000000000 +0200 +++ bigmemory/configure 2016-03-02 12:05:54.465799000 +0100 diff --git a/easybuild/easyconfigs/r/R/glasso-1.8-ifort-no-fixed.patch b/easybuild/easyconfigs/r/R/glasso-1.8-ifort-no-fixed.patch index aaa1fda26e..aed6efc0bf 100644 --- a/easybuild/easyconfigs/r/R/glasso-1.8-ifort-no-fixed.patch +++ b/easybuild/easyconfigs/r/R/glasso-1.8-ifort-no-fixed.patch @@ -1,3 +1,5 @@ +add -wd308 compiler option to dance around harmless compiler warning being treated as en error +author: Kenneth Hoste (HPC-UGent) diff -ru glasso.orig/configure glasso/configure --- glasso.orig/configure 2014-07-22 00:12:05.000000000 +0200 +++ glasso/configure 2016-03-02 14:01:48.276280000 +0100 -- GitLab From c0af084db1f46d524f026189fccd86c852a2b54e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 14:30:18 +0100 Subject: [PATCH 0749/2133] fix remarks, add OpenSSL 1.0.1s easyconfig --- .../c/cURL/cURL-7.47.0-intel-2016a.eb | 2 +- .../d/Doxygen/Doxygen-1.8.11-intel-2016a.eb | 2 +- .../o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb | 21 +++++++++++++++++++ 3 files changed, 23 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb index d47702643f..f21ebdf8a9 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016a.eb @@ -18,7 +18,7 @@ source_urls = ['http://curl.haxx.se/download/'] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -# dependencies = [('OpenSSL', '1.0.1r')] +# dependencies = [('OpenSSL', '1.0.1s')] # configopts = "--with-ssl=$EBROOTOPENSSL" modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb index dd1ad80d3a..2d5dc8597f 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb @@ -11,7 +11,7 @@ sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] builddependencies = [ - ('CMake', '3.4.1'), + ('CMake', '3.4.3'), ('flex', '2.6.0'), ('Bison', '3.0.4'), ] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb new file mode 100644 index 0000000000..976aa24ab2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1s' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-1.0.1q_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From 66966aef18254219342fce2186e7f6e35a6d401d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 2 Mar 2016 15:04:53 +0100 Subject: [PATCH 0750/2133] {vis}[intel-2016a] Tk 8.6.4 witg libX11 1.6.3 (REVIEW) --- .../l/libICE/libICE-1.0.9-intel-2016a.eb | 27 ++++++++++++ .../l/libSM/libSM-1.2.2-intel-2016a.eb | 28 +++++++++++++ .../l/libXft/libXft-2.3.2-intel-2016a.eb | 32 ++++++++++++++ .../libXrender-0.9.9-intel-2016a.eb | 28 +++++++++++++ .../l/libXt/libXt-1.1.5-intel-2016a.eb | 39 +++++++++++++++++ .../renderproto-0.11-intel-2016a.eb | 20 +++++++++ .../t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb | 42 +++++++++++++++++++ 7 files changed, 216 insertions(+) create mode 100644 easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb new file mode 100644 index 0000000000..0038b41047 --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libICE' +version = '1.0.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xtrans', '1.3.5'), +] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb new file mode 100644 index 0000000000..b34ef0db33 --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libSM' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Session Management library, which allows for applications to both manage sessions, + and make use of session managers to save and restore their state for later use.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libICE', '1.0.9'), +] +builddependencies = [ + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb new file mode 100644 index 0000000000..98289122be --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + + +dependencies = [ + ('libX11', '1.6.3'), + ('libXrender', '0.9.9'), + ('freetype', '2.6.2'), + ('fontconfig', '2.11.94'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb new file mode 100644 index 0000000000..fefc99f4eb --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb new file mode 100644 index 0000000000..66391ee4ad --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'libXt' +version = '1.1.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are + based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('kbproto', '1.0.7'), +] + +dependencies = [ + ('libSM', '1.2.2'), + ('libICE', '1.0.9'), + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', + 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', + 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', + 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', + 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb new file mode 100644 index 0000000000..37b516e535 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb new file mode 100644 index 0000000000..b69472a7b1 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +libx11 = 'libX11' +libxver = '1.6.3' +versionsuffix = '-%s-%s' % (libx11, libxver) + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +builddependencies = [ + ('xextproto', '7.3.0'), +# ('xcb-proto', '1.11', '', True), +# ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), +# ('libpthread-stubs', '0.3'), +# ('kbproto', '1.0.7'), +# ('xtrans', '1.3.5'), +] + +dependencies = [ + ('Tcl', version), + (libx11, libxver), + ('libXt', '1.1.5'), + ('libXext', '1.3.3'), + ('libXft', '2.3.2'), +] + +configopts = '--disable-xss --enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 2ccf836645880dfe1416b2b5f67b90938d4d8ee9 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 15:15:03 +0100 Subject: [PATCH 0751/2133] boost craygnu python 2.7.11 --- ...1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb new file mode 100644 index 0000000000..5be4348909 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb @@ -0,0 +1,29 @@ +# contributed by Luca Marsella (CSCS) +easyblock = 'boostcray' + +name = 'Boost' +version = "1.60.0" + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.bz2' % '_'.join(version.split('.'))] + +pythonversion = '2.7.11' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' -- GitLab From f669a4e28dba8416dcbf49b2d6bdc421a65c1a67 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 15:29:32 +0100 Subject: [PATCH 0752/2133] cp2k 3.0 cray support --- .../c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..f495713dbd --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb @@ -0,0 +1,47 @@ +# contributed by Luca Marsella (CSCS) +name = 'CP2K' +version = "3.0" + +easyblock = 'cp2kcray' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.2'), +] + +builddependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test +runtest = False +# regression test reports failures +#ignore_regtest_fails = True + +# build type +type = 'psmp' + +moduleclass = 'chem' -- GitLab From 4e983088251031f5355c41109844cee106825b6e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 15:35:53 +0100 Subject: [PATCH 0753/2133] {bio}[intel/2016a] BCFtools 1.3 + HTSlib 1.3 --- .../b/BCFtools/BCFtools-1.3-intel-2016a.eb | 41 +++++++++++++++++++ .../BCFtools-1.3_extHTSlib_Makefile.patch | 38 +++++++++++++++++ .../h/HTSlib/HTSlib-1.3-intel-2016a.eb | 27 ++++++++++++ 3 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.3_extHTSlib_Makefile.patch create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb new file mode 100644 index 0000000000..7bccf00035 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.3' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('HTSlib', '1.3'), + ('GSL', '2.1'), +] + +parallel = 1 + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1' +installopts = ' prefix=%(installdir)s' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/plugins', + 'cp plugins/*.so %(installdir)s/lib/plugins/.', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['lib/plugins'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3_extHTSlib_Makefile.patch b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3_extHTSlib_Makefile.patch new file mode 100644 index 0000000000..e8a56d6411 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3_extHTSlib_Makefile.patch @@ -0,0 +1,38 @@ +patch Makefile to pick up HTSlib, GSL and zlib provided thorugh EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- bcftools-1.3/Makefile.orig 2015-12-15 22:58:35.000000000 +0100 ++++ bcftools-1.3/Makefile 2016-03-02 15:22:03.656821071 +0100 +@@ -29,11 +29,10 @@ + all: $(PROG) $(TEST_PROG) + + # Adjust $(HTSDIR) to point to your top-level htslib directory +-HTSDIR = htslib-1.3 +-include $(HTSDIR)/htslib.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip +-TABIX = $(HTSDIR)/tabix ++HTSDIR = $(EBROOTHTSLIB)/include ++HTSLIB = $(EBROOTHTSLIB)/lib/libhts.a ++BGZIP = $(EBROOTHTSLIB)/bin/bgzip ++TABIX = $(EBROOTHTSLIB)/bin/tabix + + CC = gcc + CPPFLAGS = +@@ -57,7 +56,7 @@ + ifdef USE_GPL + EXTRA_CPPFLAGS += -DUSE_GPL + OBJS += polysomy.o peakfit.o +- GSL_LIBS = -lgsl -lcblas ++ GSL_LIBS = -L${EBROOTGSL}/lib -lgsl -lcblas + endif + + prefix = /usr/local +@@ -181,7 +180,7 @@ + $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS) + + bcftools: $(HTSLIB) $(OBJS) +- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) ++ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -L${EBROOTZLIB}/lib -lz -lm -ldl $(GSL_LIBS) $(LIBS) + + doc/bcftools.1: doc/bcftools.txt + cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb new file mode 100644 index 0000000000..19f0d7bea8 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.3' + +homepage = "http://www.htslib.org/" +description = """ A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 9b308d6910033d8142b7f089f7308cef33a0e759 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 15:40:14 +0100 Subject: [PATCH 0754/2133] fix remark --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb index 1e64be716a..2ee4f62216 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb @@ -28,7 +28,7 @@ installopts = ' prefix=%(installdir)s' postinstallcmds = [ 'mkdir -p %(installdir)s/lib/plugins', - 'cp plugins/*.so %(installdir)s/lib/plugins/.', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb index 2143e1fd78..f9319eca14 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb @@ -28,7 +28,7 @@ installopts = ' prefix=%(installdir)s' postinstallcmds = [ 'mkdir -p %(installdir)s/lib/plugins', - 'cp plugins/*.so %(installdir)s/lib/plugins/.', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb index 7bccf00035..bd1b04228a 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb @@ -30,7 +30,7 @@ installopts = ' prefix=%(installdir)s' postinstallcmds = [ 'mkdir -p %(installdir)s/lib/plugins', - 'cp plugins/*.so %(installdir)s/lib/plugins/.', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', ] sanity_check_paths = { -- GitLab From 2de552a1a8ab1e33afa8970a301623c577cdc669 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 15:43:23 +0100 Subject: [PATCH 0755/2133] fix spacing remark in description --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb | 4 ++-- easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb | 4 ++-- easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb | 4 ++-- easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb | 4 ++-- 6 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb index d99049bc6c..2f2abef4e6 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb @@ -9,8 +9,8 @@ name = 'HTSlib' version = '1.1' homepage = 'http://www.htslib.org/' -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb index b9abe470f0..36facf37a3 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb @@ -9,8 +9,8 @@ name = 'HTSlib' version = '1.2.1' homepage = "http://www.htslib.org/" -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb index 742be3ddc0..7f25a2acfb 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb @@ -11,8 +11,8 @@ name = 'HTSlib' version = '1.2.1' homepage = "http://www.htslib.org/" -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'goolf', 'version': '1.7.20'} diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb index a5f315ea84..258f48d92e 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb @@ -9,8 +9,8 @@ name = 'HTSlib' version = '1.2.1' homepage = "http://www.htslib.org/" -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb index ced9e05617..8c0f7d5ac6 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb @@ -9,8 +9,8 @@ name = 'HTSlib' version = '1.2.1' homepage = "http://www.htslib.org/" -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb index 19f0d7bea8..7b22333e99 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb @@ -9,8 +9,8 @@ name = 'HTSlib' version = '1.3' homepage = "http://www.htslib.org/" -description = """ A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix """ +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" toolchain = {'name': 'intel', 'version': '2016a'} -- GitLab From 4fbfd47001198b9fca3ca6598613a318ad758925 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 16:45:27 +0200 Subject: [PATCH 0756/2133] add easyconfig Platypus-0.8.1-intel-2016a-Python-2.7.11.eb --- ...latypus-0.8.1-intel-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..c28a1d2040 --- /dev/null +++ b/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Platypus' +version = '0.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.well.ox.ac.uk/platypus' +description = """Platypus is a tool designed for efficient and accurate variant-detection + in high-throughput sequencing data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# download requires registration, see http://www.well.ox.ac.uk/software-download-registration +sources = ['%(name)s_%(version)s.tgz'] + +dependencies = [ + ('Python', '2.7.11'), + ('HTSlib', '1.3'), +] + +unpack_options = '--strip-components=1' +buildininstalldir = True + +options = {'modulename': 'platypusutils'} + +sanity_check_paths = { + 'files': ['Platypus.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' -- GitLab From 901b2a16159c00487b53cedb78da279cd319935e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 17:10:25 +0200 Subject: [PATCH 0757/2133] modify easyconfig Platypus-0.8.1-intel-2016a-Python-2.7.11.eb --- .../p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb index c28a1d2040..bb40e835e4 100644 --- a/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb @@ -23,6 +23,8 @@ buildininstalldir = True options = {'modulename': 'platypusutils'} +postinstallcmds = ["mkdir %(installdir)s/bin && cd %(installdir)s/bin && ln ../Platypus.py"] + sanity_check_paths = { 'files': ['Platypus.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], -- GitLab From d50e69f69c5727371e52d564c8abd92a0e7f12a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 17:13:40 +0200 Subject: [PATCH 0758/2133] SYMlink --- .../p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb index bb40e835e4..b661d0c21a 100644 --- a/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Platypus/Platypus-0.8.1-intel-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ buildininstalldir = True options = {'modulename': 'platypusutils'} -postinstallcmds = ["mkdir %(installdir)s/bin && cd %(installdir)s/bin && ln ../Platypus.py"] +postinstallcmds = ["mkdir %(installdir)s/bin && cd %(installdir)s/bin && ln -s ../Platypus.py"] sanity_check_paths = { 'files': ['Platypus.py'], -- GitLab From 9529f5c2bc18861f28ffd1f00b5cc1126155b9cc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 2 Mar 2016 16:49:59 +0100 Subject: [PATCH 0759/2133] Comments removed --- .../easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb index b69472a7b1..8ada7cd405 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb @@ -19,12 +19,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] builddependencies = [ ('xextproto', '7.3.0'), -# ('xcb-proto', '1.11', '', True), -# ('inputproto', '2.3.1'), ('xproto', '7.0.28'), -# ('libpthread-stubs', '0.3'), -# ('kbproto', '1.0.7'), -# ('xtrans', '1.3.5'), ] dependencies = [ -- GitLab From 114d3585825bdfa4918ad6d6e95be8374c45b964 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 16:50:30 +0100 Subject: [PATCH 0760/2133] use CMake 3.4.3 --- .../c/CMake/CMake-2.8.4-intel-2016a.eb | 22 ------------- .../c/CMake/CMake-3.1.3-intel-2016a.eb | 22 ------------- .../c/CMake/CMake-3.2.3-intel-2016a.eb | 31 ------------------- .../g/GATE/GATE-6.2-intel-2016a.eb | 2 +- .../g/GATE/GATE-7.0-intel-2016a.eb | 7 ++--- .../g/Geant4/Geant4-9.5.p01-intel-2016a.eb | 2 +- .../g/Geant4/Geant4-9.6.p04-intel-2016a.eb | 5 +-- .../LLVM-3.6.2-intel-2016a-Python-2.7.9.eb | 2 +- 8 files changed, 9 insertions(+), 84 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb deleted file mode 100644 index 6e790f2a9a..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2016a.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '2.8.4' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '6.0')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb deleted file mode 100644 index afe0d69bd0..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2016a.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.1.3' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '6.0')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb deleted file mode 100644 index bf57c1d381..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2016a.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.2.3' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = '-- -DCMAKE_USE_OPENSSL=1' - -dependencies = [ - ('ncurses', '6.0'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb index 502c8f56f7..389d60bab7 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb @@ -21,6 +21,6 @@ dependencies = [ ('CLHEP', '2.1.1.0'), ('ROOT', 'v5.34.01'), ] -builddependencies = [('CMake', '2.8.4')] +builddependencies = [('CMake', '3.4.3')] moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb index a0a092ac93..7d392aa8b1 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb @@ -16,14 +16,13 @@ patches = [ 'GATE-%(version)s_unistdh.patch', ] -builddependencies = [ - ('CMake', '3.1.3'), -] - dependencies = [ ('Geant4', '9.6.p04'), ('CLHEP', '2.1.3.1'), ('ROOT', 'v5.34.26'), ] +builddependencies = [ + ('CMake', '3.4.3'), +] moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb index 5b065cc9f0..a4c1b85fa8 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb @@ -16,7 +16,7 @@ dependencies = [ ('CLHEP', '2.1.1.0'), ] -builddependencies = [('CMake', '2.8.4')] +builddependencies = [('CMake', '3.4.3')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" configopts += "-DGEANT4_INSTALL_DATA=OFF" diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb index 0496cd5322..8fa06aa9f5 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb @@ -15,8 +15,9 @@ dependencies = [ ('expat', '2.1.0'), ('CLHEP', '2.1.3.1'), ] - -builddependencies = [('CMake', '3.1.3')] +builddependencies = [ + ('CMake', '3.4.3'), +] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" configopts += "-DGEANT4_INSTALL_DATA=OFF" diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb index 6139d93743..e4b5b40821 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb @@ -22,7 +22,7 @@ source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ - ('CMake', '3.2.3'), + ('CMake', '3.4.3'), (python, pyver), ] -- GitLab From 24ecfa75bf35dcddcd0e895ff0ce3a029d4ade3f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 2 Mar 2016 16:53:20 +0100 Subject: [PATCH 0761/2133] Extra ampty line removed --- easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb index 98289122be..17ddfd09d9 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb @@ -16,7 +16,6 @@ builddependencies = [ ('renderproto', '0.11'), ] - dependencies = [ ('libX11', '1.6.3'), ('libXrender', '0.9.9'), -- GitLab From 7fd15a76581d533a36e0320a545bd267fb9a6eac Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Wed, 2 Mar 2016 18:23:21 +0100 Subject: [PATCH 0762/2133] Updated psmpi easyconfig files to use the new psmpi easyblock --- .../easyconfigs/p/pscom/pscom-5.0.48-1.eb | 23 ++++++++++++ .../p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 37 +++++++------------ .../psmpi-5.1.0-1-iccifort-2015.1.133.eb | 28 +++----------- .../p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb | 27 ++++++++++++++ .../psmpi-5.1.5-1-iccifort-2015.1.133.eb | 27 ++++++++++++++ 5 files changed, 95 insertions(+), 47 deletions(-) create mode 100644 easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb create mode 100644 easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb create mode 100644 easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb new file mode 100644 index 0000000000..13b9a47c54 --- /dev/null +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'pscom' +version = '5.0.48-1' + +homepage = 'http://www.par-tec.com' +description = "ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer." + +toolchain = {'version': '', 'name': 'dummy'} + +sources = ['%(version)s.zip'] +source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] + +builddependencies = [ + ('popt', '1.16'), +] + +sanity_check_paths = { + 'files': ['include/%(name)s.h', ('lib/libpscom.so', 'lib64/libpscom.so'), ('lib/libpscom4mxm.so', 'lib64/libpscom4mxm.so')], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 3e04c7775f..87539a2e7d 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -1,13 +1,15 @@ -easyblock = 'ConfigureMake' - name = 'psmpi' version = '5.1.0-1' homepage = 'https://github.com/ParaStation/psmpi2' -description = """ParaStation MPI as part of the ParaStationV5 cluster suite provides robust, flexible and scalable communication and management functions for Linux-based compute clusters. Beside parallel applications based on the Message Passing Interface specification, version 2 (MPI2), also serial applications are supported.""" - +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'defaultopt': True} + sources = [ '%(version)s.tar.gz', 'openpa-1.0.4.tar.gz', @@ -17,26 +19,13 @@ source_urls = [ 'https://trac.mpich.org/projects/openpa/raw-attachment/wiki/Downloads/', ] -# MPICH configure wants F90/F90FLAGS to be renamed to FC/FCFLAGS. -preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset F90FLAGS; ' - -# Build shared libraries -configopts = '--with-confset=gcc --enable-shared --enable-static' - -dependencies = [('pscom', '5.0.44-1')] +dependencies = [ + ('pscom', '5.0.44-1', '', True), +] -sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', - ('lib/libfmpich.a', 'lib64/libfmpich.a'), - ('lib/libfmpich.%s' % SHLIB_EXT, 'lib64/libfmpich.%s' % SHLIB_EXT), - ('lib/libmpich.a', 'lib64/libmpich.a'), - ('lib/libmpich.%s' % SHLIB_EXT, 'lib64/libmpich.%s' % SHLIB_EXT), - ('lib/libmpichcxx.a', 'lib64/libmpichcxx.a'), - ('lib/libmpichcxx.%s' % SHLIB_EXT, 'lib64/libmpichcxx.%s' % SHLIB_EXT), - ('lib/libmpichf90.a', 'lib64/libmpichf90.a'), - ('lib/libmpichf90.%s' % SHLIB_EXT, 'lib64/libmpichf90.%s' % SHLIB_EXT)], - 'dirs': [], -} +hiddendependencies = [ + ('pscom', '5.0.44-1', '', True), +] +configopts = '--with-confset=gcc PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index 4bb1ff6f7a..a57afdf688 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -1,11 +1,11 @@ -easyblock = 'ConfigureMake' - name = 'psmpi' version = '5.1.0-1' homepage = 'https://github.com/ParaStation/psmpi2' -description = """ParaStation MPI as part of the ParaStationV5 cluster suite provides robust, flexible and scalable communication and management functions for Linux-based compute clusters. Beside parallel applications based on the Message Passing Interface specification, version 2 (MPI2), also serial applications are supported.""" - +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" toolchain = {'name': 'iccifort', 'version': '2015.1.133'} sources = [ @@ -17,26 +17,8 @@ source_urls = [ 'https://trac.mpich.org/projects/openpa/attachment/wiki/Downloads', ] -# MPICH configure wants F90/F90FLAGS to be renamed to FC/FCFLAGS. -preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset F90FLAGS; ' - -# Build shared libraries -configopts = '--with-confset=intel --enable-shared --enable-static --enable-romio --enable-mpe' +configopts = '--with-confset=intel' dependencies = [('pscom', '5.0.44-1')] -sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', - ('lib/libfmpich.a', 'lib64/libfmpich.a'), - ('lib/libfmpich.%s' % SHLIB_EXT, 'lib64/libfmpich.%s' % SHLIB_EXT), - ('lib/libmpich.a', 'lib64/libmpich.a'), - ('lib/libmpich.%s' % SHLIB_EXT, 'lib64/libmpich.%s' % SHLIB_EXT), - ('lib/libmpichcxx.a', 'lib64/libmpichcxx.a'), - ('lib/libmpichcxx.%s' % SHLIB_EXT, 'lib64/libmpichcxx.%s' % SHLIB_EXT), - ('lib/libmpichf90.a', 'lib64/libmpichf90.a'), - ('lib/libmpichf90.%s' % SHLIB_EXT, 'lib64/libmpichf90.%s' % SHLIB_EXT)], - 'dirs': [], -} - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb new file mode 100644 index 0000000000..b7c5d500a2 --- /dev/null +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb @@ -0,0 +1,27 @@ +name = 'psmpi' +version = '5.1.5-1' + +homepage = 'https://github.com/ParaStation/psmpi2' +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" + +toolchain = {'version': '4.9.3', 'name': 'GCC'} + +toolchainopts = {'defaultopt': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] + +dependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +hiddendependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +configopts = ' --with-confset=gcc PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb new file mode 100644 index 0000000000..92f6033fa8 --- /dev/null +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb @@ -0,0 +1,27 @@ +name = 'psmpi' +version = '5.1.5-1' + +homepage = 'https://github.com/ParaStation/psmpi2' +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" + +toolchain = {'version': '2015.1.133', 'name': 'iccifort'} + +toolchainopts = {'defaultopt': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] + +dependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +hiddendependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +configopts = ' --with-confset=intel PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' + +moduleclass = 'mpi' -- GitLab From 861f5a1e81be0a986ff0f31a27762ca148c61852 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Wed, 2 Mar 2016 18:29:44 +0100 Subject: [PATCH 0763/2133] Small fixes --- .../easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 3 +-- .../p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb | 10 ++++++++-- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 87539a2e7d..34f4d57dd7 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -8,8 +8,6 @@ various batch systems for tighter process control. """ toolchain = {'name': 'GCC', 'version': '4.9.2'} -toolchainopts = {'defaultopt': True} - sources = [ '%(version)s.tar.gz', 'openpa-1.0.4.tar.gz', @@ -26,6 +24,7 @@ dependencies = [ hiddendependencies = [ ('pscom', '5.0.44-1', '', True), ] + configopts = '--with-confset=gcc PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index a57afdf688..ac08d5c585 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -17,8 +17,14 @@ source_urls = [ 'https://trac.mpich.org/projects/openpa/attachment/wiki/Downloads', ] -configopts = '--with-confset=intel' +dependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +hiddendependencies = [ + ('pscom', '5.0.48-1', '', True), +] -dependencies = [('pscom', '5.0.44-1')] +configopts = '--with-confset=intel PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' moduleclass = 'mpi' -- GitLab From 42f838992f1526a957c91a6f05161466394b3636 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 18:43:11 +0100 Subject: [PATCH 0764/2133] rename to intel/2016.02-GCC-5.3 --- ...1-intel-2016.02.eb => HPL-2.1-intel-2016.02-GCC-5.3.eb} | 2 +- .../i/intel/{intel-2016.02.eb => intel-2016.02-GCC-5.3.eb} | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/h/HPL/{HPL-2.1-intel-2016.02.eb => HPL-2.1-intel-2016.02-GCC-5.3.eb} (91%) rename easybuild/easyconfigs/i/intel/{intel-2016.02.eb => intel-2016.02-GCC-5.3.eb} (85%) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb similarity index 91% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb index f4c0fccb16..ffa453cdb4 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'intel', 'version': '2016.02'} +toolchain = {'name': 'intel', 'version': '2016.02-GCC-5.3'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb similarity index 85% rename from easybuild/easyconfigs/i/intel/intel-2016.02.eb rename to easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb index 47932a57f9..4d1e0dddac 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb @@ -1,8 +1,9 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild -easyblock = "Toolchain" +easyblock = 'Toolchain' name = 'intel' version = '2016.02' +gcc_maj_min = '5.3' +versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" @@ -10,7 +11,7 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.2.181' -gccver = '5.3.0' +gccver = '%s.0' % gcc_maj_min binutilsver = '2.26' gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ -- GitLab From 0886e5027a7736285c13f867627a2a8673d9a4cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 19:57:33 +0200 Subject: [PATCH 0765/2133] add easyconfig HPL-2.1-intel-2016.02-GCC-4.9.eb, add easyconfig binutils-2.26-GCCcore-4.9.3.eb, add easyconfig flex-2.6.0-GCCcore-4.9.3.eb, add easyconfig icc-2016.2.181-GCC-4.9.3-2.26.eb, add easyconfig iccifort-2016.2.181-GCC-4.9.3-2.26.eb, add easyconfig ifort-2016.2.181-GCC-4.9.3-2.26.eb, add easyconfig iimpi-2016.02-GCC-4.9.3-2.26.eb, add easyconfig imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb, add easyconfig impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb, add easyconfig intel-2016.02-GCC-4.9.eb --- .../b/binutils/binutils-2.26-GCCcore-4.9.3.eb | 41 +++++++++++++++++++ .../f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 21 ++++++++++ .../h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb | 18 ++++++++ .../i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb | 35 ++++++++++++++++ .../iccifort-2016.2.181-GCC-4.9.3-2.26.eb | 18 ++++++++ .../ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb | 35 ++++++++++++++++ .../i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb | 22 ++++++++++ ...11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb | 38 +++++++++++++++++ ....181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb | 34 +++++++++++++++ .../i/intel/intel-2016.02-GCC-4.9.eb | 26 ++++++++++++ 10 files changed, 288 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..0d3fdd2d17 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..5a3de111fc --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -0,0 +1,21 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +parallel = 1 + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..977c7d487d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..ec73b70b03 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['d6f8529a44231e427219c8e025dec3b2'] + +gccver = '4.9.3' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..93577bed54 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.2.181' +versionsuffix = '-GCC-4.9.3-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..c55e928942 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] + +gccver = '4.9.3' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..0be81ea753 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb @@ -0,0 +1,22 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.02' +versionsuffix = '-GCC-4.9.3-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '2.181' +compver = '2016.%s' % suff + +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..78baf11191 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.2.181' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-4.9.3-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..147e9c1ec1 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-4.9.3-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..955db91710 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.02' +gcc_maj_min = '4.9' +versionsuffix = '-GCC-%s' % gcc_maj_min + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.2.181' +gccver = '%s.3' % gcc_maj_min +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.2.181', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' -- GitLab From 6cc138ca5ec6cd4aaea6917159a494a892746d8a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 2 Mar 2016 17:59:17 +0000 Subject: [PATCH 0766/2133] Use existing non-bare Perl 5.20.3 --- ...erl-5.22.0.eb => PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/PRINSEQ/{PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb => PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb} (98%) diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb similarity index 98% rename from easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb rename to easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb index 9d69ec6346..1d36878e90 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb @@ -19,11 +19,11 @@ source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] sources = ['%(namelower)s-lite-%(version)s.tar.gz'] perl = 'Perl' -perlver = '5.22.0' +perlver = '5.20.3' versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ - (perl, perlver, '-bare'), + (perl, perlver), ] # these are the perl libraries dependencies -- GitLab From b8e4a25cec60fe50c037e9614ac6d497a916b47e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 2 Mar 2016 18:09:15 +0000 Subject: [PATCH 0767/2133] First version of Subread --- .../s/Subread/Subread-1.5.0p1-foss-2015b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb new file mode 100644 index 0000000000..245a7b2f5a --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb @@ -0,0 +1,30 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# It was auto-generated based on a template easyconfig, so it should be used with care. +easyblock = 'MakeCp' + +name = 'Subread' +version = '1.5.0p1' + +homepage = 'http://subread.sourceforge.net/' +description = """TEMPLATE DESCRIPTION""" + +# toolchain name should be 'TEMPLATE' if this is a template, so EasyBuild knows and is willing to use it as a template +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... + +# For sources line to work correctly with --try-software-version, you MUST employ %s OR use a construct like SOURCE_TAR_GZ +sources = ['%(namelower)s-%version)s-source.tar.gz'] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [] + +dependencies = [] + +# The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From ee51c965aac480debb113fe46bd326cca373dbac Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 19:10:53 +0100 Subject: [PATCH 0768/2133] modified to use stock easyblock for cp2k --- easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb index f495713dbd..55e00d968f 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb @@ -2,8 +2,6 @@ name = 'CP2K' version = "3.0" -easyblock = 'cp2kcray' - homepage = 'http://www.cp2k.org/' description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different -- GitLab From 5c42a24484a4db4563a78da1ed3c4d4ebc444adb Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 19:43:23 +0100 Subject: [PATCH 0769/2133] adding cuda enable version of cp2k --- .../CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb new file mode 100644 index 0000000000..aeb506b2a1 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb @@ -0,0 +1,48 @@ +# contributed by Luca Marsella (CSCS) +name = 'CP2K' +version = "3.0" +cudaversion = '7.0' +versionsuffix = '-cuda-%s' % cudaversion + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.2'), +] + +builddependencies = [ + ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test +runtest = False +# regression test reports failures +#ignore_regtest_fails = True + +# build type +type = 'psmp' + +moduleclass = 'chem' -- GitLab From 2bfcc9dfe12d917a4a60532d2fbc9df1066e6cf9 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 20:01:42 +0100 Subject: [PATCH 0770/2133] add missing dep --- .../l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..99ad1db263 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb @@ -0,0 +1,33 @@ +# contributed by Luca Marsella (CSCS) +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From 997c2da874253518cdb275ee70bfb3232257af8c Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 3 Mar 2016 06:11:16 +1030 Subject: [PATCH 0771/2133] Set toolchain version to '' so the Java dep is actually loaded --- easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb | 2 +- easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb index 0d15ad9204..6e8d731733 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb @@ -5,7 +5,7 @@ homepage = 'http://broadinstitute.github.io/picard/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb index 3c1e54038f..a7d48bf6b0 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb @@ -5,7 +5,7 @@ homepage = 'http://broadinstitute.github.io/picard/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb index 2d067163eb..742c2507d1 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb @@ -5,7 +5,7 @@ homepage = 'http://broadinstitute.github.io/picard/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb index 2c1613a976..88bda5b21f 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb @@ -5,7 +5,7 @@ homepage = 'http://broadinstitute.github.io/picard/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] sources = ['%(name)s-tools-%(version)s.zip'] -- GitLab From f038794ebafd3137021e07532136e6b116b631ce Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 2 Mar 2016 21:43:15 +0000 Subject: [PATCH 0772/2133] Add first draft of RSeQC including numpy dep --- .../numpy-1.9.2-foss-2015b-Python-2.7.10.eb | 27 ++++++++++++++ .../r/RSeQC/RSeQC-2.6.3-foss-2015b.eb | 35 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..f55df325cf --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,27 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SuiteSparse', '4.4.5', '-METIS-5.1.0'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb new file mode 100644 index 0000000000..c0f1f917f6 --- /dev/null +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'RSeQC' +version = '2.6.3' + +homepage = 'http://rseqc.sourceforge.net/' +description = """RSeQC provides a number of useful modules that can + comprehensively evaluate high throughput sequence data especially RNA-seq + data. Some basic modules quickly inspect sequence quality, nucleotide + composition bias, PCR bias and GC bias, while RNA-seq specific modules + evaluate sequencing saturation, mapped reads distribution, coverage + uniformity, strand specificity, transcript level RNA integrity etc.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [] + +Python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + ('R', '3.2.3'), + ('numpy', '1.9.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From ff5e2fde5d662b1f667c5a4268d029d98a49eaf8 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 22:44:24 +0100 Subject: [PATCH 0773/2133] fixed remarks and separated matplot lib as independent module --- ...b => freetype-2.6.2-CrayGNU-2015.11-XC.eb} | 5 +- ...eb => libpng-1.6.21-CrayGNU-2015.11-XC.eb} | 6 +- ...-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb | 45 ++++++++++ .../Python-2.7.11-CrayGNU-2015.11-XC.eb | 89 +++++++++++++++---- 4 files changed, 123 insertions(+), 22 deletions(-) rename easybuild/easyconfigs/f/freetype/{freetype-2.5.5-CrayGNU-2015.11-XC.eb => freetype-2.6.2-CrayGNU-2015.11-XC.eb} (88%) rename easybuild/easyconfigs/l/libpng/{libpng-1.6.16-CrayGNU-2015.11-XC.eb => libpng-1.6.21-CrayGNU-2015.11-XC.eb} (77%) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb similarity index 88% rename from easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb index 5231cd9418..97d02aea84 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb @@ -1,5 +1,5 @@ name = 'freetype' -version = '2.5.5' +version = '2.6.2' homepage = 'http://freetype.org' description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and @@ -7,12 +7,11 @@ description = """FreeType 2 is a software font engine that is designed to be sma servers, font conversion tools, text image generation tools, and many other products as well.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'dynamic': True} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.16')] +dependencies = [('libpng', '1.6.21')] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb similarity index 77% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb index 6191aef3b9..f58ee3b579 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb @@ -1,19 +1,17 @@ easyblock = 'ConfigureMake' name = 'libpng' -version = '1.6.16' +version = '1.6.21' homepage = 'http://www.libpng.org/pub/png/libpng.html' description = "libpng is the official PNG reference library" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'dynamic': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.8')] -configopts = "--disable-static" - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb new file mode 100644 index 0000000000..9a9609ca9e --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c "import %(ext_name)s"', '') + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index e7139b7c31..0169075b4a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -1,4 +1,4 @@ -# contributed by Luca MArsella and GPPezzi (CSCS) +# contributed by Luca Marsella and GPPezzi (CSCS) name = 'Python' version = "2.7.11" @@ -7,7 +7,7 @@ homepage = 'http://python.org/' description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'dynamic': True, 'pic': True, 'opt': True, 'optarch': True} +toolchainopts = {'pic': True} numpyversion = '1.10.4' scipyversion = '0.16.1' @@ -23,25 +23,21 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - ('freetype', '2.5.5'), - ('libpng', '1.6.16'), ] -osdependencies = [('libopenssl-devel')] - -buildopts = 'LINKCC="$CC -dynamic"' +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # order is important! # package versions updated Mar 1st 2016 exts_list = [ ('setuptools', '20.2.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '8.0.3', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.7', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,24 +47,87 @@ exts_list = [ }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), ('Cython', '0.23.4', { 'source_urls': ['http://www.cython.org/release/'], }), ('six', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), - ('virtualenv', '14.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), - ('matplotlib', '1.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), ] -- GitLab From 56deacea6672aab9c732fee0e9246bdc39b0b932 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 3 Mar 2016 09:34:25 +0100 Subject: [PATCH 0774/2133] SHLIB_EXT --- .../l/libdrm/libdrm-2.4.67-intel-2016a.eb | 4 +-- .../l/libxml2/libxml2-2.9.3-intel-2016a.eb | 29 ------------------- .../m/Mesa/Mesa-11.1.2-intel-2016a.eb | 17 +++++------ 3 files changed, 9 insertions(+), 41 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-intel-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-intel-2016a.eb index 5a91110f77..f4e9adac9a 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-intel-2016a.eb @@ -20,8 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb deleted file mode 100644 index b762d96901..0000000000 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxml2' -version = '2.9.3' - -homepage = 'http://xmlsoft.org/' -description = """Libxml2 is the XML C parser and -toolchain developed for the Gnome project - (but usable outside of the Gnome platform).""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True} - -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] - -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - -dependencies = [('zlib', '1.2.8')] - -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 9f80ae7c43..7d84452191 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -45,8 +45,9 @@ dependencies = [ #osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' @@ -55,14 +56,10 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { - 'files': ['lib/libGL.so', 'lib/libOSMesa.so', - 'lib/libGLESv1_CM.so', 'lib/libGLESv2.so', - 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GLES/gl.h', 'include/GLES2/gl2.h', - 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } -- GitLab From 2c44567470e8aef1bb2abfe26c78758d2fb2951c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 3 Mar 2016 09:57:28 +0100 Subject: [PATCH 0775/2133] {lang}[intel-2016a] Python 2.7.11 with libX11 1.6.3 (REVIEW) --- .../Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 139 ++++++++++++++++++ 1 file changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb new file mode 100644 index 0000000000..00997213ad --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -0,0 +1,139 @@ +name = 'Python' +version = '2.7.11' + +libx11 = 'libX11' +libxver = '1.6.3' +versionsuffix = '-%s-%s' % (libx11, libxver) + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + (libx11, libxver), + ('Tk', '8.6.4', versionsuffix), + ('GMP', '6.1.0'), + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%s-sse42.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), +] + +moduleclass = 'lang' -- GitLab From ec0b5b1c54f6a5f9605d3560f78932c745b24002 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 3 Mar 2016 09:59:58 +0100 Subject: [PATCH 0776/2133] " corrected --- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 7d84452191..3ee16e73ea 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -45,7 +45,7 @@ dependencies = [ #osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" configopts += " --with-osmesa-bits=32 --enable-texture-float " -- GitLab From 3f371ecc086c53fec4de195d9aa8e8bf79a5ea9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 11:51:56 +0100 Subject: [PATCH 0777/2133] bump deps: ROOT v5.34.34, Mesa 11.1.2 (cfr. #2610), Python 2.7.11, CLHEP 2.3.1.1, Geant 9.6.p04 --- .../Autotools-20150119-intel-2016a.eb | 17 --- .../b/Bison/Bison-3.0.2-intel-2016a.eb | 22 ---- .../c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb | 20 --- ...-2016a.eb => CLHEP-2.3.1.1-intel-2016a.eb} | 7 +- .../e/eudev/eudev-3.0-intel-2016a.eb | 33 ----- ... => GATE-6.2-intel-2016a-Python-2.7.11.eb} | 7 +- ... => GATE-7.1-intel-2016a-Python-2.7.11.eb} | 7 +- .../easyconfigs/g/GSL/GSL-1.15-intel-2016a.eb | 18 --- .../g/Geant4/Geant4-9.5.p01-intel-2016a.eb | 24 ---- .../g/Geant4/Geant4-9.6.p04-intel-2016a.eb | 2 +- .../LLVM-3.6.2-intel-2016a-Python-2.7.9.eb | 38 ------ .../libX11-1.6.3-intel-2016a-Python-2.7.9.eb | 37 ------ .../libXft-2.3.2-intel-2016a-libX11-1.6.3.eb | 2 +- .../libXrender-0.9.9-intel-2016a.eb | 2 +- .../l/libdrm/libdrm-2.4.59-intel-2016a.eb | 25 ---- .../libpciaccess-0.13.1-intel-2016a.eb | 26 ---- .../libreadline-6.2-intel-2016a.eb | 30 ----- .../l/libtool/libtool-2.4.5-intel-2016a.eb | 17 --- .../libxml2-2.8.0-intel-2016a-Python-2.7.3.eb | 33 ----- .../libxml2-2.9.2-intel-2016a-Python-2.7.9.eb | 28 ----- .../Mesa-10.4.5-intel-2016a-Python-2.7.9.eb | 75 ----------- .../n/ncurses/ncurses-5.9-intel-2016a.eb | 36 ------ .../p/PCRE/PCRE-8.36-intel-2016a.eb | 18 --- .../p/Python/Python-2.7.3-intel-2016a.eb | 89 ------------- .../p/Python/Python-2.7.9-intel-2016a.eb | 117 ------------------ .../pkg-config/pkg-config-0.28-intel-2016a.eb | 27 ---- .../r/ROOT/ROOT-v5.34.01-intel-2016a.eb | 39 ------ ...OOT-v5.34.34-intel-2016a-Python-2.7.11.eb} | 14 +-- .../s/SQLite/SQLite-3.8.8.1-intel-2016a.eb | 38 ------ .../t/Tcl/Tcl-8.6.3-intel-2016a.eb | 25 ---- .../t/Tk/Tk-8.6.3-intel-2016a-no-X11.eb | 24 ---- ...xcb-proto-1.11-intel-2016a-Python-2.7.9.eb | 27 ---- .../xorg-macros-1.17-intel-2016a.eb | 22 ---- .../x/xproto/xproto-7.0.27-intel-2016a.eb | 24 ---- 34 files changed, 19 insertions(+), 951 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb rename easybuild/easyconfigs/c/CLHEP/{CLHEP-2.1.3.1-intel-2016a.eb => CLHEP-2.3.1.1-intel-2016a.eb} (85%) delete mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2016a.eb rename easybuild/easyconfigs/g/GATE/{GATE-6.2-intel-2016a.eb => GATE-6.2-intel-2016a-Python-2.7.11.eb} (87%) rename easybuild/easyconfigs/g/GATE/{GATE-7.0-intel-2016a.eb => GATE-7.1-intel-2016a-Python-2.7.11.eb} (87%) delete mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2016a-Python-2.7.3.eb delete mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2016a-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2016a-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2016a.eb rename easybuild/easyconfigs/r/ROOT/{ROOT-v5.34.26-intel-2016a.eb => ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb} (90%) delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2016a-no-X11.eb delete mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2016a.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2016a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2016a.eb deleted file mode 100644 index 8d512386b5..0000000000 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2016a.eb +++ /dev/null @@ -1,17 +0,0 @@ -easyblock = 'Bundle' - -name = 'Autotools' -version = '20150119' # date of the most recent change - -homepage = 'http://autotools.io' -description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.5'), # 20150119 -] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2016a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2016a.eb deleted file mode 100644 index 4fdbf98d8f..0000000000 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2016a.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.0.2' - -homepage = 'http://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [('M4', '1.4.17')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb deleted file mode 100644 index ceed3e9cd3..0000000000 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CLHEP' -version = '2.1.1.0' - -homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' -description = """The CLHEP project is intended to be a set of HEP-specific foundation and - utility classes such as random generators, physics vectors, geometry and linear algebra. - CLHEP is structured in a set of packages independent of any external package.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TGZ] -source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] - -# CLHEP compiles with icc instead of icpc -configopts = 'CXX="$CC" CXXFLAGS="$CXXFLAGS -gcc"' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb similarity index 85% rename from easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb rename to easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb index 42f08bd8d9..cf3607f24f 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb @@ -1,24 +1,21 @@ easyblock = 'CMakeMake' name = 'CLHEP' -version = '2.1.3.1' +version = '2.3.1.1' homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' description = """The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package.""" - toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] -builddependencies = [('CMake', '3.1.3')] +builddependencies = [('CMake', '3.4.3')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' - moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2016a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2016a.eb deleted file mode 100644 index 246e9d0730..0000000000 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2016a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'eudev' -version = '3.0' - -homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' -description = """eudev is a fork of systemd-udev with the goal of obtaining - better compatibility with existing software such as - OpenRC and Upstart, older kernels, various toolchains - and anything else required by users and various distributions.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'cstd': 'c99'} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] -patches = ['%(name)s-%(version)s_pre-2.6.34_kernel.patch'] - -builddependencies = [ - ('gperf', '3.0.4'), -] - -osdependencies = [('kernel-headers', 'linux-libc-dev')] - -configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' -runtest = 'check' - -sanity_check_paths = { - 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], - 'dirs': [], -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb similarity index 87% rename from easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb rename to easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb index 389d60bab7..c48ea46984 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'GATE' version = '6.2' +versionsuffix = '-Python-2.7.11' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and @@ -17,9 +18,9 @@ patches = [ ] dependencies = [ - ('Geant4', '9.5.p01'), - ('CLHEP', '2.1.1.0'), - ('ROOT', 'v5.34.01'), + ('Geant4', '9.6.p04'), + ('CLHEP', '2.3.1.1'), + ('ROOT', 'v5.34.34', versionsuffix), ] builddependencies = [('CMake', '3.4.3')] diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb similarity index 87% rename from easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb rename to easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb index 7d392aa8b1..6e9809e000 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'GATE' -version = '7.0' +version = '7.1' +versionsuffix = '-Python-2.7.11' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and @@ -18,8 +19,8 @@ patches = [ dependencies = [ ('Geant4', '9.6.p04'), - ('CLHEP', '2.1.3.1'), - ('ROOT', 'v5.34.26'), + ('CLHEP', '2.3.1.1'), + ('ROOT', 'v5.34.34', versionsuffix), ] builddependencies = [ ('CMake', '3.4.3'), diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2016a.eb deleted file mode 100644 index 714d2f9de8..0000000000 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2016a.eb +++ /dev/null @@ -1,18 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -homepage = 'http://www.gnu.org/software/gsl/' -description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb deleted file mode 100644 index a4c1b85fa8..0000000000 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2016a.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'Geant4' -version = '9.5.p01' - -homepage = 'http://geant4.cern.ch/' -description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. - Its areas of application include high energy, nuclear and accelerator physics, - as well as studies in medical and space science.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://geant4.cern.ch/support/source'] -sources = ['%(namelower)s.%(version)s.tar.gz'] - -dependencies = [ - ('expat', '2.1.0'), - ('CLHEP', '2.1.1.0'), -] - -builddependencies = [('CMake', '3.4.3')] - -configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb index 8fa06aa9f5..356c780edf 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb @@ -13,7 +13,7 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), - ('CLHEP', '2.1.3.1'), + ('CLHEP', '2.3.1.1'), ] builddependencies = [ ('CMake', '3.4.3'), diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb deleted file mode 100644 index e4b5b40821..0000000000 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2016a-Python-2.7.9.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'LLVM' -version = '3.6.2' -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) - -homepage = "http://llvm.org/" -description = """The LLVM Core libraries provide a modern source- and target-independent - optimizer, along with code generation support for many popular CPUs - (as well as some less common ones!) These libraries are built around a well - specified code representation known as the LLVM intermediate representation - ("LLVM IR"). The LLVM Core libraries are well documented, and it is - particularly easy to invent your own language (or port an existing compiler) - to use LLVM as an optimizer and code generator.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'cstd': 'gnu++11'} - -source_urls = ["http://llvm.org/releases/%(version)s"] -sources = ["llvm-%(version)s.src.tar.xz"] - -builddependencies = [ - ('CMake', '3.4.3'), - (python, pyver), -] - -configopts = '-DBUILD_SHARED_LIBS=ON ' - -sanity_check_paths = { - 'files': ['bin/llvm-ar'], - 'dirs': ['include/llvm', 'include/llvm-c'], -} - -separate_build_dir = True - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a-Python-2.7.9.eb deleted file mode 100644 index 060a6e35d0..0000000000 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a-Python-2.7.9.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libX11' -version = '1.6.3' -versionsuffix = '-Python-2.7.9' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = """X11 client-side library""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = [SOURCE_TAR_GZ] -source_urls = [XORG_LIB_SOURCE] - -builddependencies = [ - ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', versionsuffix), - ('inputproto', '2.3.1'), - ('xproto', '7.0.27'), - ('kbproto', '1.0.6'), -] - -dependencies = [ - ('libxcb', '1.11', versionsuffix), - ('xtrans', '1.3.5'), -] - -sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] - ], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb index ab04e0520c..95e636b60d 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb @@ -20,7 +20,7 @@ libx11ver = '1.6.3' versionsuffix = '-libX11-%s' % libx11ver dependencies = [ - ('libX11', libx11ver, '-Python-2.7.9'), + ('libX11', libx11ver), ('libXrender', '0.9.9'), ('freetype', '2.5.5'), ('fontconfig', '2.11.93'), diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb index 06b460f5f2..fefc99f4eb 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ] dependencies = [ - ('libX11', '1.6.3', '-Python-2.7.9'), + ('libX11', '1.6.3'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2016a.eb deleted file mode 100644 index 8d7f8591ba..0000000000 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2016a.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libdrm' -version = '2.4.59' - -homepage = 'http://dri.freedesktop.org' -description = """Direct Rendering Manager runtime library.""" - -source_urls = ['http://dri.freedesktop.org/libdrm/'] -sources = [SOURCELOWER_TAR_GZ] - -toolchain = {'name': 'intel', 'version': '2016a'} - -dependencies = [ - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.1'), -] - -sanity_check_paths = { - 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, - 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], - 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2016a.eb deleted file mode 100644 index eeafddf420..0000000000 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2016a.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpciaccess' -version = '0.13.1' - -homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' -description = """Generic PCI access library.""" - -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] -sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'intel', 'version': '2016a'} - -builddependencies = [ - ('Autotools', '20150119', '', ('GCC', '4.9.2')), - ('xorg-macros', '1.17'), -] - -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - -sanity_check_paths = { - 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb deleted file mode 100644 index 3c775612ac..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2016a.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '6.2' - -homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' -description = """The GNU Readline library provides a set of functions for use by applications that - allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. - The Readline library includes additional functions to maintain a list of previously-entered command lines, - to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '6.0')] - -# for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" - -sanity_check_paths = { - 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2016a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2016a.eb deleted file mode 100644 index 4219e58cfd..0000000000 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2016a.eb +++ /dev/null @@ -1,17 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libtool' -version = '2.4.5' - -homepage = 'http://www.gnu.org/software/libtool' -description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries - behind a consistent, portable interface.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -dependencies = [('M4', '1.4.17')] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2016a-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2016a-Python-2.7.3.eb deleted file mode 100644 index d4cc4b5eb1..0000000000 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2016a-Python-2.7.3.eb +++ /dev/null @@ -1,33 +0,0 @@ -name = 'libxml2' -version = '2.8.0' - -homepage = 'http://xmlsoft.org/' -description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable - outside of the Gnome platform).""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True} - -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] - -configopts = 'CC="$CC" CXX="$CXX" --with-pic' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - -dependencies = [ - ('zlib', '1.2.8'), - ('Python', pythonver), -] - -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2016a-Python-2.7.9.eb deleted file mode 100644 index e000b25261..0000000000 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2016a-Python-2.7.9.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'libxml2' -version = '2.9.2' - -homepage = 'http://xmlsoft.org/' -description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable - outside of the Gnome platform).""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True} - -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] - -configopts = 'CC="$CC" CXX="$CXX" --with-pic' - -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - -dependencies = [ - ('zlib', '1.2.8'), - ('Python', pythonver), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2016a-Python-2.7.9.eb deleted file mode 100644 index 712aaf2f8b..0000000000 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2016a-Python-2.7.9.eb +++ /dev/null @@ -1,75 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Mesa' -version = '10.4.5' - -homepage = 'http://www.mesa3d.org/' -description = """Mesa is an open-source implementation of the OpenGL specification - - a system for rendering interactive 3D graphics.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} - -sources = ['%(name)sLib-%(version)s.tar.gz'] -source_urls = [ - 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', -] - -patches = ['Mesa-%(version)s_sse4_1.patch'] - -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - -builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.2'), - ('Automake', '1.15'), - ('makedepend', '1.0.5'), - ('kbproto', '1.0.6'), - ('xextproto', '7.3.0'), - ('xproto', '7.0.27'), - ('libtool', '2.4.5'), - ('pkg-config', '0.28'), - ('glproto', '1.4.17'), - ('M4', '1.4.17') -] - -dependencies = [ - ('Python', pythonver), - ('libxml2', '2.9.2', versionsuffix), - ('libdrm', '2.4.59'), - ('libX11', '1.6.3', versionsuffix), - ('libXext', '1.3.3'), - ('libXfixes', '5.0.1'), - ('libXdamage', '1.1.4'), - ('libXfont', '1.5.1'), - ('LLVM', '3.6.2', versionsuffix), - ('eudev', '3.0'), -] - -# Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] - -# GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --disable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl""" - -# package-config files for os dependencies are in an os specific place -#preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' - -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' - -sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/wmesa.h'], - 'dirs': [] -} - -maxparallel = 1 - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016a.eb deleted file mode 100644 index f16049293d..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016a.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['ncurses-%(version)s_configure_darwin.patch'] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2016a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2016a.eb deleted file mode 100644 index dabda6ed92..0000000000 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2016a.eb +++ /dev/null @@ -1,18 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PCRE' -version = '8.36' - -homepage = 'http://www.pcre.org/' -description = """The PCRE library is a set of functions that implement regular expression pattern matching using - the same syntax and semantics as Perl 5.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic --disable-cpp" - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb deleted file mode 100644 index 2d8bea6dd7..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2016a.eb +++ /dev/null @@ -1,89 +0,0 @@ -name = 'Python' -version = '2.7.3' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.6.1' -scipyversion = '0.10.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.2'), - ('ncurses', '6.0'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -# order is important! -exts_list = [ - ('setuptools', '0.6c11', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('mpi4py', '1.3', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('lockfile', '0.9.1', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.1', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '0.9.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '1.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.8', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.12.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb deleted file mode 100644 index 37aa3417d0..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2016a.eb +++ /dev/null @@ -1,117 +0,0 @@ -name = 'Python' -version = '2.7.9' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.9.1' -scipyversion = '0.14.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '6.0'), - ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -# order is important! -# package versions updated Jan 19th 2015 -exts_list = [ - ('setuptools', '11.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': ['numpy-1.8.0-mkl.patch'], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('pbr', '0.10.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.4.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.13', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('mock', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2014.10', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2016a.eb deleted file mode 100644 index 9a712cb3b4..0000000000 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2016a.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pkg-config' -version = '0.28' - -homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' -description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the - correct compiler options on the command line so an application can use - gcc -o test test.c `pkg-config --libs --cflags glib-2.0` - for instance, rather than hard-coding values on where to find glib (or other libraries).""" - -# don't use PAX, it might break. -tar_config_opts = True - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] - -configopts = " --with-internal-glib" - -sanity_check_paths = { - 'files': ['bin/pkg-config'], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2016a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2016a.eb deleted file mode 100644 index a76d8e6f3c..0000000000 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2016a.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'ROOT' -version = 'v5.34.01' - -homepage = 'http://root.cern.ch/drupal/' -description = """The ROOT system provides a set of OO frameworks with all the functionality - needed to handle and analyze large amounts of data in a very efficient way.""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True} - -sources = ['%s_%s.source.tar.gz' % (name.lower(), version)] -source_urls = ['ftp://root.cern.ch/root/'] -patches = [ - 'configure_FftwFromMkl_28.patch', - 'ROOT-%(version)s_recent-ifort.patch', -] - -python = 'Python' -pyver = '2.7.3' - -dependencies = [ - ('GSL', '1.15'), - ('libxml2', '2.8.0', '-%s-%s' % (python, pyver)), - (python, pyver), -] - -# architecture -arch = 'linuxx8664icc' - -# disable features -configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' -# enable features -configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' -configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' -configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' -configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' -configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2016a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb similarity index 90% rename from easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2016a.eb rename to easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index face3c9641..01dbe6c33b 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2016a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'ROOT' -version = 'v5.34.26' +version = 'v5.34.34' +versionsuffix = '-Python-2.7.11' homepage = 'http://root.cern.ch/drupal/' description = """The ROOT system provides a set of OO frameworks with all the functionality @@ -16,17 +17,14 @@ patches = [ 'ROOT-v5.34.26_libX.patch', ] -python = 'Python' -pyver = '2.7.9' - dependencies = [ ('GSL', '1.16'), - ('Mesa', '10.4.5', '-%s-%s' % (python, pyver)), - ('libxml2', '2.9.2', '-%s-%s' % (python, pyver)), - ('PCRE', '8.36'), + ('Mesa', '11.1.2'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), ('CFITSIO', '3.37'), ('freetype', '2.5.5'), - (python, pyver), + ('Python', '2.7.11'), ('zlib', '1.2.8'), ('libXft', '2.3.2', '-libX11-1.6.3'), ('libXpm', '3.5.11'), diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2016a.eb deleted file mode 100644 index 4421de3277..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2016a.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -easyblock = 'ConfigureMake' - -name = 'SQLite' -version = '3.8.8.1' - -homepage = 'http://www.sqlite.org/' -description = 'SQLite: SQL Database Engine in a C Library' - -toolchain = {'name': 'intel', 'version': '2016a'} - -# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz -source_urls = ['http://www.sqlite.org/2015/'] -version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) -sources = ['sqlite-autoconf-%s.tar.gz' % version_str] - -dependencies = [ - ('libreadline', '6.3'), - ('Tcl', '8.6.3'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2016a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2016a.eb deleted file mode 100644 index e368b2b5ef..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2016a.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.3' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2016a-no-X11.eb deleted file mode 100644 index c673514d37..0000000000 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2016a-no-X11.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tk' -version = '8.6.3' -versionsuffix = '-no-X11' - -homepage = 'http://www.tcl.tk/' -description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building - a graphical user interface (GUI) in many different programming languages.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('Tcl', version), -] - -configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' - -start_dir = 'unix' - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb deleted file mode 100644 index 7cbfd9e916..0000000000 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2016a-Python-2.7.9.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xcb-proto' -version = '1.11' - -homepage = 'http://xcb.freedesktop.org/' -description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, -latency hiding, direct access to the protocol, improved threading support, and extensibility.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://xcb.freedesktop.org/dist/'] -sources = [SOURCELOWER_TAR_GZ] - -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) -dependencies = [(python, pyver)] - -pyshortver = '.'.join(pyver.split('.')[0:2]) - -sanity_check_paths = { - 'files': ['lib/pkgconfig/xcb-proto.pc'], - 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2016a.eb deleted file mode 100644 index f26da7ae49..0000000000 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2016a.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xorg-macros' -version = '1.17' - -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' -description = """X.org macros utilities.""" -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! -sources = ['util-macros-%(version)s.tar.gz'] - -dependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] - -preconfigopts = './autogen.sh && ' - -sanity_check_paths = { - 'files': ['share/pkgconfig/xorg-macros.pc'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2016a.eb deleted file mode 100644 index 2f1b41c474..0000000000 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2016a.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xproto' -version = '7.0.27' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] - -sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs': [] -} - -moduleclass = 'devel' -- GitLab From 6cefbee52b4720471811de4119587e039c1b11b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 11:58:29 +0100 Subject: [PATCH 0778/2133] remove unused easyconfigs --- .../g/glproto/glproto-1.4.17-intel-2016a.eb | 20 ----------- .../k/kbproto/kbproto-1.0.6-intel-2016a.eb | 19 ----------- .../libXft-2.3.2-intel-2016a-libX11-1.6.3.eb | 2 +- .../libxcb-1.11-intel-2016a-Python-2.7.9.eb | 34 ------------------- .../makedepend-1.0.5-intel-2016a.eb | 20 ----------- 5 files changed, 1 insertion(+), 94 deletions(-) delete mode 100644 easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2016a-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb deleted file mode 100644 index c26a1ac08a..0000000000 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'glproto' -version = '1.4.17' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] - -sanity_check_paths = { - 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2016a.eb deleted file mode 100644 index 3a33382528..0000000000 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2016a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'kbproto' -version = '1.0.6' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = """X.org KBProto protocol headers.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] - -sanity_check_paths = { - 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb index 95e636b60d..5072a7bef7 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb @@ -12,7 +12,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ - ('kbproto', '1.0.6'), + ('kbproto', '1.0.7'), ('renderproto', '0.11'), ] diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2016a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2016a-Python-2.7.9.eb deleted file mode 100644 index 4279354d1f..0000000000 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2016a-Python-2.7.9.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxcb' -version = '1.11' - -homepage = 'http://xcb.freedesktop.org/' -description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, -latency hiding, direct access to the protocol, improved threading support, and extensibility.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://xcb.freedesktop.org/dist/'] -sources = [SOURCELOWER_TAR_GZ] - -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('xcb-proto', '1.11', versionsuffix), - ('libXau', '1.0.8'), - ('libpthread-stubs', '0.3'), -] - -sanity_check_paths = { - 'files': ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], - 'dirs': ['include/xcb', 'lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb deleted file mode 100644 index 1158bd68be..0000000000 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'makedepend' -version = '1.0.5' - -homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] - -sanity_check_paths = { - 'files': ['bin/makedepend'], - 'dirs': [], -} - -moduleclass = 'devel' -- GitLab From 2d9daae084f24546174edd296d33a348427d0e5b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 12:07:34 +0100 Subject: [PATCH 0779/2133] bump fontconfig/freetype/gettext dep versions --- .../fontconfig-2.11.93-intel-2016a.eb | 22 ------------------- .../f/freetype/freetype-2.5.5-intel-2016a.eb | 21 ------------------ .../g/gettext/gettext-0.19.4-intel-2016a.eb | 18 --------------- .../libXft-2.3.2-intel-2016a-libX11-1.6.3.eb | 4 ++-- .../l/libXpm/libXpm-3.5.11-intel-2016a.eb | 2 +- .../l/libpng/libpng-1.6.16-intel-2016a.eb | 19 ---------------- ...ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 2 +- 7 files changed, 4 insertions(+), 84 deletions(-) delete mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2016a.eb deleted file mode 100644 index f906761e9b..0000000000 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2016a.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = "fontconfig" -version = '2.11.93' - -homepage = 'http://www.freedesktop.org/software/fontconfig' -description = """Fontconfig is a library designed to provide system-wide font configuration, customization and -application access.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('expat', '2.1.0'), - ('freetype', '2.5.5'), -] - -configopts = '--disable-docs ' - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2016a.eb deleted file mode 100644 index 35f4da2da2..0000000000 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2016a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'freetype' -version = '2.5.5' - -homepage = 'http://freetype.org' -description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and - portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display - servers, font conversion tools, text image generation tools, and many other products as well.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = [GNU_SAVANNAH_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [('libpng', '1.6.16')] - -sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], - 'dirs': ['include/freetype2'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2016a.eb deleted file mode 100644 index 069f899a71..0000000000 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2016a.eb +++ /dev/null @@ -1,18 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gettext' -version = '0.19.4' - -homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may -build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools -and documentation""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = [SOURCE_TAR_GZ] -source_urls = [GNU_SOURCE] - -configopts = '--without-emacs' - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb index 5072a7bef7..d4214779d1 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb @@ -22,8 +22,8 @@ versionsuffix = '-libX11-%s' % libx11ver dependencies = [ ('libX11', libx11ver), ('libXrender', '0.9.9'), - ('freetype', '2.5.5'), - ('fontconfig', '2.11.93'), + ('freetype', '2.6.2'), + ('fontconfig', '2.11.94'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb index 39b2ff6653..80b08e7922 100644 --- a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] -builddependencies = [('gettext', '0.19.4', '', ('GCC', '4.9.2'))] +builddependencies = [('gettext', '0.19.6')] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.%s' % SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2016a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2016a.eb deleted file mode 100644 index d9a7ed9527..0000000000 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2016a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpng' -version = '1.6.16' - -homepage = 'http://www.libpng.org/pub/png/libpng.html' -description = "libpng is the official PNG reference library" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('zlib', '1.2.8')] - -configopts = "--with-pic" - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index 01dbe6c33b..f600e1e7a8 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ dependencies = [ ('libxml2', '2.9.3'), ('PCRE', '8.38'), ('CFITSIO', '3.37'), - ('freetype', '2.5.5'), + ('freetype', '2.6.2'), ('Python', '2.7.11'), ('zlib', '1.2.8'), ('libXft', '2.3.2', '-libX11-1.6.3'), -- GitLab From 3c8e1178fa4b5b96293742cef97702bb71b63fac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 13:11:03 +0200 Subject: [PATCH 0780/2133] add easyconfig libXft-2.3.2-intel-2016a-libX11-1.6.3.eb, add easyconfig libXpm-3.5.11-intel-2016a.eb, add easyconfig libXrender-0.9.9-intel-2016a.eb, add easyconfig renderproto-0.11-intel-2016a.eb --- .../libXft-2.3.2-intel-2016a-libX11-1.6.3.eb | 34 +++++++++++++++++++ .../l/libXpm/libXpm-3.5.11-intel-2016a.eb | 22 ++++++++++++ .../libXrender-0.9.9-intel-2016a.eb | 28 +++++++++++++++ .../renderproto-0.11-intel-2016a.eb | 20 +++++++++++ 4 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb new file mode 100644 index 0000000000..95e636b60d --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.6'), + ('renderproto', '0.11'), +] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver + +dependencies = [ + ('libX11', libx11ver), + ('libXrender', '0.9.9'), + ('freetype', '2.5.5'), + ('fontconfig', '2.11.93'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb new file mode 100644 index 0000000000..39b2ff6653 --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libXpm' +version = '3.5.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [('gettext', '0.19.4', '', ('GCC', '4.9.2'))] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb new file mode 100644 index 0000000000..fefc99f4eb --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb new file mode 100644 index 0000000000..37b516e535 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 2bff6a516cf9fc7130c0bdc2b37bf9647d67d494 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 13:16:16 +0200 Subject: [PATCH 0781/2133] fix dep versions --- .../l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb | 6 +++--- easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb index 95e636b60d..d4214779d1 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb @@ -12,7 +12,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ - ('kbproto', '1.0.6'), + ('kbproto', '1.0.7'), ('renderproto', '0.11'), ] @@ -22,8 +22,8 @@ versionsuffix = '-libX11-%s' % libx11ver dependencies = [ ('libX11', libx11ver), ('libXrender', '0.9.9'), - ('freetype', '2.5.5'), - ('fontconfig', '2.11.93'), + ('freetype', '2.6.2'), + ('fontconfig', '2.11.94'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb index 39b2ff6653..80b08e7922 100644 --- a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] -builddependencies = [('gettext', '0.19.4', '', ('GCC', '4.9.2'))] +builddependencies = [('gettext', '0.19.6')] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.%s' % SHLIB_EXT]], -- GitLab From 6a6a05bbb3e3c49da360c9e3ddde31093092e6cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 12:43:25 +0100 Subject: [PATCH 0782/2133] drop versionsuffix for libXft as ROOT dep --- .../libXft-2.3.2-intel-2016a-libX11-1.6.3.eb | 34 ------------------- ...ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 1 insertion(+), 35 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb deleted file mode 100644 index d4214779d1..0000000000 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libXft' -version = '2.3.2' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = """X11 client-side library""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = [SOURCE_TAR_GZ] -source_urls = [XORG_LIB_SOURCE] - -builddependencies = [ - ('kbproto', '1.0.7'), - ('renderproto', '0.11'), -] - -libx11ver = '1.6.3' -versionsuffix = '-libX11-%s' % libx11ver - -dependencies = [ - ('libX11', libx11ver), - ('libXrender', '0.9.9'), - ('freetype', '2.6.2'), - ('fontconfig', '2.11.94'), -] - -sanity_check_paths = { - 'files': ['lib/libXft.a'], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index f600e1e7a8..d82a30d946 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -26,7 +26,7 @@ dependencies = [ ('freetype', '2.6.2'), ('Python', '2.7.11'), ('zlib', '1.2.8'), - ('libXft', '2.3.2', '-libX11-1.6.3'), + ('libXft', '2.3.2'), ('libXpm', '3.5.11'), ('libXext', '1.3.3'), ] -- GitLab From 7e83e512599ebcacbce927c0f32a9994c6b5c50d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 12:50:37 +0100 Subject: [PATCH 0783/2133] drop libXft easyconfig with versionsuffix --- .../libXft-2.3.2-intel-2016a-libX11-1.6.3.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb deleted file mode 100644 index d4214779d1..0000000000 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-libX11-1.6.3.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libXft' -version = '2.3.2' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = """X11 client-side library""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = [SOURCE_TAR_GZ] -source_urls = [XORG_LIB_SOURCE] - -builddependencies = [ - ('kbproto', '1.0.7'), - ('renderproto', '0.11'), -] - -libx11ver = '1.6.3' -versionsuffix = '-libX11-%s' % libx11ver - -dependencies = [ - ('libX11', libx11ver), - ('libXrender', '0.9.9'), - ('freetype', '2.6.2'), - ('fontconfig', '2.11.94'), -] - -sanity_check_paths = { - 'files': ['lib/libXft.a'], - 'dirs': [], -} - -moduleclass = 'vis' -- GitLab From 3aa50aba64564f13fe8b44feaa7997cfaf646e17 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 13:49:57 +0100 Subject: [PATCH 0784/2133] bump to latest CFITSIO version --- ...{CFITSIO-3.37-intel-2016a.eb => CFITSIO-3.38-intel-2016a.eb} | 2 +- .../r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/CFITSIO/{CFITSIO-3.37-intel-2016a.eb => CFITSIO-3.38-intel-2016a.eb} (97%) diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2016a.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb similarity index 97% rename from easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2016a.eb rename to easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb index 7af022d137..6291c97147 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'CFITSIO' -version = '3.37' +version = '3.38' homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index d82a30d946..fa81ad980b 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ ('Mesa', '11.1.2'), ('libxml2', '2.9.3'), ('PCRE', '8.38'), - ('CFITSIO', '3.37'), + ('CFITSIO', '3.38'), ('freetype', '2.6.2'), ('Python', '2.7.11'), ('zlib', '1.2.8'), -- GitLab From cadbf9619dacee2b0df04dc31a4712631e483c00 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 3 Mar 2016 13:57:19 +0100 Subject: [PATCH 0785/2133] Use directly '--with-mpe' configopt for MVAPICH2 1.7 instead of to-be-removed 'withmpe' from MVAPICH2 EB --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index cee59253ac..8208f0a521 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -15,7 +15,7 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] rdma_type = "gen2" # 'gen2' or 'udapl' # enable building of MPE routines -withmpe = True +configopts = '--with-mpe ' # enable hwloc support withhwloc = True diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb index 22a7f9f02e..429ab72ae0 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb @@ -16,7 +16,7 @@ builddependencies = [('Bison', '2.5')] rdma_type = "gen2" # 'gen2' or 'udapl' # enable building of MPE routines -withmpe = True +configopts = '--with-mpe ' # parallel build tends to fail parallel = 1 -- GitLab From 6db12d99703e23e76336abbe58be66dee5b71902 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 3 Mar 2016 13:57:41 +0100 Subject: [PATCH 0786/2133] Use directly '--with-hwloc' configopt for MVAPICH2 1.7 instead of to-be-removed 'withhwloc' from MVAPICH2 EB --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 8208f0a521..7f3c50d87a 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -18,7 +18,7 @@ rdma_type = "gen2" # 'gen2' or 'udapl' configopts = '--with-mpe ' # enable hwloc support -withhwloc = True +configopts += '--with-hwloc ' dependencies = [('hwloc', '1.5.1')] # enable checkpointing support -- GitLab From 0f56d11a401e34e1a91890dee825e1da94a1c984 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 3 Mar 2016 14:08:23 +0100 Subject: [PATCH 0787/2133] Remove option rdma_type = "gen2" because it is actually the default This makes this EasyConfig files more uniform with the recent ones --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 -- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 7f3c50d87a..137b9059fe 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -12,8 +12,6 @@ sources = [SOURCELOWER_TGZ] # note: this URL will only work for the most recent version (previous versions no longer available?) source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] -rdma_type = "gen2" # 'gen2' or 'udapl' - # enable building of MPE routines configopts = '--with-mpe ' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb index 429ab72ae0..4c2eead91f 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb @@ -13,8 +13,6 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] builddependencies = [('Bison', '2.5')] -rdma_type = "gen2" # 'gen2' or 'udapl' - # enable building of MPE routines configopts = '--with-mpe ' -- GitLab From d2e3b5810c31a9d9e155587647dc3459588f9df4 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 3 Mar 2016 14:11:07 +0100 Subject: [PATCH 0788/2133] Add checksum if known --- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb | 3 +++ .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb | 3 +++ .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb | 3 +++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb | 3 +++ .../m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb | 3 +++ 5 files changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb index 9be4dedbf3..dbf130a107 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb @@ -9,6 +9,9 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['ef4ae05e3b5ad485326505db7381246c'] + builddependencies = [('Bison', '2.7')] # parallel build doesn't work diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb index 6d98d3a032..f8ed601fa4 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb @@ -9,6 +9,9 @@ toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['5dc58ed08fd3142c260b70fe297e127c'] + dependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb index e1fdfb364f..ec3097f101 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb @@ -9,6 +9,9 @@ toolchain = {'name': 'ClangGCC', 'version': '1.2.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['5dc58ed08fd3142c260b70fe297e127c'] + dependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb index 602d1c4c80..fc82223d21 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb @@ -9,6 +9,9 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['5dc58ed08fd3142c260b70fe297e127c'] + builddependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb index f87ce5fafe..2ff528acce 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb @@ -10,6 +10,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['5dc58ed08fd3142c260b70fe297e127c'] + builddependencies = [('Bison', '2.7')] # the hydra launcher start's before LD_LIBRARY_PATH is forwarded, so we provide this hint on where to find some libs -- GitLab From b925fbf66d62634be351293cb92ed5b4283979af Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 3 Mar 2016 14:50:49 +0100 Subject: [PATCH 0789/2133] {lang}[intel-2016a] R 3.2.3 with libX11 1.6.3 (WIP) --- .../cairo-1.14.6-intel-2016a-libX11-1.6.3.eb | 56 +++ .../GDAL-2.0.2-intel-2016a-libX11-1.6.3.eb | 30 ++ .../GLib-2.47.5-intel-2016a-libX11-1.6.3.eb | 39 ++ ...-intel-2016a-Python-2.7.11-libX11-1.6.3.eb | 29 ++ .../r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 453 ++++++++++++++++++ 5 files changed, 607 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-libX11-1.6.3.eb new file mode 100644 index 0000000000..6db4212fb3 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-libX11-1.6.3.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +libx11 = 'libX11' +libxver = '1.6.3' +versionsuffix = '-%s-%s' % (libx11, libxver) + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +glibver = '2.47.5' + +builddependencies = [ + ('renderproto', '0.11'), +] + +dependencies = [ + (libx11, libxver), + ('libXrender', '0.9.9'), + ('libdrm', '2.4.67'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), + ('GLib', glibver, versionsuffix), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a-libX11-1.6.3.eb new file mode 100644 index 0000000000..78e94ccbb6 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a-libX11-1.6.3.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.2' +versionsuffix = '-libX11-1.6.3' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.3.3.1'), + ('expat', '2.1.0'), + ('libxml2', '2.9.3', '-Python-2.7.11%s' % versionsuffix), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb new file mode 100644 index 0000000000..a93ed50f9f --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +versionsuffix = '-libX11-1.6.3' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +pysuffix = '-Python-%s%s' % (pyver, versionsuffix) + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3', pysuffix), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', pyver)] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11-libX11-1.6.3.eb new file mode 100644 index 0000000000..230d903622 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11-libX11-1.6.3.eb @@ -0,0 +1,29 @@ +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +libx11suffix = '-libX11-1.6.3' +versionsuffix = '-Python-%s%s' % (pyver, libx11suffix) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pyver, libx11suffix), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb new file mode 100644 index 0000000000..e0608b0939 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -0,0 +1,453 @@ +name = 'R' +version = '3.2.3' + +libx11 = 'libX11' +libxver = '1.6.3' +versionsuffix = '-%s-%s' % (libx11, libxver) + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib" +#Actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + (libx11, libxver), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('libpng', '1.6.21'), # for plotting in R + ('libjpeg-turbo', '1.4.2'), # for plottting in R + ('LibTIFF', '4.0.6'), # for plotting in R + ('cairo', '1.14.6', versionsuffix), # for plotting in R + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', versionsuffix), # for tcltk + ('cURL', '7.47.0'), # for RCurl + ('libxml2', '2.9.3', '-Python-2.7.11%s' % versionsuffix), # for XML + ('GDAL', '2.0.2', versionsuffix), # for rgdal + ('PROJ', '4.9.2'), # for rgdal +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 21st 2016 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.3', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.9', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2.1', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5.1', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-22', ext_options), + ('mime', '0.4', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.1', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.7-0', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-3', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.60.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('checkmate', '1.6.3', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-4', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.1', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.0.2', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.3-0', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringi', '1.0-1', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.8', ext_options), + ('logspline', '2.1.8', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.6-1', ext_options), + ('randomForest', '4.6-12', ext_options), + ('scatterplot3d', '0.3-36', ext_options), + ('SparseM', '1.7', ext_options), + ('tripack', '1.3-7', ext_options), + ('irace', '1.07', ext_options), + ('rJava', '0.9-7', ext_options), + ('lattice', '0.20-33', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-3', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.12.2', ext_options), + ('RcppArmadillo', '0.6.400.2.2', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.3', ext_options), + ('rlecuyer', '0.3-4', ext_options), + ('snow', '0.4-1', ext_options), + ('MASS', '7.3-45', ext_options), + ('tree', '1.0-36', ext_options), + ('pls', '2.5-0', ext_options), + ('class', '7.3-14', ext_options), + ('e1071', '1.6-7', ext_options), + ('nnet', '7.3-11', ext_options), + ('nlme', '3.1-122', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.5.1', ext_options), + ('MatrixModels', '0.4-1', ext_options), + ('quantreg', '5.19', ext_options), + ('mgcv', '1.8-10', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-5', ext_options), + ('sp', '1.2-1', ext_options), + ('zoo', '1.7-12', ext_options), + ('lmtest', '0.9-34', ext_options), + ('vcd', '1.4-1', ext_options), + ('snowfall', '1.84-6.1', ext_options), + ('rpart', '4.1-10', ext_options), + ('survival', '2.38-3', ext_options), + ('mice', '2.25', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + 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ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-1', ext_options), + ('rms', '4.4-1', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6-2', ext_options), + ('TraMineR', '1.8-11', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-5', ext_options), + ('statmod', '1.4.23', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.3-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('optparse', '1.3.2', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '1.0.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.50.1', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-10', ext_options), + ('pbkrtest', '0.4-4', ext_options), + ('car', '2.1-1', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.31.4', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-10', ext_options), + ('BiasedUrn', '1.07', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '1.1', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.9.1', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.1.3', ext_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('VennDiagram', '1.6.16', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-2', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.8-37', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.44-1', ext_options), + ('rgdal', '1.1-3', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.8.8', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-4', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), + ('SuperLearner', '2.0-15', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('caret', '6.0-64', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.6', ext_options), + ('ggvis', '0.4.2', ext_options), + ('mlr', '2.7', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-7', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.10', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.2', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.4.0', ext_options), + ('roxygen2', '5.0.1', ext_options), + ('git2r', '0.13.1', ext_options), + ('xml2', '0.1.2', ext_options), + ('rversions', '1.0.2', ext_options), + ('devtools', '1.9.1', ext_options), + ('Rook', '1.1-1', ext_options), + ('rjson', '0.2.15', ext_options), + ('Cairo', '1.5-9', ext_options), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.1-6', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-7', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-9', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), + ('ks', '1.10.1', ext_options), + ('logcondens', '2.1.4', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-45', ext_options), + ('coin', '1.1-2', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.0.7', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.5.8', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-20', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.8-6', ext_options), + ('mi', '1.0', ext_options), + ('htmlwidgets', '0.6', ext_options), + ('visNetwork', '0.2.1', ext_options), + ('DiagrammeR', '0.8.2', ext_options), + ('sem', '3.1-6', ext_options), + ('jpeg', '0.1-8', ext_options), + ('sna', '2.3-2', ext_options), + ('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.3.2', ext_options), + ('diveRsity', '1.9.89', ext_options), +] + +moduleclass = 'lang' -- GitLab From 2fdcbaedb5a5cfb03e132fc95142378761a1a91f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 3 Mar 2016 14:54:43 +0100 Subject: [PATCH 0790/2133] vesrionsuffix and libX11 fixes --- .../p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 00997213ad..87032c0ef5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -1,9 +1,7 @@ name = 'Python' version = '2.7.11' -libx11 = 'libX11' -libxver = '1.6.3' -versionsuffix = '-%s-%s' % (libx11, libxver) +versionsuffix = '-libX11-1.6.3' homepage = 'http://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems @@ -25,7 +23,6 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - (libx11, libxver), ('Tk', '8.6.4', versionsuffix), ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -- GitLab From c0b90b90ff6dc24a40e0d5f148dced00cd393875 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 3 Mar 2016 14:58:16 +0100 Subject: [PATCH 0791/2133] Enhanced easyconfigs that need the new psmpi.py easyblock --- .../p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 4 +-- .../psmpi-5.1.0-1-iccifort-2015.1.133.eb | 4 +-- .../p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb | 30 +++++++++++++++++++ .../p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb | 4 +-- .../psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb | 30 +++++++++++++++++++ .../psmpi-5.1.5-1-iccifort-2015.1.133.eb | 4 +-- 6 files changed, 68 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb create mode 100644 easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 34f4d57dd7..3b8d70635f 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -17,6 +17,8 @@ source_urls = [ 'https://trac.mpich.org/projects/openpa/raw-attachment/wiki/Downloads/', ] +mpich_opts = '--enable-static' + dependencies = [ ('pscom', '5.0.44-1', '', True), ] @@ -25,6 +27,4 @@ hiddendependencies = [ ('pscom', '5.0.44-1', '', True), ] -configopts = '--with-confset=gcc PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index ac08d5c585..a5c1e058f0 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -17,6 +17,8 @@ source_urls = [ 'https://trac.mpich.org/projects/openpa/attachment/wiki/Downloads', ] +mpich_opts = '--enable-static' + dependencies = [ ('pscom', '5.0.48-1', '', True), ] @@ -25,6 +27,4 @@ hiddendependencies = [ ('pscom', '5.0.48-1', '', True), ] -configopts = '--with-confset=intel PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb new file mode 100644 index 0000000000..c783f37b64 --- /dev/null +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb @@ -0,0 +1,30 @@ +name = 'psmpi' +version = '5.1.5-1' +versionsuffix = '-mt' + +homepage = 'https://github.com/ParaStation/psmpi2' +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" + +toolchain = {'version': '4.9.3', 'name': 'GCC'} + +toolchainopts = {'defaultopt': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] + +mpich_opts = '--enable-static' + +threaded = True + +dependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +hiddendependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb index b7c5d500a2..aac098925c 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb @@ -14,6 +14,8 @@ toolchainopts = {'defaultopt': True} sources = ['%(version)s.tar.gz'] source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] +mpich_opts = '--enable-static' + dependencies = [ ('pscom', '5.0.48-1', '', True), ] @@ -22,6 +24,4 @@ hiddendependencies = [ ('pscom', '5.0.48-1', '', True), ] -configopts = ' --with-confset=gcc PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb new file mode 100644 index 0000000000..c33effaedb --- /dev/null +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb @@ -0,0 +1,30 @@ +name = 'psmpi' +version = '5.1.5-1' +versionsuffix = '-mt' + +homepage = 'https://github.com/ParaStation/psmpi2' +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" + +toolchain = {'version': '2015.1.133', 'name': 'iccifort'} + +toolchainopts = {'defaultopt': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] + +mpich_opts = '--enable-static' + +threaded = True + +dependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +hiddendependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb index 92f6033fa8..22468a4f7f 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb @@ -14,6 +14,8 @@ toolchainopts = {'defaultopt': True} sources = ['%(version)s.tar.gz'] source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] +mpich_opts = '--enable-static' + dependencies = [ ('pscom', '5.0.48-1', '', True), ] @@ -22,6 +24,4 @@ hiddendependencies = [ ('pscom', '5.0.48-1', '', True), ] -configopts = ' --with-confset=intel PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' - moduleclass = 'mpi' -- GitLab From 2b3091bb02481b40409f90235487ac60ad611bf9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 14:58:53 +0100 Subject: [PATCH 0792/2133] use recommended Geant4/CLHEP versions --- .../c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb | 23 +++++++++++++++++ .../GATE-7.1-intel-2016a-Python-2.7.11.eb | 8 +++--- .../g/Geant4/Geant4-10.02.p01-intel-2016a.eb | 25 +++++++++++++++++++ .../g/Geant4/Geant4-9.6.p04-intel-2016a.eb | 3 ++- 4 files changed, 54 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb new file mode 100644 index 0000000000..0e16a66612 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.1.3.1' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '3.4.3')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb index 6e9809e000..42cc40aaaf 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb @@ -9,16 +9,16 @@ description = """GATE is an advanced opensource software developed by the intern toolchain = {'name': 'intel', 'version': '2016a'} -sources = [('%(namelower)s_v%(version)s.tar_.gz', "tar xfvz %s")] +sources = [('%(namelower)s_v%(version)s.tar.gz', "tar xfvz %s")] source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/'] patches = [ - 'GATE-%(version)s_Makefile-prefix.patch', - 'GATE-%(version)s_unistdh.patch', + 'GATE-7.0_Makefile-prefix.patch', + 'GATE-7.0_unistdh.patch', ] dependencies = [ - ('Geant4', '9.6.p04'), + ('Geant4', '10.02.p01'), ('CLHEP', '2.3.1.1'), ('ROOT', 'v5.34.34', versionsuffix), ] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb new file mode 100644 index 0000000000..300557f7e0 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb @@ -0,0 +1,25 @@ +name = 'Geant4' +version = '10.02.p01' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.10.2.html#2. + ('CLHEP', '2.3.1.1'), +] + +builddependencies = [('CMake', '3.4.3')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += "-DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb index 356c780edf..554b9825d7 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb @@ -13,7 +13,8 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), - ('CLHEP', '2.3.1.1'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.6.html#2. + ('CLHEP', '2.1.3.1'), ] builddependencies = [ ('CMake', '3.4.3'), -- GitLab From 486a02d0e4540eeb24860025ee710312218582db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 15:00:36 +0100 Subject: [PATCH 0793/2133] add comment on recommended CLHEP version in Geant4 easyconfigs --- easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb | 1 + easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb | 1 + .../easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb | 1 + easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb | 1 + easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb | 1 + easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb | 1 + easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb | 1 + 8 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb index 412c19225c..468e4e32f4 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb @@ -13,6 +13,7 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.10.1.html#2. ('CLHEP', '2.2.0.5'), ] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb index dd53f85088..1e0d6874fa 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb @@ -13,6 +13,7 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.4.html#2. ('CLHEP', '2.1.1.0'), ] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb index fbf3b03c0b..b7af10a848 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb @@ -13,6 +13,7 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. ('CLHEP', '2.1.1.0'), ] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb index 7db2e910b2..59a0ae794e 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb @@ -13,6 +13,7 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. ('CLHEP', '2.1.1.0'), ] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb index 8eb3941ded..3f34b45154 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb @@ -13,6 +13,7 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. ('CLHEP', '2.1.1.0'), ] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb index cbe91d153a..ec55937829 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb @@ -13,6 +13,7 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. ('CLHEP', '2.1.1.0'), ] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb index bfe0be4aaf..5a4e622db8 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb @@ -13,6 +13,7 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. ('CLHEP', '2.1.1.0'), ] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb index 791ce6652f..e8b5782036 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb @@ -13,6 +13,7 @@ sources = ['%(namelower)s.%(version)s.tar.gz'] dependencies = [ ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.6.html#2. ('CLHEP', '2.1.3.1'), ] -- GitLab From 8e40fa6502203e3856da598dd906e031f06cb0db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 15:06:45 +0100 Subject: [PATCH 0794/2133] stick to recommended Geant4/CLHEP versions for GATE 6.2 --- .../c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb | 20 +++++++++++++++ .../GATE-6.2-intel-2016a-Python-2.7.11.eb | 4 +-- .../g/Geant4/Geant4-9.5.p02-intel-2016a.eb | 25 +++++++++++++++++++ 3 files changed, 47 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb new file mode 100644 index 0000000000..ceed3e9cd3 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'CLHEP' +version = '2.1.1.0' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +# CLHEP compiles with icc instead of icpc +configopts = 'CXX="$CC" CXXFLAGS="$CXXFLAGS -gcc"' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb index c48ea46984..c8044cb0a3 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb @@ -18,8 +18,8 @@ patches = [ ] dependencies = [ - ('Geant4', '9.6.p04'), - ('CLHEP', '2.3.1.1'), + ('Geant4', '9.5.p02'), + ('CLHEP', '2.1.1.0'), ('ROOT', 'v5.34.34', versionsuffix), ] builddependencies = [('CMake', '3.4.3')] diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb new file mode 100644 index 0000000000..b790b2a3f8 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb @@ -0,0 +1,25 @@ +name = 'Geant4' +version = '9.5.p02' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.9.5.html#2. + ('CLHEP', '2.1.1.0'), +] + +builddependencies = [('CMake', '3.4.3')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += "-DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' -- GitLab From be7882c7c86d1265dbaea105e03db457b48159de Mon Sep 17 00:00:00 2001 From: perettig Date: Thu, 3 Mar 2016 17:15:30 +0100 Subject: [PATCH 0795/2133] added sanity check for libpng --- .../l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb | 7 +++++++ .../p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 1 + 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb index f58ee3b579..bb061f924f 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb @@ -14,4 +14,11 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.8')] +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 0169075b4a..7eef88d995 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -15,6 +15,7 @@ scipyversion = '0.16.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +# patch needed for building h5py patches = ['unixccompiler-Python-2.7.11.patch'] # python needs bzip2 to build the bz2 package -- GitLab From 2d1318995610e78436b943b65f3a42f81f01bc2c Mon Sep 17 00:00:00 2001 From: perettig Date: Thu, 3 Mar 2016 18:12:35 +0100 Subject: [PATCH 0796/2133] fixed remarks --- .../freetype-2.6.2-CrayGNU-2015.11-XC.eb | 3 +- .../g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb | 24 +++++++++++ .../Python-2.7.11-CrayGNU-2015.11-XC.eb | 3 ++ .../SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb | 40 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb | 25 ++++++++++++ .../Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb | 26 ++++++++++++ 6 files changed, 120 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb index 97d02aea84..113ad0ada9 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..9fa2e217a8 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb @@ -0,0 +1,24 @@ +# contributed by Luca Marsella (CSCS) +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +preconfigopts = 'export CFLAGS=-mcmodel=large && ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 7eef88d995..5c7827f5c1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -24,6 +24,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..f8f253cac7 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..45169d651c --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb new file mode 100644 index 0000000000..e34216f215 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 1d8ec9a842b80101489f7b669885afbd540d5e39 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2016 20:55:57 +0100 Subject: [PATCH 0797/2133] fix Geant4/CHLEP dep versions for GATE 7.1, add easyconfig for GATE 7.2 --- .../c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb | 21 +++++++++++++ .../GATE-7.1-intel-2016a-Python-2.7.11.eb | 7 +++-- .../g/GATE/GATE-7.1_std-isnan.patch | 11 +++++++ .../GATE-7.2-intel-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ .../g/Geant4/Geant4-10.01.p03-intel-2016a.eb | 25 +++++++++++++++ 5 files changed, 93 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch create mode 100644 easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb new file mode 100644 index 0000000000..c7863dcbd1 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.2.0.8' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '3.4.3')] + +separate_build_dir = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb index 42cc40aaaf..a0b0cfc7ac 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb @@ -15,15 +15,18 @@ source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration patches = [ 'GATE-7.0_Makefile-prefix.patch', 'GATE-7.0_unistdh.patch', + 'GATE-7.1_std-isnan.patch', ] dependencies = [ - ('Geant4', '10.02.p01'), - ('CLHEP', '2.3.1.1'), + ('Geant4', '10.01.p03'), + ('CLHEP', '2.2.0.8'), ('ROOT', 'v5.34.34', versionsuffix), ] builddependencies = [ ('CMake', '3.4.3'), ] +buildopts = 'LD="$CXX"' + moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch b/easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch new file mode 100644 index 0000000000..58dbb69bb2 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch @@ -0,0 +1,11 @@ +--- gate_v7.1/source/digits_hits/src/GateToRoot.cc.orig 2016-03-03 19:41:50.569854028 +0100 ++++ gate_v7.1/source/digits_hits/src/GateToRoot.cc 2016-03-03 19:43:09.370590639 +0100 +@@ -765,7 +765,7 @@ + if (dzg1 > dzg2) {dev = acos(-dev)*180/Pi;} + else {dev = acos(dev)*180/Pi - 180;} + +- if (isnan(dev) ) dev = 0.; ++ if (std::isnan(dev) ) dev = 0.; + + // G4cout<< " dev = " << dev << G4endl; + diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f372f2e488 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +name = 'GATE' +version = '7.2' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [('%(namelower)s_v%(version)s.tar.gz', "tar xfvz %s")] +source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/'] + +patches = [ + 'GATE-7.0_Makefile-prefix.patch', + 'GATE-7.0_unistdh.patch', +] + +dependencies = [ + ('Geant4', '10.02.p01'), + ('CLHEP', '2.3.1.1'), + ('ROOT', 'v5.34.34', versionsuffix), +] +builddependencies = [ + ('CMake', '3.4.3'), +] + +buildopts = 'LD="$CXX"' + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb new file mode 100644 index 0000000000..f30dcb1a76 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb @@ -0,0 +1,25 @@ +name = 'Geant4' +version = '10.01.p03' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/geant4/support/ReleaseNotes4.10.1.html#2. + ('CLHEP', '2.2.0.8'), +] + +builddependencies = [('CMake', '3.4.3')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += "-DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' -- GitLab From a3d04d9a93681559f65a7f2cb9dbc51e9cf481d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 09:31:09 +0100 Subject: [PATCH 0798/2133] add comment in patch file for GATE --- easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch b/easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch index 58dbb69bb2..b8d39150f4 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch +++ b/easybuild/easyconfigs/g/GATE/GATE-7.1_std-isnan.patch @@ -1,3 +1,5 @@ +fix for compiler error ""error: more than one instance of overloaded function isnan matches the argument list" +author: Kenneth Hoste (HPC-UGent) --- gate_v7.1/source/digits_hits/src/GateToRoot.cc.orig 2016-03-03 19:41:50.569854028 +0100 +++ gate_v7.1/source/digits_hits/src/GateToRoot.cc 2016-03-03 19:43:09.370590639 +0100 @@ -765,7 +765,7 @@ -- GitLab From 2dd40478d824d178be19b517743b30ac62118a57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 09:31:35 +0100 Subject: [PATCH 0799/2133] add -DCMAKE_BUILD_TYPE=Release config option in all recent CLHEP easyconfigs --- easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb | 2 ++ easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb | 2 ++ easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb index 9408c50361..cf96d8d47a 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb @@ -18,4 +18,6 @@ builddependencies = [('CMake', '3.2.2')] separate_build_dir = True +configopts = '-DCMAKE_BUILD_TYPE=Release' + moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb index c7863dcbd1..fb7adb464b 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb @@ -18,4 +18,6 @@ builddependencies = [('CMake', '3.4.3')] separate_build_dir = True +configopts = '-DCMAKE_BUILD_TYPE=Release' + moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb index cf3607f24f..0c5534a737 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb @@ -18,4 +18,6 @@ builddependencies = [('CMake', '3.4.3')] separate_build_dir = True +configopts = '-DCMAKE_BUILD_TYPE=Release' + moduleclass = 'numlib' -- GitLab From cf470891e60fc625b3d01976d11699a94769bc1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 09:47:57 +0100 Subject: [PATCH 0800/2133] fix long line in GATE descriptions --- easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb | 2 +- .../easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb | 2 +- .../easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb | 2 +- .../easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb index f6983e6ed6..24800cedc7 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb @@ -4,7 +4,7 @@ version = '6.1' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'ictce', 'version': '4.0.6'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb index 8cd12c59aa..b344b3f548 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb @@ -4,7 +4,7 @@ version = '6.2' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb index 3bac12bc2c..89a8046f2f 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb @@ -4,7 +4,7 @@ version = '6.2' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb index cf9f93f198..2c2c954a1c 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb @@ -4,7 +4,7 @@ version = '6.2' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'ictce', 'version': '4.0.6'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb index b6ef9ed9c1..1a6ef28db9 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb @@ -4,7 +4,7 @@ version = '6.2' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb index c8044cb0a3..d237afef62 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb @@ -5,7 +5,7 @@ versionsuffix = '-Python-2.7.11' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'intel', 'version': '2016a'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb index e93ce79175..85541021f4 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb @@ -4,7 +4,7 @@ version = '7.0' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb index a0b0cfc7ac..b1e10c6404 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb @@ -5,7 +5,7 @@ versionsuffix = '-Python-2.7.11' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'intel', 'version': '2016a'} diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb index f372f2e488..80a5207676 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb @@ -5,7 +5,7 @@ versionsuffix = '-Python-2.7.11' homepage = 'http://www.opengatecollaboration.org/' description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography - (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'intel', 'version': '2016a'} -- GitLab From 8dd88a2c7e9fd4d59fc3d4f405561b1725357bbd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 09:53:30 +0100 Subject: [PATCH 0801/2133] fix long line in GSL descr --- easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb | 3 ++- easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb | 4 ++-- 24 files changed, 48 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb index 85ec8681aa..f4197820e5 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb @@ -5,7 +5,8 @@ version = '1.15' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb index 2bc7e232eb..d9295adc89 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb @@ -5,7 +5,8 @@ version = '1.15' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. -The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" +The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb index d19efed940..3230d895d1 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb @@ -5,7 +5,8 @@ version = '1.15' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. -The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb index 3ee18f98a2..93b875b8e7 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb @@ -5,7 +5,8 @@ version = '1.15' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb index a0f7045209..3e17c8b5d6 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb @@ -5,7 +5,8 @@ version = '1.15' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb index 3d34fbf06f..9ef4e74b99 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb @@ -5,7 +5,8 @@ version = '1.15' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. -The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb index 9cfba7ecd1..2c856c0c22 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb @@ -5,7 +5,8 @@ version = '1.15' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb index b20d7731f8..426a5fa702 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb index ed67148304..681aa2648b 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb index 108a2f3dc5..7481f95582 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. -The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb index ffcd9e4804..493418d259 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. -The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb index 875d7306f5..0336ef456f 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. -The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolfc', 'version': '1.3.12'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb index 9d9ca82812..0e558d5644 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. -The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'goolfc', 'version': '2.6.10'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb index 7005ed5e6a..e3cf37d1e5 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb index 9d1699e64d..1ee8967b14 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb index 1291647435..cc561c1cbf 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb index 958500b4dd..e1a049a993 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'ictce', 'version': '6.2.5'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb index 3587bf11b9..f93fbb1090 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb index 79f876ac1d..207992d0eb 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb index f9f59f712b..33c068c25d 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb index 75f289b550..aaffd974f5 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb @@ -5,7 +5,8 @@ version = '1.16' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb index 812faf4e0f..64966f0023 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb @@ -5,7 +5,8 @@ version = "2.1" homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'version': '2015b', 'name': 'foss'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb index cae4fccd47..d363055a95 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb @@ -5,7 +5,8 @@ version = '2.1' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb index 4184830813..6ff19555c3 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb @@ -5,8 +5,8 @@ version = '2.1' homepage = 'http://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, - special functions and least-squares fitting.""" + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -- GitLab From 3fb1e69deb7b7ba5f8e980ed0c46e41a85c9b4a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 10:04:10 +0100 Subject: [PATCH 0802/2133] use %(pyver)s --- .../r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index fa81ad980b..59556c19fd 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -1,6 +1,6 @@ name = 'ROOT' version = 'v5.34.34' -versionsuffix = '-Python-2.7.11' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://root.cern.ch/drupal/' description = """The ROOT system provides a set of OO frameworks with all the functionality -- GitLab From cd3f12ae6a78b0d3f0b5f4c9facec4fb1509d424 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 10:05:46 +0100 Subject: [PATCH 0803/2133] $LD is set correctly in GATE easyblock, so remove from easyconfig (cfr. https://github.com/hpcugent/easybuild-easyblocks/pull/855) --- .../easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb | 2 -- .../easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb index b1e10c6404..ddcd9aaa7c 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb @@ -27,6 +27,4 @@ builddependencies = [ ('CMake', '3.4.3'), ] -buildopts = 'LD="$CXX"' - moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb index 80a5207676..91e8c30f8c 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb @@ -26,6 +26,4 @@ builddependencies = [ ('CMake', '3.4.3'), ] -buildopts = 'LD="$CXX"' - moduleclass = 'cae' -- GitLab From 9a96199c4192b0b8fee1479c25a43b14b630a5fd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 4 Mar 2016 10:18:25 +0100 Subject: [PATCH 0804/2133] X libs are fixed --- .../l/libXmu/libXmu-1.1.2-intel-2016a.eb | 25 +++++++++++++++++++ .../l/libXpm/libXpm-3.5.11-intel-2016a.eb | 22 ++++++++++++++++ .../r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 2 ++ 3 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2016a.eb new file mode 100644 index 0000000000..5611aadb4b --- /dev/null +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXmu' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. + libXmuu is a lighter-weight version that does not depend on libXt or libXext""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libXt', '1.1.5'), + ('libXpm', '3.5.11'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%%(name)s.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb new file mode 100644 index 0000000000..80b08e7922 --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libXpm' +version = '3.5.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [('gettext', '0.19.6')] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index e0608b0939..61bf28051c 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -24,6 +24,8 @@ configopts += " --with-recommended-packages=no" dependencies = [ (libx11, libxver), + ('libXt', '1.1.5'), + ('libXmu', '1.1.2'), ('libreadline', '6.3'), ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R -- GitLab From 8aa7badee4c785afcbf70c2cf8351efb7a0826fc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 4 Mar 2016 10:41:31 +0100 Subject: [PATCH 0805/2133] GLib builddependency fixed (to use Python with X) --- .../easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb index a93ed50f9f..3ae73ffc00 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb @@ -15,7 +15,6 @@ source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) pysuffix = '-Python-%s%s' % (pyver, versionsuffix) dependencies = [ @@ -25,7 +24,7 @@ dependencies = [ ('PCRE', '8.38'), ] -builddependencies = [('Python', pyver)] +builddependencies = [('Python', pyver, versionsuffix)] configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" -- GitLab From f95c1cd2d0e1c9758bcb8b3a8a525e06cd1056fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 12:25:25 +0200 Subject: [PATCH 0806/2133] add easyconfig PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb --- ...penGL-3.1.1a1-intel-2016a-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..c284cf8453 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyOpenGL' +version = '3.1.1a1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('Mesa', '11.1.2'), +] + +options = {'modulename': 'OpenGL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' -- GitLab From 9d202a7e73953c2e17fb64e6476bd3b75edfe3fd Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Fri, 4 Mar 2016 11:45:49 +0100 Subject: [PATCH 0807/2133] Revert "Use directly '--with-hwloc' configopt for MVAPICH2 1.7 instead of to-be-removed 'withhwloc' from MVAPICH2 EB" This reverts commit 6db12d99703e23e76336abbe58be66dee5b71902. --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 137b9059fe..95bd5200b6 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -16,7 +16,7 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] configopts = '--with-mpe ' # enable hwloc support -configopts += '--with-hwloc ' +withhwloc = True dependencies = [('hwloc', '1.5.1')] # enable checkpointing support -- GitLab From 43112ab3f8c4fe9e7c9cf9dce36fb392ac6fd1c3 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Fri, 4 Mar 2016 11:45:55 +0100 Subject: [PATCH 0808/2133] Revert "Use directly '--with-mpe' configopt for MVAPICH2 1.7 instead of to-be-removed 'withmpe' from MVAPICH2 EB" This reverts commit cadbf9619dacee2b0df04dc31a4712631e483c00. --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 95bd5200b6..a20b1e03f0 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TGZ] source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] # enable building of MPE routines -configopts = '--with-mpe ' +withmpe = True # enable hwloc support withhwloc = True diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb index 4c2eead91f..76de06e6fd 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb @@ -14,7 +14,7 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] builddependencies = [('Bison', '2.5')] # enable building of MPE routines -configopts = '--with-mpe ' +withmpe = True # parallel build tends to fail parallel = 1 -- GitLab From e6490b9b37771398ad0362f479803e695d7ffef7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Mar 2016 11:51:56 +0100 Subject: [PATCH 0809/2133] Move to intel 2016a --- .../{bbFTP-3.2.1-foss-2015b.eb => bbFTP-3.2.1-intel-2016a.eb} | 2 +- .../{Perl-5.22.0-foss-2015b.eb => Perl-5.22.1-intel-2016a.eb} | 4 ++-- .../{shift-4.0-foss-2015b.eb => shift-4.0-intel-2016a.eb} | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/b/bbFTP/{bbFTP-3.2.1-foss-2015b.eb => bbFTP-3.2.1-intel-2016a.eb} (96%) rename easybuild/easyconfigs/p/Perl/{Perl-5.22.0-foss-2015b.eb => Perl-5.22.1-intel-2016a.eb} (99%) rename easybuild/easyconfigs/s/shift/{shift-4.0-foss-2015b.eb => shift-4.0-intel-2016a.eb} (90%) diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-intel-2016a.eb similarity index 96% rename from easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-foss-2015b.eb rename to easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-intel-2016a.eb index ec80570d1a..3c955962eb 100644 --- a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-intel-2016a.eb @@ -21,7 +21,7 @@ description = """bbFTP is a file transfer software. It implements its own transf * Automatic retry * Customizable time-outs * Transfer simulation * AFS authentication integration * RFIO interface""" -toolchain = {'name': 'foss', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2016a'} # fi. http://doc.in2p3.fr/bbftp/dist/bbftp-client-3.2.0.tar.gz sources = ['%s-client-%s.tar.gz' % (name.lower(), version)] diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb similarity index 99% rename from easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b.eb rename to easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index 37c67413c1..b46dec87b6 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -1,10 +1,10 @@ name = 'Perl' -version = '5.22.0' +version = '5.22.1' homepage = 'http://www.perl.org/' description = """Larry Wall's Practical Extraction and Report Language""" -toolchain = {'name': 'foss', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://www.cpan.org/src/5.0'] diff --git a/easybuild/easyconfigs/s/shift/shift-4.0-foss-2015b.eb b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb similarity index 90% rename from easybuild/easyconfigs/s/shift/shift-4.0-foss-2015b.eb rename to easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb index 7adef50aac..24ac3912b7 100644 --- a/easybuild/easyconfigs/s/shift/shift-4.0-foss-2015b.eb +++ b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb @@ -9,13 +9,13 @@ Shift is a framework for Self-Healing Independent File Transfer that provides hi performance and resilience for local and remote transfers through a variety of techniques. """ -toolchain = {'name': 'foss', 'version': '2015b'} +toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TGZ] source_urls = [('http://sourceforge.net/projects/shiftc/files', 'download')] dependencies = [ - ('Perl', '5.22.0'), + ('Perl', '5.22.1'), ('bbFTP', '3.2.1'), ] -- GitLab From 7ab9d464e410a7361524941d15fdc07645908474 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Mar 2016 12:32:27 +0100 Subject: [PATCH 0810/2133] Update gnutls to intel/2016a --- .../g/gnutls/gnutls-3.3.21-intel-2016a.eb | 40 +++++++++++++++++++ .../g/guile/guile-1.8.8-intel-2016a.eb | 32 +++++++++++++++ .../l/libidn/libidn-1.32-intel-2016a.eb | 19 +++++++++ .../l/libtasn1/libtasn1-4.7-intel-2016a.eb | 22 ++++++++++ .../libunistring-0.9.3-intel-2016a.eb | 24 +++++++++++ .../n/nettle/nettle-3.1.1-intel-2016a.eb | 28 +++++++++++++ .../p/p11-kit/p11-kit-0.23.2-intel-2016a.eb | 29 ++++++++++++++ 7 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnutls/gnutls-3.3.21-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.32-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.3.21-intel-2016a.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.3.21-intel-2016a.eb new file mode 100644 index 0000000000..62fd6a4ca6 --- /dev/null +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.3.21-intel-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'gnutls' +version = '3.3.21' + +homepage = 'http://www.gnutls.org/' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCE_TAR_XZ] + +guilever = '1.8.8' +guileshortver = '.'.join(guilever.split('.')[:2]) +dependencies = [ + ('GMP', '6.1.0'), + ('nettle', '3.1.1'), + ('guile', guilever), + ('libtasn1', '4.7'), + ('libidn', '1.32'), + ('p11-kit', '0.23.2'), +] + +configopts = "--with-guile-site-dir=$EBROOTGUILE --enable-openssl-compatibility " + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['certtool', 'crywrap', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]] + + ['lib/guile/%s/guile-gnutls-v-2.so' % guileshortver], + 'dirs': ['include/gnutls'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2016a.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2016a.eb new file mode 100644 index 0000000000..a7e7520df8 --- /dev/null +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.0'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.29'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-intel-2016a.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-intel-2016a.eb new file mode 100644 index 0000000000..92af944d43 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.32' + +homepage = 'http://www.gnu.org/software/libidn' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb new file mode 100644 index 0000000000..f8867d1ca7 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.7' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. + It was written by Fabio Fiorina, and has been shipped as part of GnuTLS + for some time but is now a proper GNU package.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', 'so', 'so.6']], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2016a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2016a.eb new file mode 100644 index 0000000000..8b6d4e58c5 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb new file mode 100644 index 0000000000..c725853009 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.1.1' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-intel-2016a.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-intel-2016a.eb new file mode 100644 index 0000000000..671c3febaa --- /dev/null +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'p11-kit' +version = '0.23.2' + +homepage = 'http://p11-glue.freedesktop.org/p11-kit.html' +description = """Provides a way to load and enumerate PKCS#11 modules. + Provides a standard configuration setup for installing + PKCS#11 modules in such a way that they're discoverable. + Also solves problems with coordinating the use of PKCS#11 + by different components or libraries living in the same process.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://p11-glue.freedesktop.org/releases/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libtasn1', '4.7'), + ('libffi', '3.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/p11-kit', 'bin/trust'] + + ['lib/libp11-kit.%s' % x for x in ['so', 'so.0']], + 'dirs': ['include/p11-kit-1/p11-kit'], +} + +moduleclass = 'lib' -- GitLab From 326e6c8c0d65c30d79250a00556c5b51df9475ec Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Mar 2016 13:00:20 +0100 Subject: [PATCH 0811/2133] Add libgcrypt and libgpg-error --- .../libgcrypt/libgcrypt-1.6.5-intel-2016a.eb | 21 +++++++++++++++++++ .../libgpg-error-1.21-intel-2016a.eb | 19 +++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.21-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb new file mode 100644 index 0000000000..9c3e1eaa05 --- /dev/null +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'libgcrypt' +version = '1.6.5' + +homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] + +dependencies = [('libgpg-error', '1.21')] + +sanity_check_paths = { + 'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.21-intel-2016a.eb b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.21-intel-2016a.eb new file mode 100644 index 0000000000..a3d7d6c682 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.21-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libgpg-error' +version = '1.21' + +homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] + +sanity_check_paths = { + 'files': ['bin/gpg-error-config', 'include/gpg-error.h', 'lib/libgpg-error.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' -- GitLab From 3fef96ccf2febe599e601a0a131bbeeecb84b267 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Mar 2016 13:13:27 +0100 Subject: [PATCH 0812/2133] Fix remarks --- easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb index f8867d1ca7..273a3cb53b 100644 --- a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] sanity_check_paths = { 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + - ['lib/libtasn1.%s' % x for x in ['a', 'so', 'so.6']], + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-intel-2016a.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-intel-2016a.eb index 671c3febaa..d945ad10e0 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-intel-2016a.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-intel-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/p11-kit', 'bin/trust'] + - ['lib/libp11-kit.%s' % x for x in ['so', 'so.0']], + ['lib/libp11-kit.%s' % SHLIB_EXT], 'dirs': ['include/p11-kit-1/p11-kit'], } -- GitLab From 1970b762c7f3291281d22cbd47bbf53259c4fed3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 13:27:53 +0100 Subject: [PATCH 0813/2133] add missing dependencies for cairo, fix build vs runtime deps in X11 libs --- easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb | 3 +++ easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb | 2 +- 6 files changed, 8 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb index 0a62de36aa..3b52cb336a 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb @@ -24,6 +24,9 @@ dependencies = [ ('fontconfig', '2.11.94'), ('expat', '2.1.0'), ('GLib', glibver), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb index 5df5e13e43..e4f9296663 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb @@ -17,12 +17,12 @@ builddependencies = [ ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), - ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), ] dependencies = [ ('libxcb', '1.11.1'), + ('kbproto', '1.0.7'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb index 243dbd6f22..f18fd04337 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb @@ -13,7 +13,7 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] -builddependencies = [ +dependencies = [ ('xproto', '7.0.28'), ] diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 3e89327b58..44f12d56c2 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -14,11 +14,11 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] builddependencies = [ ('xproto', '7.0.28'), - ('xextproto', '7.3.0'), ] dependencies = [ ('libX11', '1.6.3'), + ('xextproto', '7.3.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb index fefc99f4eb..74f683ec01 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -13,11 +13,11 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), - ('renderproto', '0.11'), ] dependencies = [ ('libX11', '1.6.3'), + ('renderproto', '0.11'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index 098e8569bb..db46240f22 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -15,11 +15,11 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), - ('libpthread-stubs', '0.3'), ] dependencies = [ ('libXau', '1.0.8'), ('libXdmcp', '1.1.2'), + ('libpthread-stubs', '0.3'), ] sanity_check_paths = { -- GitLab From f5c8261c454f335bdcd61395e780a4d33bfa3e76 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Mar 2016 13:30:42 +0100 Subject: [PATCH 0814/2133] Fix url for libgcrypt --- .../easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb index 9c3e1eaa05..437c5cc9a2 100644 --- a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.6.5-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libgcrypt' version = '1.6.5' -homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +homepage = 'https://gnupg.org/related_software/libgcrypt/index.html' description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" toolchain = {'name': 'intel', 'version': '2016a'} -- GitLab From 05d9c8be573e9dbb3c6d2bc59397c43d5dc25ac2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Mar 2016 13:31:10 +0100 Subject: [PATCH 0815/2133] Fix typo --- easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb index 273a3cb53b..4bb22e3a8f 100644 --- a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-intel-2016a.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] sanity_check_paths = { 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + - ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT], + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include'], } -- GitLab From 2f9e2de8866be0f3782c767e374db93191301d2c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Mar 2016 13:44:19 +0100 Subject: [PATCH 0816/2133] Add mutil --- .../m/mutil/mutil-1.822.3-intel-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb new file mode 100644 index 0000000000..a12dea39eb --- /dev/null +++ b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb @@ -0,0 +1,32 @@ +name = 'mutil' +version = '1.822.3' + +homepage = 'http://people.nas.nasa.gov/~kolano/projects/mutil.html' +description = """Mutil is a set of standard utilities that have been parallelized to maximize performance on +modern file systems. These currently include multi-threaded drop-in replacements for cp and md5sum from +GNU coreutils, which have achieved 10/30x rates on one/many nodes. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [ + "coreutils-8.22.tar.xz", + SOURCE_TGZ, +] +source_urls = [ + ('http://sourceforge.net/projects/mutil/files', 'download'), + GNU_SOURCE, +] + +dependencies = [ + ('gnutls', '3.3.21'), + ('libgpg-error', '1.21'), + ('libgcrypt', '1.6.5'), +] + +sanity_check_paths = { + 'files': ['bin/cp', 'bin/md5sum'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' -- GitLab From a2eea3f20f47dcaad498d6bfb8b108880aac6499 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 14:13:16 +0100 Subject: [PATCH 0817/2133] don't include proto header libs as runtime deps --- easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb index e4f9296663..5df5e13e43 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb @@ -17,12 +17,12 @@ builddependencies = [ ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), ] dependencies = [ ('libxcb', '1.11.1'), - ('kbproto', '1.0.7'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb index f18fd04337..243dbd6f22 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb @@ -13,7 +13,7 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] -dependencies = [ +builddependencies = [ ('xproto', '7.0.28'), ] diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 44f12d56c2..3e89327b58 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -14,11 +14,11 @@ source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] builddependencies = [ ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), ] dependencies = [ ('libX11', '1.6.3'), - ('xextproto', '7.3.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb index 74f683ec01..fefc99f4eb 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -13,11 +13,11 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), + ('renderproto', '0.11'), ] dependencies = [ ('libX11', '1.6.3'), - ('renderproto', '0.11'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index db46240f22..098e8569bb 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -15,11 +15,11 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), ] dependencies = [ ('libXau', '1.0.8'), ('libXdmcp', '1.1.2'), - ('libpthread-stubs', '0.3'), ] sanity_check_paths = { -- GitLab From b55cd2298377b5c8cb875d267f9b718a9aacd97c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 14:20:17 +0100 Subject: [PATCH 0818/2133] add libX11 as explicit dep to cairo --- easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb index 3b52cb336a..ef5f023e09 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb @@ -24,6 +24,7 @@ dependencies = [ ('fontconfig', '2.11.94'), ('expat', '2.1.0'), ('GLib', glibver), + ('libX11', '1.6.3'), ('libxcb', '1.11.1'), ('libXrender', '0.9.9'), ('libXext', '1.3.3'), -- GitLab From 57fc835c13032f86b54d80a0cdb798ed175b88cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 14:26:22 +0100 Subject: [PATCH 0819/2133] add renderproto as build dep for cairo --- easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb index ef5f023e09..2966a85fa7 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb @@ -29,6 +29,9 @@ dependencies = [ ('libXrender', '0.9.9'), ('libXext', '1.3.3'), ] +builddependencies = [ + ('renderproto', '0.11'), +] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " -- GitLab From beb89b7c4232ffbe815a690432620a1f0196fab4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 15:29:19 +0200 Subject: [PATCH 0820/2133] add easyconfig Glade-3.8.5-intel-2016a-Python-2.7.11.eb, add easyconfig intltool-0.51.0-intel-2016a.eb, add easyconfig XML-Parser-2.41-intel-2016a-Perl-5.20.3.eb --- .../Glade-3.8.5-intel-2016a-Python-2.7.11.eb | 40 +++++++++++++++++++ .../i/intltool/intltool-0.51.0-intel-2016a.eb | 24 +++++++++++ ...XML-Parser-2.41-intel-2016a-Perl-5.20.3.eb | 27 +++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2016a-Perl-5.20.3.eb diff --git a/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a592f1d91d --- /dev/null +++ b/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Glade' +version = '3.8.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://glade.gnome.org/' +description = """Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit + and the GNOME desktop environment.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s%(version_major)s/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version_major)s-%(version)s.tar.xz'] + +dependencies = [ + ('Python', '2.7.11'), + ('GTK+', '2.24.28'), + ('PyGTK', '2.24.0', versionsuffix), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3', versionsuffix), +] +builddependencies = [ + ('intltool', '0.51.0'), + ('pkg-config', '0.29'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('renderproto', '0.11'), +] + +sanity_check_paths = { + 'files': ['bin/glade-%(version_major)s', 'lib/libgladeui-1.%s' % SHLIB_EXT, 'lib/pkgconfig/gladeui-1.0.pc', + 'lib/glade%%(version_major)s/modules/libgladegtk.%s' % SHLIB_EXT, + 'lib/glade%%(version_major)s/modules/libgladepython.%s' % SHLIB_EXT], + 'dirs': ['include/libgladeui-1.0/gladeui', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a.eb new file mode 100644 index 0000000000..1b3568a509 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.41', '-Perl-5.20.3'), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2016a-Perl-5.20.3.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2016a-Perl-5.20.3.eb new file mode 100644 index 0000000000..2ef054ad23 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2016a-Perl-5.20.3.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.41' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.20.3'), + ('expat', '2.1.0') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], +} + +moduleclass = 'data' -- GitLab From 7a43b7c24a4b2f3f87f7117241bf461282856f30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 14:37:11 +0100 Subject: [PATCH 0821/2133] add PyOpenGL and Glade as deps for p4vasp --- .../p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb index 7903d62ba9..699eafed53 100644 --- a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'p4vasp' version = '0.3.29' -versionsuffix = '-Python-2.7.11' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.p4vasp.at/' description = """Visualization suite for VASP""" @@ -13,7 +13,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TGZ] dependencies = [ + ('Python', '2.7.11'), ('PyGTK', '2.24.0', versionsuffix), + ('PyOpenGL', '3.1.1a1', versionsuffix), + ('Glade', '3.8.5', versionsuffix), ] skipsteps = ['configure', 'build'] -- GitLab From ae86fbb5e227b6c05b1baf7181a756d9086d19bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 15:18:26 +0100 Subject: [PATCH 0822/2133] GLib doesn't require libxml2 with Python bindings --- easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb index 3dcfe3ad19..2b30216f8c 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a.eb @@ -12,18 +12,14 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) -pysuffix = '-Python-%s' % pyver - dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), - ('libxml2', '2.9.3', pysuffix), + ('libxml2', '2.9.3'), ('PCRE', '8.38'), ] -builddependencies = [('Python', pyver)] +builddependencies = [('Python', '2.7.11')] configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" -- GitLab From 0a740288d25794de4b67b34db1a9f06d7f9ef89d Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 4 Mar 2016 15:20:48 +0100 Subject: [PATCH 0823/2133] vcftools latest version --- ...CFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..fec3b7a05c --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.14' + +homepage = 'https://vcftools.github.io/' +description = """A set of tools written in Perl and C++ for working with VCF files.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/vcftools/vcftools/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl , perlver), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["vcftools", "fill-fs", "vcf-compare", "vcf-contrast", + "vcf-fix-ploidy", "vcf-merge"]], + 'dirs': [], +} + +modextrapaths = { 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) } + +moduleclass = 'bio' -- GitLab From 0edfa0e1c01e00e4762a690993d689938c83b956 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 15:42:33 +0100 Subject: [PATCH 0824/2133] add patch file to imkl 10.2.6.038 32-bit easyconfig to fix installer not being able to deal with -- in build path] --- .../easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb | 2 ++ .../imkl-10.2.6.038_fix-install-double-dash.patch | 14 ++++++++++++++ 2 files changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-10.2.6.038_fix-install-double-dash.patch diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb index 2312f4b388..39b3d7cf7b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['l_mkl_p_%(version)s.tar.gz'] +patches = ['imkl-%(version)s_fix-install-double-dash.patch'] + dontcreateinstalldir = 'True' # deps for interface build diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038_fix-install-double-dash.patch b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038_fix-install-double-dash.patch new file mode 100644 index 0000000000..929b9c7069 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038_fix-install-double-dash.patch @@ -0,0 +1,14 @@ +fix regex that doesn't handle directory names with a double dash (--) in them correctly +this fix is specific to using '-32bit' as versionsuffix +author: Kenneth Hoste (HPC-UGent) +--- l_mkl_p_10.2.6.038/pset/install.sh.orig 2016-03-04 15:28:03.092055076 +0100 ++++ l_mkl_p_10.2.6.038/pset/install.sh 2016-03-04 15:27:44.071603046 +0100 +@@ -1281,7 +1281,7 @@ + + [ $err -eq ${ERR_OK} ] || return 1 + +- RS=$(echo $CMD_STR | sed s/.*--$cmd[[:blank:]]*//g | sed 's/[[:blank:]]*--.*$//g') ++ RS=$(echo $CMD_STR | sed s/.*--$cmd[[:blank:]]*//g | sed 's/[[:blank:]]*--[^3].*$//g') + [[ -z "$RS" ]] && return 1 + echo $RS + -- GitLab From a2943853e4799c2fb32b8a40e17638533ca5fffe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 16:49:04 +0200 Subject: [PATCH 0825/2133] use libxml2 without Python bindings as dep in Glade easyconfig --- .../g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb index a592f1d91d..a60c5a250c 100644 --- a/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb @@ -18,7 +18,7 @@ dependencies = [ ('GTK+', '2.24.28'), ('PyGTK', '2.24.0', versionsuffix), ('gettext', '0.19.6'), - ('libxml2', '2.9.3', versionsuffix), + ('libxml2', '2.9.3'), ] builddependencies = [ ('intltool', '0.51.0'), -- GitLab From 2b7f0e2f3e1875274240bd090d4c7c82ec66b532 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 15:55:58 +0100 Subject: [PATCH 0826/2133] add -Perl-5.20.3 to versionsuffix for intltool --- .../g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb | 2 +- ...el-2016a.eb => intltool-0.51.0-intel-2016ab-Perl-5.20.3.eb} | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/i/intltool/{intltool-0.51.0-intel-2016a.eb => intltool-0.51.0-intel-2016ab-Perl-5.20.3.eb} (89%) diff --git a/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb index a60c5a250c..7b4701d28d 100644 --- a/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/Glade/Glade-3.8.5-intel-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ dependencies = [ ('libxml2', '2.9.3'), ] builddependencies = [ - ('intltool', '0.51.0'), + ('intltool', '0.51.0', '-Perl-5.20.3'), ('pkg-config', '0.29'), ('libpthread-stubs', '0.3'), ('kbproto', '1.0.7'), diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016ab-Perl-5.20.3.eb similarity index 89% rename from easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a.eb rename to easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016ab-Perl-5.20.3.eb index 1b3568a509..8fd4cb48f8 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016ab-Perl-5.20.3.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'intltool' version = '0.51.0' +versionsuffix = '-Perl-5.20.3' homepage = 'http://freedesktop.org/wiki/Software/intltool/' description = """intltool is a set of tools to centralize translation of @@ -13,7 +14,7 @@ source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] dependencies = [ - ('XML-Parser', '2.41', '-Perl-5.20.3'), + ('XML-Parser', '2.41', versionsuffix), ] sanity_check_paths = { -- GitLab From 45f1afd8d292d62ec5d0951d53f19d75599cc881 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 16:35:34 +0100 Subject: [PATCH 0827/2133] add libglade as dependency for PyGTK --- .../l/libglade/libglade-2.6.4-intel-2016a.eb | 27 +++++++++++++++++++ .../PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb | 6 ++++- 2 files changed, 32 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libglade/libglade-2.6.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libglade/libglade-2.6.4-intel-2016a.eb b/easybuild/easyconfigs/l/libglade/libglade-2.6.4-intel-2016a.eb new file mode 100644 index 0000000000..479f939d5a --- /dev/null +++ b/easybuild/easyconfigs/l/libglade/libglade-2.6.4-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libglade' +version = '2.6.4' + +homepage = 'https://developer.gnome.org/libglade/' +description = """Libglade is a library for constructing user interfaces dynamically from XML descriptions.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/libglade/%(version_major_minor)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('ATK', '2.18.0'), + ('GTK+', '2.24.28'), + ('GLib', '2.47.5'), + ('libxml2', '2.9.3'), +] + +sanity_check_paths = { + 'files': ['bin/libglade-convert', 'lib/libglade-2.0.a', 'lib/libglade-2.0.%s' % SHLIB_EXT, + 'lib/pkgconfig/libglade-2.0.pc'], + 'dirs': ['include/libglade-2.0/glade', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb index d470f598fa..3e012eb7c3 100644 --- a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2016a-Python-2.7.11.eb @@ -24,6 +24,7 @@ dependencies = [ ('GTK+', '2.24.28'), ('ATK', '2.18.0'), ('PyCairo', '1.10.0', versionsuffix), + ('libglade', '2.6.4'), ] postinstallcmds = [ @@ -45,6 +46,9 @@ sanity_check_paths = { 'dirs': ['lib/pygtk'], } -sanity_check_commands = [('python', "-c 'import gtk'")] +sanity_check_commands = [ + ('python', "-c 'import gtk'"), + ('python', "-c 'import gtk.glade'"), +] moduleclass = 'vis' -- GitLab From c58caeb36055f219eb3e75840916513277fe7702 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 17:24:59 +0100 Subject: [PATCH 0828/2133] PyOpenGL doesn't need usempi... thx @ocaisa --- .../p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb index c284cf8453..cd4aac12db 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-intel-2016a-Python-2.7.11.eb @@ -8,7 +8,6 @@ homepage = 'http://pyopengl.sourceforge.net' description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -- GitLab From c60e315399ea6e25ac118a06baaa654910b1721f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 17:25:28 +0100 Subject: [PATCH 0829/2133] fix $PYTHONPATH for PyGObject, make sure 'import gio' works --- ...Object-2.28.6-intel-2016a-Python-2.7.11.eb | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb index 3291d71bff..2098c7c9b3 100644 --- a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.6-intel-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'PyGObject' version = '2.28.6' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.pygtk.org/' description = """Python Bindings for GLib/GObject/GIO/GTK+""" @@ -15,11 +16,10 @@ patches = ['PyGObject-%(version)s_enum-types.patch'] pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-Python-%s' % pyver glibver = '2.47.5' dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ('GLib', glibver), ('GObject-Introspection', '1.47.1'), ('PyCairo', '1.10.0', versionsuffix), @@ -28,13 +28,24 @@ dependencies = [ configopts = "--disable-introspection" modextrapaths = { - 'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver], + 'PYTHONPATH': [ + 'lib/python%(pyshortver)s/site-packages', + 'lib/python%(pyshortver)s/site-packages/gtk-2.0', + 'lib64/python%(pyshortver)s/site-packages', + 'lib64/python%(pyshortver)s/site-packages/gtk-2.0', + ], } sanity_check_paths = { 'files': ['include/pygtk-%(version_major)s.0/pyglib.h', 'include/pygtk-%(version_major)s.0/pygobject.h', 'lib/libpyglib-%(version_major)s.0-python.so'], - 'dirs': ['bin', 'lib/python%s/site-packages/' % pyshortver], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/'], } +sanity_check_commands = [ + ('python', "-c 'import gobject'"), + ('python', "-c 'import glib'"), + ('python', "-c 'import gio'"), +] + moduleclass = 'vis' -- GitLab From c0cfc0015d2ac1f35ed8d593fa2883dad927f97f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 17:30:26 +0100 Subject: [PATCH 0830/2133] fix filename for intltool easyconfig --- ...ntltool-0.51.0-intel-2016ab-Perl-5.20.3.eb | 25 ------------------- 1 file changed, 25 deletions(-) delete mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016ab-Perl-5.20.3.eb diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016ab-Perl-5.20.3.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016ab-Perl-5.20.3.eb deleted file mode 100644 index 8fd4cb48f8..0000000000 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016ab-Perl-5.20.3.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'intltool' -version = '0.51.0' -versionsuffix = '-Perl-5.20.3' - -homepage = 'http://freedesktop.org/wiki/Software/intltool/' -description = """intltool is a set of tools to centralize translation of - many different file formats using GNU gettext-compatible PO files.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('XML-Parser', '2.41', versionsuffix), -] - -sanity_check_paths = { - 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], - 'dirs': [] -} - -moduleclass = 'devel' -- GitLab From ee82bbaf6b5c4ea6f4f1b64fb641f5ee62058e2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 17:49:47 +0100 Subject: [PATCH 0831/2133] add back intltool easyconfig --- ...intltool-0.51.0-intel-2016a-Perl-5.20.3.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb new file mode 100644 index 0000000000..8fd4cb48f8 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.20.3' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.41', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 330716efb83e0e4a5cf01e160c121b8c1d333d37 Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 4 Mar 2016 17:52:06 +0100 Subject: [PATCH 0832/2133] removed tk (seems to break matplotlib) --- .../easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 5c7827f5c1..8b756292a1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -25,7 +25,6 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), ] -- GitLab From 1e71cfadbe1f76240557d31d81ba34b2d30ed971 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2016 18:28:30 +0100 Subject: [PATCH 0833/2133] {geo}[intel/2016a] rgeos 0.3-17 w/ R 3.2.3 --- .../GEOS-3.5.0-intel-2016a-Python-2.7.11.eb | 28 +++++++++++++++++++ .../rgeos/rgeos-0.3-17-intel-2016a-R-3.2.3.eb | 26 +++++++++++++++++ .../SWIG-3.0.8-intel-2016a-Python-2.7.11.eb | 20 +++++++++++++ 3 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/r/rgeos/rgeos-0.3-17-intel-2016a-R-3.2.3.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..b8bf09f57e --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('Python', '2.7.11')] + +builddependencies = [('SWIG', '3.0.8', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rgeos/rgeos-0.3-17-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/rgeos/rgeos-0.3-17-intel-2016a-R-3.2.3.eb new file mode 100644 index 0000000000..de838e34c0 --- /dev/null +++ b/easybuild/easyconfigs/r/rgeos/rgeos-0.3-17-intel-2016a-R-3.2.3.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'rgeos' +version = '0.3-17' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rgeos/' +description = """R interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations + on geometries""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://cran.r-project.org/src/contrib/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('R', '3.2.3'), + ('GEOS', '3.5.0', '-Python-2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..43296c33fb --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.8' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' -- GitLab From 16dfb07be9d450b2658fdee641b29c0657aeae2f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 4 Mar 2016 19:50:01 +0100 Subject: [PATCH 0834/2133] Glib libxml2 dep without Python --- .../cairo-1.14.6-intel-2016a-libX11-1.6.3.eb | 56 ------------------- .../GDAL-2.0.2-intel-2016a-libX11-1.6.3.eb | 30 ---------- .../GLib-2.47.5-intel-2016a-libX11-1.6.3.eb | 38 ------------- ...-intel-2016a-Python-2.7.11-libX11-1.6.3.eb | 29 ---------- .../r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 6 +- 5 files changed, 3 insertions(+), 156 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-libX11-1.6.3.eb delete mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a-libX11-1.6.3.eb delete mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb delete mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11-libX11-1.6.3.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-libX11-1.6.3.eb deleted file mode 100644 index 6db4212fb3..0000000000 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-libX11-1.6.3.eb +++ /dev/null @@ -1,56 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'cairo' -version = '1.14.6' - -libx11 = 'libX11' -libxver = '1.6.3' -versionsuffix = '-%s-%s' % (libx11, libxver) - -homepage = 'http://cairographics.org' -description = """Cairo is a 2D graphics library with support for multiple output devices. - Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, - PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://cairographics.org/releases/'] -sources = [SOURCE_TAR_XZ] - -glibver = '2.47.5' - -builddependencies = [ - ('renderproto', '0.11'), -] - -dependencies = [ - (libx11, libxver), - ('libXrender', '0.9.9'), - ('libdrm', '2.4.67'), - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libpng', '1.6.21'), - ('freetype', '2.6.2'), - ('pixman', '0.34.0'), - ('fontconfig', '2.11.94'), - ('expat', '2.1.0'), - ('GLib', glibver, versionsuffix), -] - -# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " - -# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" -buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' - -sanity_check_paths = { - 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', - 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', - 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + - ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', - '-script', '-script-interpreter', '-svg', '-version', '-xcb', - '-xlib', '-xlib-xrender']], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a-libX11-1.6.3.eb deleted file mode 100644 index 78e94ccbb6..0000000000 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-intel-2016a-libX11-1.6.3.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDAL' -version = '2.0.2' -versionsuffix = '-libX11-1.6.3' - -homepage = 'http://www.gdal.org/' -description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style - Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model - to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for - data translation and processing.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('netCDF', '4.3.3.1'), - ('expat', '2.1.0'), - ('libxml2', '2.9.3', '-Python-2.7.11%s' % versionsuffix), - ('zlib', '1.2.8'), -] - -sanity_check_paths = { - 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], - 'dirs': ['bin', 'include'] -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb deleted file mode 100644 index 3ae73ffc00..0000000000 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-intel-2016a-libX11-1.6.3.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GLib' -version = '2.47.5' - -versionsuffix = '-libX11-1.6.3' - -homepage = 'http://www.gtk.org/' -description = """GLib is one of the base libraries of the GTK+ project""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] - -pyver = '2.7.11' -pysuffix = '-Python-%s%s' % (pyver, versionsuffix) - -dependencies = [ - ('libffi', '3.2.1'), - ('gettext', '0.19.6'), - ('libxml2', '2.9.3', pysuffix), - ('PCRE', '8.38'), -] - -builddependencies = [('Python', pyver, versionsuffix)] - -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" - -postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] - -sanity_check_paths = { - 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11-libX11-1.6.3.eb deleted file mode 100644 index 230d903622..0000000000 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11-libX11-1.6.3.eb +++ /dev/null @@ -1,29 +0,0 @@ -name = 'libxml2' -version = '2.9.3' - -homepage = 'http://xmlsoft.org/' -description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable - outside of the Gnome platform).""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True} - -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] - -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) -libx11suffix = '-libX11-1.6.3' -versionsuffix = '-Python-%s%s' % (pyver, libx11suffix) - -dependencies = [ - ('zlib', '1.2.8'), - ('Python', pyver, libx11suffix), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index 61bf28051c..8df021253b 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -31,13 +31,13 @@ dependencies = [ ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R ('LibTIFF', '4.0.6'), # for plotting in R - ('cairo', '1.14.6', versionsuffix), # for plotting in R + ('cairo', '1.14.6'), # for plotting in R ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', versionsuffix), # for tcltk ('cURL', '7.47.0'), # for RCurl - ('libxml2', '2.9.3', '-Python-2.7.11%s' % versionsuffix), # for XML - ('GDAL', '2.0.2', versionsuffix), # for rgdal + ('libxml2', '2.9.3'), # for XML + ('GDAL', '2.0.2'), # for rgdal ('PROJ', '4.9.2'), # for rgdal ] -- GitLab From c1dbd131ac40d265ea7549d5973e94535fa2c4ad Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 4 Mar 2016 19:59:36 +0100 Subject: [PATCH 0835/2133] extra empty line deleted --- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index 8df021253b..60dfecc0d6 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -51,7 +51,6 @@ ext_options = { 'source_tmpl': name_tmpl, } - # !! order of packages is important !! # packages updated on January 21st 2016 exts_list = [ -- GitLab From e59867b60cf61ccdd5d696db15784e88d712b3fe Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Sat, 5 Mar 2016 06:30:52 +1030 Subject: [PATCH 0836/2133] Add missing libxml2 dep to Glib --- easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb index 55b64d46c2..0b0d4ce37c 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb @@ -15,6 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.7'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] -- GitLab From cfb939cec91b83b385b7b303f5036172a2d9c4e8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 4 Mar 2016 21:07:48 +0000 Subject: [PATCH 0837/2133] Remove unnecessary files_to_copy after easyblock change --- .../v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb index 926d8c8707..9d1e642f25 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb @@ -30,8 +30,6 @@ dependencies = [ (perl, perlver), ] -files_to_copy = ["bin", "lib", "examples", (["bin/man1"], 'man')] - modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} sanity_check_paths = { -- GitLab From a833a112bf35362c1bfb476838dfbc4f6be6419d Mon Sep 17 00:00:00 2001 From: perettig Date: Sat, 5 Mar 2016 00:27:53 +0100 Subject: [PATCH 0838/2133] removed Tk version suffix to workaround matplotlib detection bug --- .../easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 1 + ...ayGNU-2015.11-XC-no-X11.eb => Tk-8.6.4-CrayGNU-2015.11-XC.eb} | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb => Tk-8.6.4-CrayGNU-2015.11-XC.eb} (96%) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 8b756292a1..45a3845e6a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -25,6 +25,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), + ('Tk', '8.6.4'), ('GMP', '6.1.0'), ] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb similarity index 96% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb index e34216f215..8aeedf1e3d 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb @@ -2,7 +2,6 @@ easyblock = 'ConfigureMake' name = 'Tk' version = '8.6.4' -versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building -- GitLab From 8a638f2ff59bf591d224df458e7010e4bdb2004c Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Sun, 6 Mar 2016 07:29:02 +1030 Subject: [PATCH 0839/2133] Added missing libxml2 dependency --- easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015b.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb | 1 + .../easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb | 1 + 11 files changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb index 8949f8ac3a..d5179c2d3f 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb index 30174bd67f..8a3283f98f 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb @@ -14,6 +14,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015b.eb index b79abecbd3..f78f797967 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015b.eb @@ -14,6 +14,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.10')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb index 08bf6bb8cb..94d03a2c3d 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb index e2971ec78c..1320160d1a 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb @@ -15,6 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb index 224be43936..09e94d7c70 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb @@ -15,6 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb index c6424b3f53..9b0db5c7d4 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb index 9f4e52261e..e1f3dc6096 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a-Python-2.7.10.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] python = 'Python' pyver = '2.7.10' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb index ea740d47ca..6aacfaecc2 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb index 56025316ff..1a6974652c 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb @@ -15,6 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.10')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb index d5db1754d1..90389b48f3 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.1-intel-2015b.eb @@ -15,6 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.10')] -- GitLab From 8fd4030f443c7a32e6ce06aa539b10bebbcf33f8 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Mon, 7 Mar 2016 12:38:39 +1030 Subject: [PATCH 0840/2133] Bump Python version --- easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb index 0b0d4ce37c..2d418a45be 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.2-foss-2015b.eb @@ -17,6 +17,6 @@ dependencies = [ ('gettext', '0.19.7'), ('libxml2', '2.9.2'), ] -builddependencies = [('Python', '2.7.9')] +builddependencies = [('Python', '2.7.10')] moduleclass = 'vis' -- GitLab From 807d12e700fefe7a54aa9c5a85e7793ff3af13bc Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Mon, 7 Mar 2016 13:55:16 +1030 Subject: [PATCH 0841/2133] Added easyconfig for csvkit --- .../csvkit-0.9.1-foss-2015b-Python-2.7.10.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..1b0f60b271 --- /dev/null +++ b/easybuild/easyconfigs/c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'csvkit' +version = '0.9.1' + +homepage = 'https://github.com/wireservice/csvkit' +description = """csvkit is a suite of command-line tools for converting to and working with CSV, + the king of tabular file formats.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +postinstallcmds = ["chmod -R +r %(installdir)s/lib/"] + +sanity_check_paths = { + 'files': ['bin/in2csv', 'bin/sql2csv', 'bin/csvclean', 'bin/csvcut', 'bin/csvgrep', 'bin/csvjoin', + 'bin/csvsort', 'bin/csvstack', 'bin/csvformat', 'bin/csvjson', 'bin/csvlook', 'bin/csvpy', + 'bin/csvsql', 'bin/csvstat'], + 'dirs': [], +} + +sanity_check_commands = [('csvlook','-h')] + +moduleclass = 'tools' -- GitLab From 2b459eebb7a7797b47b81f04ef6b056a31f8ac5b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 7 Mar 2016 09:47:55 +0100 Subject: [PATCH 0842/2133] easyconfig renamed --- ...opus-5.0.0-intel-2015b.eb => Octopus-5.0.0-intel-2015b-mpi.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/o/Octopus/{Octopus-5.0.0-intel-2015b.eb => Octopus-5.0.0-intel-2015b-mpi.eb} (100%) diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb similarity index 100% rename from easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b.eb rename to easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb -- GitLab From 5278cc3e88ddc3d8a0215b6f4f414341247465c3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 7 Mar 2016 11:16:26 +0100 Subject: [PATCH 0843/2133] fixes --- easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch | 4 ++++ .../o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb | 11 ++++++----- .../p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb | 4 ++-- 3 files changed, 12 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch b/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch index 981d2feb46..a5895cfc2c 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch +++ b/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch @@ -1,7 +1,11 @@ #https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en#scripts +#This patch is needed by PFFT +#https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en#pfft #Within these scripts we apply the following patches that have been submitted to FFTW but are not yet included in FFTW-3.3.4: #We add two more global transposition algorithms to the planner. #We patch file mpi/transpose-pairwise.c in order to fix a double free bug. +#The patch file is fleshed out from install_fftw-3.3.4_gcc.sh +#at https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software/install_fftw-3.3.4_gcc.sh diff -rupN fftw-3.3.4/mpi/conf.c fftw-3.3.4-patched/mpi/conf.c --- fftw-3.3.4/mpi/conf.c 2014-03-04 19:41:03.000000000 +0100 +++ fftw-3.3.4-patched/mpi/conf.c 2015-09-05 05:53:19.085516467 +0200 diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb index 932a21ffc2..31ad0d2de5 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb @@ -18,8 +18,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=%(version)s/' ] builddependencies = [ - ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), - ('Perl', '5.20.3'), + ('Bison', '3.0.4'), + ('Perl', '5.20.3', '-bare'), ] dependencies = [ @@ -34,18 +34,19 @@ dependencies = [ configopts = '--disable-openmp --enable-mpi --enable-newuoa --disable-python --disable-gdlib ' configopts += '--with-libxc-prefix=$EBROOTLIBXC --with-gsl-prefix=$EBROOTGSL ' -configopts += '--with-blas="-L$MKLROOT/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" ' +configopts += '--with-blas="-L$MKLROOT/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential ' +iconfigure += '-lmkl_core -Wl,--end-group -lpthread" ' configopts += '--with-blacs="$MKLROOT/lib/intel64/libmkl_blacs_intelmpi_lp64.a" ' configopts += '--with-scalapack="$MKLROOT/lib/intel64/libmkl_scalapack_lp64.a" ' configopts += '--with-netcdf-prefix=$EBROOTNETCDFMINFORTRAN ' configopts += '--with-etsf-io-prefix=$EBROOTETSF_IO ' configopts += '--with-pfft-prefix=$EBROOTPFFT --with-mpifftw-prefix=$EBROOTFFTW ' +runtest = 'MPIEXEC=`which mpirun` check' + sanity_check_paths = { 'files': ["bin/octopus_mpi"], 'dirs': [] } -runtest = 'MPIEXEC=`which mpirun` check' - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb b/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb index 4ee4858b6d..4e9dda8fed 100644 --- a/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb @@ -16,11 +16,11 @@ source_urls = ['http://www.tu-chemnitz.de/~potts/workgroup/pippig/software/'] dependencies = [ ('FFTW', '3.3.4-p2'), - ('Autotools', '20150215', '', ('GNU', '4.9.3-2.25')), + ('Autotools', '20150215'), ] sanity_check_paths = { - 'files': ['lib/libpfft.so.0.0.0', 'lib/libpfft.a'], + 'files': ['lib/libpfft.%s' % SHLIB_EXT, 'lib/libpfft.a'], 'dirs': [], } -- GitLab From eb98e79dda3d753f5747b718b15fbab9f0acc7fa Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 7 Mar 2016 11:26:41 +0100 Subject: [PATCH 0844/2133] FFTW patch renamed --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb | 4 ++-- ...{FFTW_3.3.4-p2.patch => FFTW_3.3.4-p2_PFFT-20150905.patch} | 0 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/f/FFTW/{FFTW_3.3.4-p2.patch => FFTW_3.3.4-p2_PFFT-20150905.patch} (100%) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb index 05f0826bb5..2c340edd6e 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb @@ -13,10 +13,10 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%s-%s.tar.gz' % (name.lower(), version.split("-")[0])] source_urls = [homepage] -patches = ['%(name)s_%(version)s.patch'] +patches = ['%(name)s_%(version)s_PFFT-20150905.patch'] builddependencies = [ - ('Autotools', '20150215', '', ('GNU', '4.9.3-2.25')), + ('Autotools', '20150215'), ] # the patch changed a Makefile.am, so we need to call autoreconf diff --git a/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch b/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2_PFFT-20150905.patch similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2.patch rename to easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2_PFFT-20150905.patch -- GitLab From fb02e13bdc60e3ecc34a010a365f7e41e7ff85fb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 7 Mar 2016 12:02:21 +0100 Subject: [PATCH 0845/2133] typo corrected --- .../easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb index 31ad0d2de5..74a81115f6 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb @@ -35,7 +35,7 @@ dependencies = [ configopts = '--disable-openmp --enable-mpi --enable-newuoa --disable-python --disable-gdlib ' configopts += '--with-libxc-prefix=$EBROOTLIBXC --with-gsl-prefix=$EBROOTGSL ' configopts += '--with-blas="-L$MKLROOT/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential ' -iconfigure += '-lmkl_core -Wl,--end-group -lpthread" ' +configopts += '-lmkl_core -Wl,--end-group -lpthread" ' configopts += '--with-blacs="$MKLROOT/lib/intel64/libmkl_blacs_intelmpi_lp64.a" ' configopts += '--with-scalapack="$MKLROOT/lib/intel64/libmkl_scalapack_lp64.a" ' configopts += '--with-netcdf-prefix=$EBROOTNETCDFMINFORTRAN ' -- GitLab From 0d55e4c1a3c55122fe237ddb6969a58c46244515 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 7 Mar 2016 12:23:52 +0100 Subject: [PATCH 0846/2133] only bare from perl 5.20.2 --- .../easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb index 74a81115f6..9d2c7d09fa 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb @@ -19,7 +19,7 @@ source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=%(version)s/ builddependencies = [ ('Bison', '3.0.4'), - ('Perl', '5.20.3', '-bare'), + ('Perl', '5.20.2', '-bare'), ] dependencies = [ -- GitLab From 829932dc3bf99d8b8e2d2ef618d2dbbee3c41773 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Mar 2016 13:03:16 +0100 Subject: [PATCH 0847/2133] use %(pyver)s --- .../easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016a-Python-2.7.11.eb index 43296c33fb..b441f92cef 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016a-Python-2.7.11.eb @@ -1,6 +1,6 @@ name = 'SWIG' version = '3.0.8' -versionsuffix = '-Python-2.7.11' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.swig.org/' description = """SWIG is a software development tool that connects programs written in C and C++ with -- GitLab From 2c5348e808184eb5e4450639d0857b083a54c4b6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 7 Mar 2016 13:07:22 +0100 Subject: [PATCH 0848/2133] Fix mutil to copy & rename --- .../m/mutil/mutil-1.822.3-intel-2016a.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb index a12dea39eb..545df3ad39 100644 --- a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb +++ b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb @@ -10,12 +10,12 @@ GNU coreutils, which have achieved 10/30x rates on one/many nodes. toolchain = {'name': 'intel', 'version': '2016a'} sources = [ - "coreutils-8.22.tar.xz", + "coreutils-8.22.tar.xz", # must be first SOURCE_TGZ, ] source_urls = [ ('http://sourceforge.net/projects/mutil/files', 'download'), - GNU_SOURCE, + 'http://ftpmirror.gnu.org/coreutils', ] dependencies = [ @@ -24,8 +24,15 @@ dependencies = [ ('libgcrypt', '1.6.5'), ] +builddependencies = [('Automake', '1.14')] + +files_to_copy = [ + (['src/cp', 'src/md5sum'], ['mcp', 'msum'], 'bin'), + (['man/cp.1', 'man/md5sum.1'], ['mcp.1', 'msum.1'], 'man/man1'), +] + sanity_check_paths = { - 'files': ['bin/cp', 'bin/md5sum'], + 'files': ['bin/mcp', 'bin/msum'], 'dirs': ['man/man1'] } -- GitLab From 5489904cf3802ea81f9c90e8c3e0f295c3534c35 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 7 Mar 2016 13:17:17 +0100 Subject: [PATCH 0849/2133] Add mutil to shift --- easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb index 24ac3912b7..d1522854fe 100644 --- a/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb @@ -17,6 +17,7 @@ source_urls = [('http://sourceforge.net/projects/shiftc/files', 'download')] dependencies = [ ('Perl', '5.22.1'), ('bbFTP', '3.2.1'), + ('mutil', '1.822.3'), ] files_to_copy = [(['perl/shiftc', 'perl/shift-mgr', 'perl/shift-aux'], 'bin'), 'etc', (['doc/shiftc.1'], 'man/man1')] -- GitLab From 64b722d1dc9a6fb778a33df127bbe5477c6d545b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 7 Mar 2016 13:25:16 +0100 Subject: [PATCH 0850/2133] blas/blacs/scalapack fixes --- .../easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb index 9d2c7d09fa..932461139a 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb @@ -34,10 +34,9 @@ dependencies = [ configopts = '--disable-openmp --enable-mpi --enable-newuoa --disable-python --disable-gdlib ' configopts += '--with-libxc-prefix=$EBROOTLIBXC --with-gsl-prefix=$EBROOTGSL ' -configopts += '--with-blas="-L$MKLROOT/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential ' -configopts += '-lmkl_core -Wl,--end-group -lpthread" ' -configopts += '--with-blacs="$MKLROOT/lib/intel64/libmkl_blacs_intelmpi_lp64.a" ' -configopts += '--with-scalapack="$MKLROOT/lib/intel64/libmkl_scalapack_lp64.a" ' +configopts += '--with-blas="-L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += ''--with-blacs="-L$BLACS_LIB_DIR $LIBBLACS" ' +configopts += '--with-scalapack="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK" ' configopts += '--with-netcdf-prefix=$EBROOTNETCDFMINFORTRAN ' configopts += '--with-etsf-io-prefix=$EBROOTETSF_IO ' configopts += '--with-pfft-prefix=$EBROOTPFFT --with-mpifftw-prefix=$EBROOTFFTW ' -- GitLab From 88f9c315deedec6896397bd14395e8a02fd4840c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 7 Mar 2016 13:55:04 +0100 Subject: [PATCH 0851/2133] typo corrected --- .../easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb index 932461139a..5501b66a20 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb @@ -35,7 +35,7 @@ dependencies = [ configopts = '--disable-openmp --enable-mpi --enable-newuoa --disable-python --disable-gdlib ' configopts += '--with-libxc-prefix=$EBROOTLIBXC --with-gsl-prefix=$EBROOTGSL ' configopts += '--with-blas="-L$BLAS_LIB_DIR $LIBBLAS" ' -configopts += ''--with-blacs="-L$BLACS_LIB_DIR $LIBBLACS" ' +configopts += '--with-blacs="-L$BLACS_LIB_DIR $LIBBLACS" ' configopts += '--with-scalapack="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK" ' configopts += '--with-netcdf-prefix=$EBROOTNETCDFMINFORTRAN ' configopts += '--with-etsf-io-prefix=$EBROOTETSF_IO ' -- GitLab From a5df502069bc1995e723c9782e7e7bbae8d1aa62 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 7 Mar 2016 14:01:31 +0100 Subject: [PATCH 0852/2133] {vis}[intel-2016a] FLTK 1.3.3 with libX11 1.6.3 (REVIEW) --- .../FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb | 43 +++++++++++++++++++ .../l/libGLU/libGLU-9.0.0-intel-2016a.eb | 24 +++++++++++ .../libXcursor-1.1.14-intel-2016a.eb | 29 +++++++++++++ .../libXinerama-1.1.3-intel-2016a.eb | 31 +++++++++++++ .../xineramaproto-1.2.1-intel-2016a.eb | 19 ++++++++ .../x/xprop/xprop-1.2.2-intel-2016a.eb | 26 +++++++++++ 6 files changed, 172 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb new file mode 100644 index 0000000000..9929d550c8 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb @@ -0,0 +1,43 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.3' + +libx11 = 'libX11' +libxver = '1.6.3' +versionsuffix = '-%s-%s' % (libx11, libxver) + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + + +dependencies = [ + (libx11, libxver), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('Tcl', '8.6.4'), + ('Tk', '8.6.4', versionsuffix), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('xprop', '1.2.2'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config','bin/fluid'], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a.eb new file mode 100644 index 0000000000..46c9710adc --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '11.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb new file mode 100644 index 0000000000..e7e9608bd8 --- /dev/null +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXcursor' +version = '1.1.14' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Cursor management library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXfixes', '5.0.1'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['include/X11/Xcursor/Xcursor.h', 'lib/libXcursor.%s' % SHLIB_EXT, 'lib/libXcursor.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb new file mode 100644 index 0000000000..5963374589 --- /dev/null +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXinerama' +version = '1.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Xinerama multiple monitor library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('xineramaproto', '1.2.1'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXinerama.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb new file mode 100644 index 0000000000..d198aa80e4 --- /dev/null +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xineramaproto' +version = '1.2.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers for xinerama" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/panoramiXproto.h'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016a.eb new file mode 100644 index 0000000000..2da94927e9 --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.2' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftp.x.org/archive/individual/app/'] + +builddependencies = [ + ('xorg-macros', '1.19.0'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 23887fcc6a89ba97fc4b5c15dcd37615f5f3cffe Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 7 Mar 2016 14:37:15 +0100 Subject: [PATCH 0853/2133] {devel}[intel-2016a] Qt 4.8.7 (REVIEW) --- .../easyconfigs/q/Qt/Qt-4.8.7-intel-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a.eb new file mode 100644 index 0000000000..b51c2c0fac --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a.eb @@ -0,0 +1,24 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +dependencies = [ + ('GLib', '2.47.5'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXrender', '0.9.9'), +] + +moduleclass = 'devel' -- GitLab From 99e3a7528420d32bb228d76261515f61f0a02766 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 7 Mar 2016 14:55:35 +0100 Subject: [PATCH 0854/2133] {math}[intel-2016a] Qhull 2015.2 (REVIEW) --- .../q/Qhull/Qhull-2015.2-intel-2016a.eb | 37 ++++++++++++++++++ .../q/Qhull/Qhull-2015.2-intel-fix.patch | 39 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-fix.patch diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb new file mode 100644 index 0000000000..67f36525e6 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2015.2' + +homepage = 'http://www.qhull.org' +description = """ +Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, +furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, +and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +#recently checkged the Unix version numbering see https://github.com/Homebrew/homebrew-science/issues/3353 +sources = ['%(namelower)s-2015-src-7.2.0.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = [ + 'Qhull-%(version)s-intel-fix.patch', + 'Qhull_pkgconfig.patch', +] + +builddependencies = [('CMake', '3.4.3')] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.%s' % SHLIB_EXT, 'lib/pkgconfig/qhull.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-fix.patch b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-fix.patch new file mode 100644 index 0000000000..d38ea52b0a --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-fix.patch @@ -0,0 +1,39 @@ +# they use some weird template thing in pure C code to avoid +# warnings, I think, but only for intel compilers +# We remove the special case for intel and use the general one +# Ward Poelmans +diff -ru qhull-2012.1.orig/src/libqhull/qhull_a.h qhull-2012.1/src/libqhull/qhull_a.h +--- qhull-2015.2/src/libqhull/qhull_a.h.orig 2016-01-18 14:32:14.000000000 +0100 ++++ qhull-2015.2/src/libqhull/qhull_a.h 2016-03-07 10:42:19.223952420 +0100 +@@ -101,13 +101,7 @@ + + */ + +-#if defined(__cplusplus) && defined(__INTEL_COMPILER) && !defined(QHULL_OS_WIN) +-template +-inline void qhullUnused(T &x) { (void)x; } +-# define QHULL_UNUSED(x) qhullUnused(x); +-#else +-# define QHULL_UNUSED(x) (void)x; +-#endif ++#define QHULL_UNUSED(x) (void)x; + + /***** -libqhull.c prototypes (alphabetical after qhull) ********************/ + +--- qhull-2015.2/src/libqhull_r/qhull_ra.h.orig 2016-01-17 17:06:10.000000000 +0100 ++++ qhull-2015.2/src/libqhull_r/qhull_ra.h 2016-03-07 14:46:03.846048341 +0100 +@@ -101,13 +101,7 @@ + + */ + +-#if defined(__cplusplus) && defined(__INTEL_COMPILER) && !defined(QHULL_OS_WIN) +-template +-inline void qhullUnused(T &x) { (void)x; } +-# define QHULL_UNUSED(x) qhullUnused(x); +-#else +-# define QHULL_UNUSED(x) (void)x; +-#endif ++#define QHULL_UNUSED(x) (void)x; + + /***** -libqhull_r.c prototypes (alphabetical after qhull) ********************/ + -- GitLab From d1128a5b76975bfa039380828881b96db206f7b5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 7 Mar 2016 15:27:56 +0100 Subject: [PATCH 0855/2133] added firefox easyconfig --- .../easyconfigs/f/Firefox/Firefox-44.0.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb diff --git a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb new file mode 100644 index 0000000000..21da1fddad --- /dev/null +++ b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'Firefox' +version = '44.0.2' + +homepage = 'https://www.mozilla.org/en-US/firefox/new/' +description = """Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code + base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy + and security measures, smart searching, and RSS live bookmarks.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://ftp.mozilla.org/pub/firefox/releases/%(version)s/linux-x86_64/en-US/'] +sources = [SOURCELOWER_TAR_BZ2] + +sanity_check_paths = { + 'files': ['firefox'], + 'dirs': [] +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': "", +} + +moduleclass = 'tools' -- GitLab From a925cd1cdc39f71047190aab6990b66862f7f12f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 7 Mar 2016 15:35:37 +0100 Subject: [PATCH 0856/2133] Adjust mutil for easyblock --- easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb index 545df3ad39..4b04365a5a 100644 --- a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb +++ b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb @@ -26,11 +26,6 @@ dependencies = [ builddependencies = [('Automake', '1.14')] -files_to_copy = [ - (['src/cp', 'src/md5sum'], ['mcp', 'msum'], 'bin'), - (['man/cp.1', 'man/md5sum.1'], ['mcp.1', 'msum.1'], 'man/man1'), -] - sanity_check_paths = { 'files': ['bin/mcp', 'bin/msum'], 'dirs': ['man/man1'] -- GitLab From 65a1af206a0010a69602cd53305a5c6278dab88d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Mar 2016 15:39:28 +0100 Subject: [PATCH 0857/2133] add doSNOW package to R 3.2.3 easyconfigs --- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 1 + easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index c3a62add2c..dcabcfedb0 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -437,6 +437,7 @@ exts_list = [ ('ggm', '2.3', ext_options), ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index eb2673295f..ddf0479c12 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -437,6 +437,7 @@ exts_list = [ ('ggm', '2.3', ext_options), ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), ] moduleclass = 'lang' -- GitLab From f473964495a75dba4ccfc76d99a15a505e05d2c4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 7 Mar 2016 17:25:39 +0100 Subject: [PATCH 0858/2133] h5py for HDF5 serial --- ...-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb new file mode 100644 index 0000000000..1366ade8a4 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.16' +hdf5versuffix = '-serial' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s%s' % (hdf5ver, hdf5versuffix) + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.11'), + ('HDF5', hdf5ver, hdf5versuffix), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From 3c765b249a4e0c23371b73296cbfd0952bad0153 Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 7 Mar 2016 17:38:21 +0100 Subject: [PATCH 0859/2133] moving Cray stuff to boost.py --- .../b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb index 5be4348909..9d5320a12a 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb @@ -1,5 +1,4 @@ # contributed by Luca Marsella (CSCS) -easyblock = 'boostcray' name = 'Boost' version = "1.60.0" -- GitLab From 0039fc555e126d50f029ba45b45656b25e4f9118 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 7 Mar 2016 17:40:27 +0100 Subject: [PATCH 0860/2133] Don't use MPI in h5py-serial --- .../h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb index 1366ade8a4..68c3c3daaf 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb @@ -18,8 +18,7 @@ hdf5ver = '1.8.16' hdf5versuffix = '-serial' versionsuffix = '-Python-%%(pyver)s-HDF5-%s%s' % (hdf5ver, hdf5versuffix) -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' +prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' dependencies = [ ('Python', '2.7.11'), -- GitLab From 62238b6b9d58baab900019598d624d8eeb2e70bd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 7 Mar 2016 17:43:01 +0100 Subject: [PATCH 0861/2133] Fix shift easyconfig --- easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb index d1522854fe..62fb0dbd9d 100644 --- a/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb @@ -1,4 +1,4 @@ -easyblock = 'CmdCp' +easyblock = 'MakeCp' name = 'shift' version = '4.0' @@ -20,8 +20,8 @@ dependencies = [ ('mutil', '1.822.3'), ] +skipsteps = ['build'] files_to_copy = [(['perl/shiftc', 'perl/shift-mgr', 'perl/shift-aux'], 'bin'), 'etc', (['doc/shiftc.1'], 'man/man1')] -cmds_map = [] sanity_check_paths = { 'files': ['bin/shiftc'], -- GitLab From 6dc78e3a90bfe946af01cf276d8fd59116109277 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 7 Mar 2016 17:58:43 +0100 Subject: [PATCH 0862/2133] Add missing dep --- .../a/Automake/Automake-1.14-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.14-intel-2016a.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14-intel-2016a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-intel-2016a.eb new file mode 100644 index 0000000000..a1f5954bb7 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14-intel-2016a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.14" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 9f5af1710bca9fc15f41ac3c8b66dacbb4e36501 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 7 Mar 2016 18:01:12 +0100 Subject: [PATCH 0863/2133] Don't use MPI in -serial for h5py --- .../h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb index 68c3c3daaf..43d2050d00 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb @@ -9,7 +9,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to amounts of data.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -- GitLab From e3dad942d607df08b50472e178a41da94693a8be Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 7 Mar 2016 18:05:38 +0100 Subject: [PATCH 0864/2133] Make all h5py serial consistent --- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb | 2 ++ ....5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 3 ++- .../h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb | 2 +- 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index c839cbc2dd..f2d854aad2 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -19,6 +19,8 @@ pythonver = '2.7.9' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s-serial' % (python, pythonver) +prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' + dependencies = [ (python, pythonver), ('HDF5', '1.8.14', '-serial'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb index f070e8c226..6588f01027 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -19,10 +19,11 @@ pyver = '%s.10' % py_maj_min hdf5ver = '1.8.15-patch1' versionsuffix = '-Python-%s-HDF5-%s-serial' % (pyver, hdf5ver) +prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' + dependencies = [ ('Python', pyver), ('HDF5', hdf5ver), - ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb index 43d2050d00..108d4c4bb8 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb @@ -9,6 +9,7 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to amounts of data.""" toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': False} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] @@ -22,7 +23,6 @@ prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' dependencies = [ ('Python', '2.7.11'), ('HDF5', hdf5ver, hdf5versuffix), - ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), ] sanity_check_paths = { -- GitLab From 89039cbf0e0e1562e43ac11459688675f38ff6ce Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 7 Mar 2016 18:54:14 +0100 Subject: [PATCH 0865/2133] Add pkg-config as build dep --- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb | 2 ++ ...2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 2 ++ .../h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index f2d854aad2..12d6705dfa 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -26,6 +26,8 @@ dependencies = [ ('HDF5', '1.8.14', '-serial'), ] +builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] + sanity_check_paths = { 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], 'dirs': [], diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb index 6588f01027..7cd0e17232 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -26,6 +26,8 @@ dependencies = [ ('HDF5', hdf5ver), ] +builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%s/site-packages/' % py_maj_min], diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb index 108d4c4bb8..2f905991c2 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb @@ -25,6 +25,8 @@ dependencies = [ ('HDF5', hdf5ver, hdf5versuffix), ] +builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -- GitLab From 1e3228ddbbea445c7ace7fc6272bbb89789b2fd3 Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 7 Mar 2016 19:35:13 +0100 Subject: [PATCH 0866/2133] GMP doesn't work with -02, using lowopt (-01) --- easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb index 9fa2e217a8..34e4ce0776 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb @@ -9,11 +9,12 @@ description = """GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. """ toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'lowopt': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = [GNU_SOURCE] -preconfigopts = 'export CFLAGS=-mcmodel=large && ' +preconfigopts = 'export CFLAGS="$CFLAGS -mcmodel=large" && ' runtest = 'check' sanity_check_paths = { -- GitLab From d5a76df46e0f6394e6d77b3327d515e14048c818 Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 7 Mar 2016 19:36:23 +0100 Subject: [PATCH 0867/2133] fixed remarks --- .../p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 45a3845e6a..8c373b7caf 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -29,7 +29,7 @@ dependencies = [ ('GMP', '6.1.0'), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated Mar 1st 2016 @@ -45,9 +45,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], -- GitLab From b6aeea2faca9c3b5b73ac8977472229edf0b445a Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 8 Mar 2016 06:25:37 +1030 Subject: [PATCH 0868/2133] Added missing libxm2 and ncurses dependencies to gettext --- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb index 26649681d7..b35aee8501 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb @@ -13,6 +13,11 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +dependencies = [ + ('libxml2', '2.9.2'), + ('ncurses', '5.9'), +] + configopts = '--without-emacs' moduleclass = 'vis' -- GitLab From 799ddb504bc88f5ed4dab6bc1e0c02dc96f89786 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 8 Mar 2016 07:11:43 +1030 Subject: [PATCH 0869/2133] More consistent sanity checks --- .../easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb | 2 +- .../easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb | 5 +++-- .../easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb | 5 +++-- .../easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb | 5 +++-- .../easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb | 6 +++--- 5 files changed, 13 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb index 905088b61a..cff5f57f05 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb @@ -33,7 +33,7 @@ postinstallcmds = ['chmod +x %(installdir)s/fastqc'] sanity_check_paths = { 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.32.jar", "cisd-jhdf5.jar"], + "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.32.jar"], 'dirs': ["Contaminants", "Help", "Templates", "uk"], } diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb index 045b3e4281..ca09cb6324 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb @@ -24,8 +24,9 @@ dependencies = [(java, javaver)] postinstallcmds = ['chmod +x %(installdir)s/fastqc'] sanity_check_paths = { - 'files': ['fastqc'], - 'dirs': [], + 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", + "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar"], + 'dirs': ["Contaminants", "Help", "Templates", "uk", 'net', 'org'], } sanity_check_commands = [('fastqc', '-v')] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb index 6b39ac8445..17029e5d5a 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb @@ -24,8 +24,9 @@ dependencies = [(java, javaver)] postinstallcmds = ['chmod +x %(installdir)s/fastqc'] sanity_check_paths = { - 'files': ['fastqc'], - 'dirs': [], + 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", "LICENSE_JHDF5.txt" + "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar", "cisd-jhdf5.jar"], + 'dirs': ['Configuration', "Contaminants", "Help", "Templates", "uk", 'net', 'org'], } sanity_check_commands = [('fastqc', '-v')] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb index 4b0d9817eb..677e8d7c74 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb @@ -24,8 +24,9 @@ dependencies = [(java, javaver)] postinstallcmds = ['chmod +x %(installdir)s/fastqc'] sanity_check_paths = { - 'files': ['fastqc'], - 'dirs': [], + 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", "LICENSE_JHDF5.txt" + "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar", "cisd-jhdf5.jar"], + 'dirs': ['Configuration', "Contaminants", "Help", "Templates", "uk", 'net', 'org'], } sanity_check_commands = [('fastqc', '-v')] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb index 64fb816e8d..ddfb27a3db 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb @@ -24,9 +24,9 @@ dependencies = [(java, javaver)] postinstallcmds = ['chmod +x %(installdir)s/fastqc'] sanity_check_paths = { - 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.32.jar", "cisd-jhdf5.jar"], - 'dirs': ["Contaminants", "Help", "Templates", "uk"], + 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", "LICENSE_JHDF5.txt" + "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar", "cisd-jhdf5.jar"], + 'dirs': ['Configuration', "Contaminants", "Help", "Templates", "uk", 'net', 'org'], } sanity_check_commands = [('fastqc', '-v')] -- GitLab From 73d1c4958ce4a18957efa2887cc148724694cce6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 7 Mar 2016 23:09:40 +0000 Subject: [PATCH 0870/2133] Initial version --- .../BamUtil-libStatGen-1.0.13-foss-2015b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamUtil/BamUtil-libStatGen-1.0.13-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/BamUtil/BamUtil-libStatGen-1.0.13-foss-2015b.eb b/easybuild/easyconfigs/b/BamUtil/BamUtil-libStatGen-1.0.13-foss-2015b.eb new file mode 100644 index 0000000000..ceee101f27 --- /dev/null +++ b/easybuild/easyconfigs/b/BamUtil/BamUtil-libStatGen-1.0.13-foss-2015b.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute +# +# This is the version bundled with the libStatGen library + +name = 'BamUtil' +version = '1.0.13' +versionsuffix = 'libStatGen' + +easyblock = 'MakeCp' + +homepage = 'http://genome.sph.umich.edu/wiki/BamUtil' +description = """BamUtil is a repository that contains several programs + that perform operations on SAM/BAM files. All of these programs + are built into a single executable, bam.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['%(name)sLibStatGen.%(version)s.tgz'] +source_urls = ['http://genome.sph.umich.edu/w/images/7/70/'] + +files_to_copy = ["bamUtil/bin", "libStatGen"] + +sanity_check_paths = { + 'files': ["bin/bam"], + 'dirs': ["libStatGen"], +} + +moduleclass = 'bio' -- GitLab From 4fe7c4af6ce486e86d3175e9572273b778518a9a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 09:03:41 +0100 Subject: [PATCH 0871/2133] {vis}[intel-2016a] gnuplot 5.0.3 (REVIEW) --- .../g/gnuplot/gnuplot-5.0.3-intel-2016a.eb | 42 +++++++++++++++++++ .../l/libcerf/libcerf-1.4-intel-2016a.eb | 28 +++++++++++++ .../l/libgd/libgd-2.1.1-intel-2016a.eb | 26 ++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.1.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-intel-2016a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-intel-2016a.eb new file mode 100644 index 0000000000..131131cfee --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-intel-2016a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.3' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.14.6'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('libgd', '2.1.1'), + ('Pango', '1.39.0'), + ('libcerf', '1.4'), + ('Qt', '4.8.7'), +] + +configopts = '--with-qt=qt4 ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-2016a.eb new file mode 100644 index 0000000000..0d21d9de2a --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libcerf' +version = '1.4' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """libcerf is a self-contained numeric library that provides an efficient and accurate + implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TGZ] +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/' + 'http://apps.jcns.fz-juelich.de/src/libcerf/old' +] + +builddependencies = [ + ('Autotools', '20150215'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.1.1-intel-2016a.eb b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-intel-2016a.eb new file mode 100644 index 0000000000..6e0e817251 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.1.1' + +homepage = 'http://libgd.bitbucket.org/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/libgd/gd-libgd/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fontconfig', '2.11.94'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' -- GitLab From 6a287dac3c85a3cca4211fbb0233bb4b6f4ae143 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 09:16:12 +0100 Subject: [PATCH 0872/2133] commas fixed in libcerf --- easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-2016a.eb index 0d21d9de2a..e0a93e776c 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-intel-2016a.eb @@ -11,8 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TGZ] source_urls = [ - 'http://apps.jcns.fz-juelich.de/src/libcerf/' - 'http://apps.jcns.fz-juelich.de/src/libcerf/old' + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', ] builddependencies = [ -- GitLab From ff58f5a467379cd7ec1f7b319b30696b83a8e9ee Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 09:36:18 +0100 Subject: [PATCH 0873/2133] back to explicit blas/blacs/scalapack and fftw version fixes --- .../easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb | 4 ++-- ...-2015b.eb => FFTW-3.3.4-intel-2015b-PFFT-20150905.eb} | 7 ++++--- ...FFT-20150905.patch => FFTW_3.3.4-PFFT-20150905.patch} | 0 .../o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb | 9 +++++---- 4 files changed, 11 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.4-p2-intel-2015b.eb => FFTW-3.3.4-intel-2015b-PFFT-20150905.eb} (91%) rename easybuild/easyconfigs/f/FFTW/{FFTW_3.3.4-p2_PFFT-20150905.patch => FFTW_3.3.4-PFFT-20150905.patch} (100%) diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb index 1e01d1ca9a..0e4a07c55e 100644 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb @@ -21,8 +21,8 @@ source_urls = ['http://www.etsf.eu/system/files'] sources = [SOURCELOWER_TAR_GZ] configopts = "--with-netcdf-prefix=$EBROOTNETCDF " -configopts += "--with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' " -configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include'" +configopts += "--with-netcdf-libs='-L$EBROOTNETCDF/lib -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdf -lnetcdff' " +configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include '" dependencies = [ ('netCDF', '4.3.3.1'), diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb similarity index 91% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb index 2c340edd6e..80bd65820f 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-p2-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb @@ -1,7 +1,8 @@ easyblock = 'ConfigureMake' name = 'FFTW' -version = '3.3.4-p2' +version = '3.3.4' +versionsuffix = '-PFFT-20150905' homepage = 'http://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) @@ -10,10 +11,10 @@ description = """FFTW is a C subroutine library for computing the discrete Fouri toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s-%s.tar.gz' % (name.lower(), version.split("-")[0])] +sources = [ source_urls = [homepage] -patches = ['%(name)s_%(version)s_PFFT-20150905.patch'] +patches = ['%(name)s_%(version)s%s.patch' % versionsuffix] builddependencies = [ ('Autotools', '20150215'), diff --git a/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2_PFFT-20150905.patch b/easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-PFFT-20150905.patch similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-p2_PFFT-20150905.patch rename to easybuild/easyconfigs/f/FFTW/FFTW_3.3.4-PFFT-20150905.patch diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb index 5501b66a20..5f7abe5f1f 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb @@ -26,7 +26,7 @@ dependencies = [ ('libxc', '2.2.2'), ('netCDF', '4.3.3.1'), ('netCDF-Fortran', '4.4.2'), - ('FFTW', '3.3.4-p2'), + ('FFTW', '3.3.4', '-PFFT-20150905'), ('PFFT', '1.0.8-alpha'), ('ETSF_IO', '1.0.4'), ('GSL', '1.16'), @@ -34,9 +34,10 @@ dependencies = [ configopts = '--disable-openmp --enable-mpi --enable-newuoa --disable-python --disable-gdlib ' configopts += '--with-libxc-prefix=$EBROOTLIBXC --with-gsl-prefix=$EBROOTGSL ' -configopts += '--with-blas="-L$BLAS_LIB_DIR $LIBBLAS" ' -configopts += '--with-blacs="-L$BLACS_LIB_DIR $LIBBLACS" ' -configopts += '--with-scalapack="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK" ' +configopts += '--with-blas="-L$MKLROOT/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential' +configopts += ' -lmkl_core -Wl,--end-group -lpthread" ' +configopts += '--with-blacs="$MKLROOT/lib/intel64/libmkl_blacs_intelmpi_lp64.a" ' +configopts += '--with-scalapack="$MKLROOT/lib/intel64/libmkl_scalapack_lp64.a" ' configopts += '--with-netcdf-prefix=$EBROOTNETCDFMINFORTRAN ' configopts += '--with-etsf-io-prefix=$EBROOTETSF_IO ' configopts += '--with-pfft-prefix=$EBROOTPFFT --with-mpifftw-prefix=$EBROOTFFTW ' -- GitLab From 99f95e5050d0a504db3893198bcdcf068d4e4933 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 09:56:13 +0100 Subject: [PATCH 0874/2133] space corrected --- .../easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb index 9929d550c8..ff45e5cf97 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb @@ -36,7 +36,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/fltk-config','bin/fluid'], + 'files': ['bin/fltk-config', 'bin/fluid'], 'dirs': ['lib'], } -- GitLab From fdfbe72fffe6f8fcd21250b3140b301796cf74f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 09:56:42 +0100 Subject: [PATCH 0875/2133] fix style & sync issues in FastQC easyconfigs --- .../f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb | 12 +++++++----- .../f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb | 10 ++++++---- .../f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb | 10 ++++++---- .../f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb | 10 ++++++---- .../f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb | 10 ++++++---- 5 files changed, 31 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb index cff5f57f05..dd8206547e 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb @@ -6,7 +6,7 @@ # License:: MIT/GPL # ## -easyblock = "PackedBinary" +easyblock = 'PackedBinary' name = 'FastQC' version = '0.10.1' @@ -29,12 +29,14 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ['chmod +x %(installdir)s/fastqc'] +postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} sanity_check_paths = { - 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.32.jar"], - 'dirs': ["Contaminants", "Help", "Templates", "uk"], + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.32.jar'], + 'dirs': ['Contaminants', 'Help', 'Templates', 'uk'], } sanity_check_commands = [('fastqc', '-v')] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb index ca09cb6324..bfe51bfeb2 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb @@ -21,12 +21,14 @@ javaver = '1.7.0_60' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ['chmod +x %(installdir)s/fastqc'] +postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} sanity_check_paths = { - 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar"], - 'dirs': ["Contaminants", "Help", "Templates", "uk", 'net', 'org'], + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], } sanity_check_commands = [('fastqc', '-v')] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb index 17029e5d5a..6cc20e3f8a 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb @@ -21,12 +21,14 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ['chmod +x %(installdir)s/fastqc'] +postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} sanity_check_paths = { - 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", "LICENSE_JHDF5.txt" - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar", "cisd-jhdf5.jar"], - 'dirs': ['Configuration', "Contaminants", "Help", "Templates", "uk", 'net', 'org'], + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], } sanity_check_commands = [('fastqc', '-v')] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb index 677e8d7c74..7046190a29 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb @@ -21,12 +21,14 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ['chmod +x %(installdir)s/fastqc'] +postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} sanity_check_paths = { - 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", "LICENSE_JHDF5.txt" - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar", "cisd-jhdf5.jar"], - 'dirs': ['Configuration', "Contaminants", "Help", "Templates", "uk", 'net', 'org'], + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], } sanity_check_commands = [('fastqc', '-v')] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb index ddfb27a3db..231ac6979f 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb @@ -21,12 +21,14 @@ javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ['chmod +x %(installdir)s/fastqc'] +postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} sanity_check_paths = { - 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", "LICENSE_JHDF5.txt" - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar", "cisd-jhdf5.jar"], - 'dirs': ['Configuration', "Contaminants", "Help", "Templates", "uk", 'net', 'org'], + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], } sanity_check_commands = [('fastqc', '-v')] -- GitLab From 92820a52fbe08d5f5c6ed49ef55527faec620549 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 10:07:43 +0100 Subject: [PATCH 0876/2133] blas/blacs/scalapack issues part III --- .../easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb | 2 +- .../easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb index 80bd65820f..51541a8e59 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [ source_urls = [homepage] -patches = ['%(name)s_%(version)s%s.patch' % versionsuffix] +patches = ['%(name)s_%(version)s%(versionsuffix)s.patch'] builddependencies = [ ('Autotools', '20150215'), diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb index 5f7abe5f1f..e3cd54d745 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb @@ -34,8 +34,7 @@ dependencies = [ configopts = '--disable-openmp --enable-mpi --enable-newuoa --disable-python --disable-gdlib ' configopts += '--with-libxc-prefix=$EBROOTLIBXC --with-gsl-prefix=$EBROOTGSL ' -configopts += '--with-blas="-L$MKLROOT/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential' -configopts += ' -lmkl_core -Wl,--end-group -lpthread" ' +configopts += '--with-blas="-L$BLAS_LIB_DIR $LIBBLAS" ' configopts += '--with-blacs="$MKLROOT/lib/intel64/libmkl_blacs_intelmpi_lp64.a" ' configopts += '--with-scalapack="$MKLROOT/lib/intel64/libmkl_scalapack_lp64.a" ' configopts += '--with-netcdf-prefix=$EBROOTNETCDFMINFORTRAN ' -- GitLab From dcabe8e69077cee6c19e782143be8baeb779c389 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 10:13:50 +0100 Subject: [PATCH 0877/2133] Tck/Tk dep deleted --- ...el-2016a-libX11-1.6.3.eb => FLTK-1.3.3-intel-2016a.eb} | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) rename easybuild/easyconfigs/f/FLTK/{FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb => FLTK-1.3.3-intel-2016a.eb} (85%) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb similarity index 85% rename from easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb rename to easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb index ff45e5cf97..97b3b63c16 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb @@ -6,10 +6,6 @@ easyblock = 'ConfigureMake' name = 'FLTK' version = '1.3.3' -libx11 = 'libX11' -libxver = '1.6.3' -versionsuffix = '-%s-%s' % (libx11, libxver) - homepage = 'http://www.fltk.org' description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL @@ -23,11 +19,9 @@ source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] dependencies = [ - (libx11, libxver), + ('libX11', '1.6.3'), ('libXcursor', '1.1.14'), ('libXinerama', '1.1.3'), - ('Tcl', '8.6.4'), - ('Tk', '8.6.4', versionsuffix), ('Mesa', '11.1.2'), ('libGLU', '9.0.0'), ('libpng', '1.6.21'), -- GitLab From 35e5db373f1eafd352cedca92094117eac01c409 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 10:19:06 +0100 Subject: [PATCH 0878/2133] fix libxml2 conflict --- easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb index 1a6974652c..d439d240eb 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb @@ -15,8 +15,8 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), - ('libxml2', '2.9.2'), + ('libxml2', '2.9.3', '-Python-2.7.11'), ] -builddependencies = [('Python', '2.7.10')] +builddependencies = [('Python', '2.7.11')] moduleclass = 'vis' -- GitLab From edaa152bd88b122534a0ea45f264dfe9793edb4f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 10:29:23 +0100 Subject: [PATCH 0879/2133] comment corrected --- easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb index 67f36525e6..0261adb42f 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb @@ -12,7 +12,8 @@ and higher dimensions. Qhull implements the Quickhull algorithm for computing th toolchain = {'name': 'intel', 'version': '2016a'} -#recently checkged the Unix version numbering see https://github.com/Homebrew/homebrew-science/issues/3353 +# Recently changed the Unix version numbering see http://www.qhull.org/src/Changes.txt +# and https://github.com/Homebrew/homebrew-science/issues/3353 sources = ['%(namelower)s-2015-src-7.2.0.tgz'] source_urls = ['http://www.qhull.org/download/'] -- GitLab From 23e89aadc1658f84565030679b8730418ea924d5 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 10:52:19 +0100 Subject: [PATCH 0880/2133] version problems --- easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb index 0261adb42f..0fcce0e702 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # Recently changed the Unix version numbering see http://www.qhull.org/src/Changes.txt # and https://github.com/Homebrew/homebrew-science/issues/3353 -sources = ['%(namelower)s-2015-src-7.2.0.tgz'] +sources = ['%(namelower)s-%(version_major)-src-7.%(version_minor).0.tgz'] source_urls = ['http://www.qhull.org/download/'] patches = [ -- GitLab From 9e66df1369e5d31eb98dac9882ef648659f760ac Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 10:55:44 +0100 Subject: [PATCH 0881/2133] fftw source corrected --- .../easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb index 51541a8e59..d127590485 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb @@ -11,7 +11,7 @@ description = """FFTW is a C subroutine library for computing the discrete Fouri toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True} -sources = [ +sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] patches = ['%(name)s_%(version)s%(versionsuffix)s.patch'] -- GitLab From fd4a651e488f06b79db7c47991207fac6005faec Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 8 Mar 2016 10:57:54 +0100 Subject: [PATCH 0882/2133] add virtualenv for python 2.7.11 --- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 3 +++ .../p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 3 +++ 5 files changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index 34c45f4ac7..b360b95e8c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -126,6 +126,9 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index deaca9e5fd..2556554c13 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -126,6 +126,9 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index 74d0c82b50..3976e80bf2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -129,6 +129,9 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 87032c0ef5..62884700e2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -131,6 +131,9 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 6819a492c9..1ecb34bdf1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -129,6 +129,9 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), ] moduleclass = 'lang' -- GitLab From 21dd43f705080266b128fc592da7e12870d4584c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 11:02:13 +0100 Subject: [PATCH 0883/2133] {tools}[intel-2016a] GLPK 4.58 (REVIEW) --- .../g/GLPK/GLPK-4.58-intel-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-2016a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-2016a.eb new file mode 100644 index 0000000000..07ed2e7997 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.58' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.1.0')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c316d78c2ab2c50039f5a85d1f4426fe4d0a0aba Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 11:34:17 +0100 Subject: [PATCH 0884/2133] intermezzo --- .../f/freeglut/freeglut-3.0.0-intel-2016a.eb | 26 ++++++++++++++++ .../g/GL2PS/GL2PS-1.3.9-intel-2016a.eb | 30 ++++++++++++++++++ .../l/libXi/libXi-1.7.6-intel-2016a.eb | 30 ++++++++++++++++++ .../libXrandr/libXrandr-1.5.0-intel-2016a.eb | 31 +++++++++++++++++++ .../randrproto-1.5.0-intel-2016a.eb | 19 ++++++++++++ 5 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb new file mode 100644 index 0000000000..50285c0962 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libXi', '1.7.6'), + ('libXrandr', '1.5.0'), +] + +sanity_check_paths = { + 'files': ['lib64/libglut.a', 'lib64/libglut.%s' % SHLIB_EXT], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a.eb new file mode 100644 index 0000000000..640e02a1af --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('freeglut', '3.0.0'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb new file mode 100644 index 0000000000..265985f5e5 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' +name = 'libXi' +version = '1.7.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('inputproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb new file mode 100644 index 0000000000..d7c99042a3 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXrandr' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Resize, Rotate and Reflection extension library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('randrproto', '1.5.0'), + ('renderproto', '0.11'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrandr.%s' % SHLIB_EXT, 'lib/libXrandr.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb new file mode 100644 index 0000000000..278cc7bbbf --- /dev/null +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'randrproto' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrandr protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ed0d9428cc22e8503c90334a23b7fdce933f00ff Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 11:35:18 +0100 Subject: [PATCH 0885/2133] ssssss.... --- easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb index 0fcce0e702..4b32731c89 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # Recently changed the Unix version numbering see http://www.qhull.org/src/Changes.txt # and https://github.com/Homebrew/homebrew-science/issues/3353 -sources = ['%(namelower)s-%(version_major)-src-7.%(version_minor).0.tgz'] +sources = ['%(namelower)s-%(version_major)s-src-7.%(version_minor)s.0.tgz'] source_urls = ['http://www.qhull.org/download/'] patches = [ -- GitLab From 165a9dcdce97de0b25aeb446876292c37e5d8e93 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 11:38:58 +0100 Subject: [PATCH 0886/2133] PFFT FFTW name corrected --- easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb b/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb index 4e9dda8fed..cbbba0ee73 100644 --- a/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PFFT/PFFT-1.0.8-alpha-intel-2015b.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.tu-chemnitz.de/~potts/workgroup/pippig/software/'] dependencies = [ - ('FFTW', '3.3.4-p2'), + ('FFTW', '3.3.4', '-PFFT-20150905'), ('Autotools', '20150215'), ] -- GitLab From 2f7107a4a43e5988e7f71ae6667ba42df3851c52 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 11:50:07 +0100 Subject: [PATCH 0887/2133] fix GLib/Python version conflict --- .../GLib-2.46.0-intel-2015b-Python-2.7.11.eb | 24 +++++++++++++++++++ .../g/GLib/GLib-2.46.0-intel-2015b.eb | 4 ++-- .../Qt/Qt-4.8.7-intel-2015b-Python-2.7.11.eb | 2 +- .../Qt5/Qt5-5.5.1-intel-2015b-Mesa-11.0.8.eb | 2 +- 4 files changed, 28 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b-Python-2.7.11.eb new file mode 100644 index 0000000000..a273876d40 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.46.0' +pyver = '2.7.11' +versionsuffix = '-Python-%s' % pyver + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3', versionsuffix), +] +builddependencies = [('Python', pyver)] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb index d439d240eb..dfa82e6a76 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb @@ -15,8 +15,8 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), - ('libxml2', '2.9.3', '-Python-2.7.11'), + ('libxml2', '2.9.3', '-Python-2.7.10'), ] -builddependencies = [('Python', '2.7.11')] +builddependencies = [('Python', '2.7.10')] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2015b-Python-2.7.11.eb index 9f56d8e9fb..de2e107422 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2015b-Python-2.7.11.eb @@ -16,7 +16,7 @@ sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] patches = ['Qt-%(version)s_phonon-export.patch'] dependencies = [ - ('GLib', '2.46.0'), + ('GLib', '2.46.0', versionsuffix), ('libX11', '1.6.3', versionsuffix), ('libXt', '1.1.5', versionsuffix), ('libXrender', '0.9.9', versionsuffix), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.5.1-intel-2015b-Mesa-11.0.8.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.5.1-intel-2015b-Mesa-11.0.8.eb index 037b082375..f213e54acc 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.5.1-intel-2015b-Mesa-11.0.8.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.5.1-intel-2015b-Mesa-11.0.8.eb @@ -18,7 +18,7 @@ sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] pysuff = '-Python-2.7.11' dependencies = [ - ('GLib', '2.46.0'), + ('GLib', '2.46.0', pysuff), ('libX11', '1.6.3', pysuff), ('libXt', '1.1.5', pysuff), ('libXi', '1.7.4', pysuff), -- GitLab From 642ff13b533609863f3432e8cfdb3f6317bf40ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 12:21:25 +0100 Subject: [PATCH 0888/2133] stick to libxml2 2.9.2 in GLib 2.46.0 easyconfig (w/ Python 2.7.10) --- easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb index dfa82e6a76..1a6974652c 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.46.0-intel-2015b.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.6'), - ('libxml2', '2.9.3', '-Python-2.7.10'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.10')] -- GitLab From 6949836c17ad9cabc49b4c8b7617067e547f2a81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 13:34:46 +0200 Subject: [PATCH 0889/2133] add easyconfig Autoconf-2.69-gimkl-2.11.5.eb, add easyconfig Automake-1.15-gimkl-2.11.5.eb, add easyconfig Autotools-20150215-gimkl-2.11.5.eb, add easyconfig GMP-6.1.0-gimkl-2.11.5.eb, add easyconfig Python-2.7.11-gimkl-2.11.5.eb, add easyconfig SQLite-3.9.2-gimkl-2.11.5.eb, add easyconfig libtool-2.4.6-gimkl-2.11.5.eb --- .../a/Autoconf/Autoconf-2.69-gimkl-2.11.5.eb | 26 ++++ .../a/Automake/Automake-1.15-gimkl-2.11.5.eb | 33 +++++ .../Autotools-20150215-gimkl-2.11.5.eb | 17 +++ .../g/GMP/GMP-6.1.0-gimkl-2.11.5.eb | 30 ++++ .../l/libtool/libtool-2.4.6-gimkl-2.11.5.eb | 17 +++ .../p/Python/Python-2.7.11-gimkl-2.11.5.eb | 134 ++++++++++++++++++ .../s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb | 40 ++++++ 7 files changed, 297 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gimkl-2.11.5.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gimkl-2.11.5.eb new file mode 100644 index 0000000000..2a267fa96b --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gimkl-2.11.5.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb new file mode 100644 index 0000000000..d521a6ebe2 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-gimkl-2.11.5.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-gimkl-2.11.5.eb new file mode 100644 index 0000000000..3f48668b12 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-gimkl-2.11.5.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-gimkl-2.11.5.eb new file mode 100644 index 0000000000..3a93d0ea86 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-gimkl-2.11.5.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-gimkl-2.11.5.eb new file mode 100644 index 0000000000..03bf53f395 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-gimkl-2.11.5.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb new file mode 100644 index 0000000000..9c41844d2f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -0,0 +1,134 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%s-sse42.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb new file mode 100644 index 0000000000..8d257ce664 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' -- GitLab From 9d19e68f0e6ccbbe6fcfd09dcad6202c4a8efd0f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 13:35:51 +0200 Subject: [PATCH 0890/2133] add easyconfig CMake-3.4.3-gimkl-2.11.5.eb --- .../c/CMake/CMake-3.4.3-gimkl-2.11.5.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000..f5527c16d6 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ca146e53fc09c370a5d2aa4f1d06bc8fb736bc51 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 13:42:00 +0200 Subject: [PATCH 0891/2133] add easyconfig fixesproto-5.0-gimkl-2.11.5.eb, add easyconfig fontsproto-2.1.3-gimkl-2.11.5.eb, add easyconfig freetype-2.6.2-gimkl-2.11.5.eb, add easyconfig inputproto-2.3.1-gimkl-2.11.5.eb, add easyconfig kbproto-1.0.7-gimkl-2.11.5.eb, add easyconfig libX11-1.6.3-gimkl-2.11.5.eb, add easyconfig libXau-1.0.8-gimkl-2.11.5.eb, add easyconfig libXdamage-1.1.4-gimkl-2.11.5.eb, add easyconfig libXdmcp-1.1.2-gimkl-2.11.5.eb, add easyconfig libXext-1.3.3-gimkl-2.11.5.eb, add easyconfig libXfixes-5.0.1-gimkl-2.11.5.eb, add easyconfig libXfont-1.5.1-gimkl-2.11.5.eb, add easyconfig libfontenc-1.1.3-gimkl-2.11.5.eb, add easyconfig libpng-1.6.21-gimkl-2.11.5.eb, add easyconfig libpthread-stubs-0.3-gimkl-2.11.5.eb, add easyconfig libxcb-1.11.1-gimkl-2.11.5.eb, add easyconfig xextproto-7.3.0-gimkl-2.11.5.eb, add easyconfig xorg-macros-1.19.0-gimkl-2.11.5.eb, add easyconfig xproto-7.0.28-gimkl-2.11.5.eb, add easyconfig xtrans-1.3.5-gimkl-2.11.5.eb --- .../fixesproto/fixesproto-5.0-gimkl-2.11.5.eb | 19 ++++++++++ .../fontsproto-2.1.3-gimkl-2.11.5.eb | 20 ++++++++++ .../f/freetype/freetype-2.6.2-gimkl-2.11.5.eb | 22 +++++++++++ .../inputproto-2.3.1-gimkl-2.11.5.eb | 19 ++++++++++ .../k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb | 19 ++++++++++ .../l/libX11/libX11-1.6.3-gimkl-2.11.5.eb | 37 +++++++++++++++++++ .../l/libXau/libXau-1.0.8-gimkl-2.11.5.eb | 25 +++++++++++++ .../libXdamage-1.1.4-gimkl-2.11.5.eb | 25 +++++++++++++ .../l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb | 25 +++++++++++++ .../l/libXext/libXext-1.3.3-gimkl-2.11.5.eb | 33 +++++++++++++++++ .../libXfixes/libXfixes-5.0.1-gimkl-2.11.5.eb | 24 ++++++++++++ .../l/libXfont/libXfont-1.5.1-gimkl-2.11.5.eb | 31 ++++++++++++++++ .../libfontenc-1.1.3-gimkl-2.11.5.eb | 23 ++++++++++++ .../l/libpng/libpng-1.6.21-gimkl-2.11.5.eb | 26 +++++++++++++ .../libpthread-stubs-0.3-gimkl-2.11.5.eb | 20 ++++++++++ .../l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb | 33 +++++++++++++++++ .../xextproto/xextproto-7.3.0-gimkl-2.11.5.eb | 24 ++++++++++++ .../xorg-macros-1.19.0-gimkl-2.11.5.eb | 22 +++++++++++ .../x/xproto/xproto-7.0.28-gimkl-2.11.5.eb | 23 ++++++++++++ .../x/xtrans/xtrans-1.3.5-gimkl-2.11.5.eb | 22 +++++++++++ 20 files changed, 492 insertions(+) create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.21-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-gimkl-2.11.5.eb diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb new file mode 100644 index 0000000000..88fa55c14d --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000..0719ec51f4 --- /dev/null +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'fontsproto' +version = '2.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X11 font extension wire protocol" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.eb new file mode 100644 index 0000000000..fec100e1f0 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000..1a5db1eefa --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb new file mode 100644 index 0000000000..050b2bda55 --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000..52b296562e --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb new file mode 100644 index 0000000000..2e88286d07 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-gimkl-2.11.5.eb new file mode 100644 index 0000000000..e140118bf0 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-gimkl-2.11.5.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdamage' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Damage extension library""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xdamage.h', 'lib/libXdamage.%s' % SHLIB_EXT, 'lib/libXdamage.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb new file mode 100644 index 0000000000..9233da540e --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000..9ce9ef676f --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000..7f710e144e --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-gimkl-2.11.5.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000..9695dfd53a --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-gimkl-2.11.5.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', '2.6.2'), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000..7e68f16635 --- /dev/null +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-gimkl-2.11.5.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfontenc' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/xlibs/' +description = """X11 font encoding library""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/fonts/fontenc.h', 'lib/libfontenc.%s' % SHLIB_EXT, 'lib/libfontenc.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-gimkl-2.11.5.eb new file mode 100644 index 0000000000..9b5b14067a --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-gimkl-2.11.5.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000..b29ddd6099 --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-gimkl-2.11.5.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000..ab5bcf6b38 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb new file mode 100644 index 0000000000..1800fbf094 --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb new file mode 100644 index 0000000000..536fa8c6ff --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb new file mode 100644 index 0000000000..2591e436f9 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-gimkl-2.11.5.eb new file mode 100644 index 0000000000..4bfb1d13fb --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-gimkl-2.11.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From d7616cf593103eb79f93c480e3e5e403d1b2e5f1 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 8 Mar 2016 13:09:12 +0100 Subject: [PATCH 0892/2133] Add easyconfigs for SuperLU library --- .../c/CMake/CMake-3.2.3-ictce-7.3.5.eb | 31 +++++++++++++ .../s/SuperLU/SuperLU-5.1.1-foss-2016a.eb | 43 +++++++++++++++++++ .../s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb | 41 ++++++++++++++++++ 3 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb new file mode 100644 index 0000000000..5ae7415b1c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb new file mode 100644 index 0000000000..7f7793d488 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'SuperLU' +version = '5.1.1' + +homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True} + +source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] +sources = ["superlu_%(version)s.tar.gz"] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['260a3cd90b2100122abff38587a8290a'] + +# Set to ON to generate shared library +configopts = "-DBUILD_SHARED_LIBS=OFF" + +# Make sure not to build the slow BLAS library included in the package +configopts += " -Denable_blaslib=OFF" + +# Set the BLAS library to use +# cf https://cmake.org/cmake/help/latest/module/FindBLAS.html +# Unfortunately, OpenBLAS is not recognized by FindBLAS from CMake, +# we have to specify the OpenBLAS library manually +configopts += ' -DBLAS_LIBRARIES="${EBROOTOPENBLAS}/lib/libopenblas.a;-pthread"' + +# Make symlink to version-numbered library filename +installopts = ' && cd %(installdir)s/lib && ln -s libsuperlu_%(version)s.a libsuperlu.a' + +builddependencies = [('CMake', '3.4.3')] +separate_build_dir = True + +runtest = "test" + +sanity_check_paths = { + 'files': ["include/supermatrix.h", "lib/libsuperlu.a"], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb new file mode 100644 index 0000000000..514dd74cfa --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'SuperLU' +version = '5.1.1' + +homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'opt': True, 'pic': True} + +source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] +sources = ["superlu_%(version)s.tar.gz"] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['260a3cd90b2100122abff38587a8290a'] + +# Set to ON to generate shared library +configopts = "-DBUILD_SHARED_LIBS=OFF" + +# Make sure not to build the slow BLAS library included in the package +configopts += " -Denable_blaslib=OFF" + +# Set the BLAS library to use +# cf https://cmake.org/cmake/help/latest/module/FindBLAS.html +configopts += " -DBLA_VENDOR=Intel10_64lp" + +# Make symlink to version-numbered library filename +installopts = ' && cd %(installdir)s/lib && ln -s libsuperlu_%(version)s.a libsuperlu.a' + +builddependencies = [('CMake', '3.2.3')] +separate_build_dir = True + +runtest = "test" + +sanity_check_paths = { + 'files': ["include/supermatrix.h", "lib/libsuperlu.a"], + 'dirs': [], +} + +moduleclass = 'numlib' -- GitLab From 4b32067d95dc828d21e9b1be3b959669c99164e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 14:02:49 +0100 Subject: [PATCH 0893/2133] remove unneeded specs in FastQC easyconfigs --- easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb | 4 +--- easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb | 4 +--- easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb | 4 +--- easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb | 4 +--- easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb | 4 +--- 5 files changed, 5 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb index dd8206547e..5441477664 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb @@ -29,9 +29,7 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] - -modextrapaths = {'PATH': ['']} +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] sanity_check_paths = { 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb index bfe51bfeb2..89f6650b3c 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb @@ -21,9 +21,7 @@ javaver = '1.7.0_60' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] - -modextrapaths = {'PATH': ['']} +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] sanity_check_paths = { 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb index 6cc20e3f8a..fd7fff1b16 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb @@ -21,9 +21,7 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] - -modextrapaths = {'PATH': ['']} +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] sanity_check_paths = { 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb index 7046190a29..7c531942b3 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb @@ -21,9 +21,7 @@ javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] - -modextrapaths = {'PATH': ['']} +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] sanity_check_paths = { 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb index 231ac6979f..5b6a4d51e9 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb @@ -21,9 +21,7 @@ javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -postinstallcmds = ["chmod +x %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] - -modextrapaths = {'PATH': ['']} +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] sanity_check_paths = { 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', -- GitLab From 9e3cbd6e8dc553bf1e75d4f20feeeb581d22fca5 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 8 Mar 2016 14:16:47 +0100 Subject: [PATCH 0894/2133] Correct filename --- .../{SuperLU-5.1.1-ictce-7.35.eb => SuperLU-5.1.1-ictce-7.3.5.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/SuperLU/{SuperLU-5.1.1-ictce-7.35.eb => SuperLU-5.1.1-ictce-7.3.5.eb} (100%) diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb similarity index 100% rename from easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb rename to easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb -- GitLab From 8f587972c5fb8c57eb837458469e82bbb9dd58c5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 8 Mar 2016 15:04:10 +0100 Subject: [PATCH 0895/2133] Fix remarks --- .../m/mutil/mutil-1.822.3-intel-2016a.eb | 10 +- .../p/Perl/Perl-5.22.1-intel-2016a.eb | 110 +++++++++--------- .../s/shift/shift-4.0-intel-2016a.eb | 2 +- 3 files changed, 63 insertions(+), 59 deletions(-) diff --git a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb index 4b04365a5a..363a280e90 100644 --- a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb +++ b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb @@ -1,5 +1,4 @@ name = 'mutil' -version = '1.822.3' homepage = 'http://people.nas.nasa.gov/~kolano/projects/mutil.html' description = """Mutil is a set of standard utilities that have been parallelized to maximize performance on @@ -9,12 +8,16 @@ GNU coreutils, which have achieved 10/30x rates on one/many nodes. toolchain = {'name': 'intel', 'version': '2016a'} +coreutils_maj = '8' +coreutils_min = '22' +version = '1.%s%s.3' % (coreutils_maj, coreutils_min) + sources = [ - "coreutils-8.22.tar.xz", # must be first + "coreutils-%s.%s.tar.xz" % (coreutils_maj, coreutils_min), # must be first SOURCE_TGZ, ] source_urls = [ - ('http://sourceforge.net/projects/mutil/files', 'download'), + SOURCEFORGE_SOURCE, 'http://ftpmirror.gnu.org/coreutils', ] @@ -24,6 +27,7 @@ dependencies = [ ('libgcrypt', '1.6.5'), ] +# needs 1.14 to work builddependencies = [('Automake', '1.14')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index b46dec87b6..2729eb6536 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -7,11 +7,11 @@ description = """Larry Wall's Practical Extraction and Report Language""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://www.cpan.org/src/5.0'] +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] exts_list = [ - ('Config::General', '2.58', { + ('Config::General', '2.60', { 'source_tmpl': 'Config-General-2.58.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], }), @@ -27,7 +27,7 @@ exts_list = [ 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), - ('TAP::Harness::Env', '3.35', { + ('TAP::Harness::Env', '3.36', { 'source_tmpl': 'Test-Harness-3.35.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), @@ -47,7 +47,7 @@ exts_list = [ 'source_tmpl': 'Text-Glob-0.09.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], }), - ('Regexp::Common', '2013031301', { + ('Regexp::Common', '2016020301', { 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], }), @@ -63,15 +63,15 @@ exts_list = [ 'source_tmpl': 'Test-Fatal-0.014.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), - ('Test::Warnings', '0.021', { + ('Test::Warnings', '0.026', { 'source_tmpl': 'Test-Warnings-0.021.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('DateTime::Locale', '0.46', { + ('DateTime::Locale', '1.02', { 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), - ('DateTime::TimeZone', '1.93', { + ('DateTime::TimeZone', '1.95', { 'source_tmpl': 'DateTime-TimeZone-1.93.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -87,11 +87,11 @@ exts_list = [ 'source_tmpl': 'Module-Runtime-0.014.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], }), - ('Try::Tiny', '0.22', { + ('Try::Tiny', '0.24', { 'source_tmpl': 'Try-Tiny-0.22.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], }), - ('Params::Validate', '1.21', { + ('Params::Validate', '1.22', { 'source_tmpl': 'Params-Validate-1.21.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -107,7 +107,7 @@ exts_list = [ 'source_tmpl': 'Class-Singleton-1.5.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], }), - ('DateTime', '1.20', { + ('DateTime', '1.25', { 'source_tmpl': 'DateTime-1.20.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -115,11 +115,11 @@ exts_list = [ 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('Module::Build', '0.4214', { + ('Module::Build', '0.4216', { 'source_tmpl': 'Module-Build-0.4214.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), - ('Readonly', '2.00', { + ('Readonly', '2.01', { 'source_tmpl': 'Readonly-2.00.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO'], }), @@ -127,7 +127,7 @@ exts_list = [ 'source_tmpl': 'Git-0.41.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], }), - ('Tree::DAG_Node', '1.27', { + ('Tree::DAG_Node', '1.29', { 'source_tmpl': 'Tree-DAG_Node-1.27.tgz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], }), @@ -143,7 +143,7 @@ exts_list = [ 'source_tmpl': 'DBI-1.634.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], }), - ('DBD::SQLite', '1.48', { + ('DBD::SQLite', '1.50', { 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], }), @@ -159,11 +159,11 @@ exts_list = [ 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD'], }), - ('Shell', '0.72', { + ('Shell', '0.73', { 'source_tmpl': 'Shell-0.72.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], }), - ('File::Spec', '3.47', { + ('File::Spec', '3.62', { 'source_tmpl': 'PathTools-3.47.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], }), @@ -203,7 +203,7 @@ exts_list = [ 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], }), - ('Test::Exception', '0.40', { + ('Test::Exception', '0.43', { 'source_tmpl': 'Test-Exception-0.40.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], }), @@ -211,7 +211,7 @@ exts_list = [ 'source_tmpl': 'Text-Table-1.130.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], }), - ('MIME::Types', '2.11', { + ('MIME::Types', '2.13', { 'source_tmpl': 'MIME-Types-2.11.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), @@ -227,7 +227,7 @@ exts_list = [ 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], }), - ('HTML::Parser', '3.71', { + ('HTML::Parser', '3.72', { 'source_tmpl': 'HTML-Parser-3.71.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], }), @@ -251,7 +251,7 @@ exts_list = [ 'source_tmpl': 'Class-ISA-0.36.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], }), - ('URI', '1.69', { + ('URI', '1.71', { 'source_tmpl': 'URI-1.69.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), @@ -271,7 +271,7 @@ exts_list = [ 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], }), - ('Pod::POM', '2.00', { + ('Pod::POM', '2.01', { 'source_tmpl': 'Pod-POM-2.00.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], }), @@ -279,7 +279,7 @@ exts_list = [ 'source_tmpl': 'Math-Round-0.07.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], }), - ('Text::Diff', '1.43', { + ('Text::Diff', '1.44', { 'source_tmpl': 'Text-Diff-1.43.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], }), @@ -287,7 +287,7 @@ exts_list = [ 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), - ('IO::Socket::SSL', '2.020', { + ('IO::Socket::SSL', '2.024', { 'source_tmpl': 'IO-Socket-SSL-2.020.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], }), @@ -311,7 +311,7 @@ exts_list = [ 'source_tmpl': 'IO-stringy-2.111.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], }), - ('Getopt::Long', '2.47', { + ('Getopt::Long', '2.48', { 'source_tmpl': 'Getopt-Long-2.47.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], }), @@ -335,7 +335,7 @@ exts_list = [ 'source_tmpl': 'Net-HTTP-6.09.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('Test::Deep', '0.117', { + ('Test::Deep', '1.120', { 'source_tmpl': 'Test-Deep-0.117.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), @@ -347,7 +347,7 @@ exts_list = [ 'source_tmpl': 'MRO-Compat-0.12.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], }), - ('Moo', '2.000002', { + ('Moo', '2.001001', { 'source_tmpl': 'Moo-2.000002.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], }), @@ -375,7 +375,7 @@ exts_list = [ 'source_tmpl': 'IPC-Run-0.94.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], }), - ('HTML::Entities::Interpolate', '1.05', { + ('HTML::Entities::Interpolate', '1.09', { 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], }), @@ -391,7 +391,7 @@ exts_list = [ 'source_tmpl': 'Class-Accessor-0.34.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], }), - ('Test::Differences', '0.63', { + ('Test::Differences', '0.64', { 'source_tmpl': 'Test-Differences-0.63.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], }), @@ -399,7 +399,7 @@ exts_list = [ 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], }), - ('Package::DeprecationManager', '0.14', { + ('Package::DeprecationManager', '0.15', { 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -411,7 +411,7 @@ exts_list = [ 'source_tmpl': 'TimeDate-2.30.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], }), - ('version', '0.9912', { + ('version', '0.9915', { 'source_tmpl': 'version-0.9912.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], }), @@ -432,7 +432,7 @@ exts_list = [ 'source_tmpl': 'Sub-Name-0.14.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('Time::Piece', '1.30', { + ('Time::Piece', '1.31', { 'source_tmpl': 'Time-Piece-1.30.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), @@ -460,7 +460,7 @@ exts_list = [ 'source_tmpl': 'Canary-Stability-2006.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], }), - ('AnyEvent', '7.11', { + ('AnyEvent', '7.12', { 'source_tmpl': 'AnyEvent-7.11.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], }), @@ -520,7 +520,7 @@ exts_list = [ 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], }), - ('Statistics::Descriptive', '3.0609', { + ('Statistics::Descriptive', '3.0612', { 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], }), @@ -528,7 +528,7 @@ exts_list = [ 'source_tmpl': 'Class-Load-0.23.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('LWP::Simple', '6.13', { + ('LWP::Simple', '6.15', { 'source_tmpl': 'libwww-perl-6.13.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), @@ -540,7 +540,7 @@ exts_list = [ 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], }), - ('GD::Graph', '1.49', { + ('GD::Graph', '1.52', { 'source_tmpl': 'GDGraph-1.49.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], }), @@ -580,19 +580,19 @@ exts_list = [ 'source_tmpl': 'Class-Inspector-1.28.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], }), - ('Parse::RecDescent', '1.967012', { + ('Parse::RecDescent', '1.967013', { 'source_tmpl': 'Parse-RecDescent-1.967012.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], }), - ('Carp', '1.36', { + ('Carp', '1.38', { 'source_tmpl': 'Carp-1.36.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), - ('XML::XPath', '1.13', { + ('XML::XPath', '1.33', { 'source_tmpl': 'XML-XPath-1.13.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT'], }), - ('Capture::Tiny', '0.30', { + ('Capture::Tiny', '0.36', { 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], }), @@ -616,7 +616,7 @@ exts_list = [ 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], }), - ('LWP', '6.13', { + ('LWP', '6.15', { 'source_tmpl': 'libwww-perl-6.13.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), @@ -648,7 +648,7 @@ exts_list = [ 'source_tmpl': 'Text-Balanced-2.03.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], }), - ('strictures', '2.000001', { + ('strictures', '2.000002', { 'source_tmpl': 'strictures-2.000001.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], }), @@ -656,7 +656,7 @@ exts_list = [ 'source_tmpl': 'Switch-2.17.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], }), - ('File::Which', '1.19', { + ('File::Which', '1.21', { 'source_tmpl': 'File-Which-1.19.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], }), @@ -692,7 +692,7 @@ exts_list = [ 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], }), - ('Exception::Class', '1.39', { + ('Exception::Class', '1.40', { 'source_tmpl': 'Exception-Class-1.39.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -724,7 +724,7 @@ exts_list = [ 'source_tmpl': 'IO-String-1.08.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], }), - ('XML::Simple', '2.20', { + ('XML::Simple', '2.22', { 'source_tmpl': 'XML-Simple-2.20.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], }), @@ -748,7 +748,7 @@ exts_list = [ 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], }), - ('Scalar::Util', '1.42', { + ('Scalar::Util', '1.43', { 'source_tmpl': 'Scalar-List-Utils-1.42.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], }), @@ -808,7 +808,7 @@ exts_list = [ 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], }), - ('Log::Handler', '0.87', { + ('Log::Handler', '0.84', { 'source_tmpl': 'Log-Handler-0.87.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], }), @@ -816,11 +816,11 @@ exts_list = [ 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], }), - ('HTML::Entities', '3.71', { + ('HTML::Entities', '3.72', { 'source_tmpl': 'HTML-Parser-3.71.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], }), - ('Devel::StackTrace', '2.00', { + ('Devel::StackTrace', '2.01', { 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -832,7 +832,7 @@ exts_list = [ 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], }), - ('Moose', '2.1603', { + ('Moose', '2.1605', { 'source_tmpl': 'Moose-2.1603.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), @@ -848,7 +848,7 @@ exts_list = [ 'source_tmpl': 'IPC-Run3-0.048.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), - ('File::Find::Rule', '0.33', { + ('File::Find::Rule', '0.34', { 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], }), @@ -868,11 +868,11 @@ exts_list = [ 'source_tmpl': 'Data-OptList-0.109.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), - ('CPANPLUS', '0.9154', { + ('CPANPLUS', '0.9156', { 'source_tmpl': 'CPANPLUS-0.9154.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), - ('Test::Harness', '3.35', { + ('Test::Harness', '3.36', { 'source_tmpl': 'Test-Harness-3.35.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), @@ -880,15 +880,15 @@ exts_list = [ 'source_tmpl': 'IO-Tty-1.12.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], }), - ('Text::Soundex', '3.04', { + ('Text::Soundex', '3.05', { 'source_tmpl': 'Text-Soundex-3.04.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), - ('Lingua::EN::PluralToSingular', '0.14', { + ('Lingua::EN::PluralToSingular', '0.18', { 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB'], }), - ('Want', '0.26', { + ('Want', '0.29', { 'source_tmpl': 'Want-0.26.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], }), diff --git a/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb index 62fb0dbd9d..14d911f6fc 100644 --- a/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb @@ -12,7 +12,7 @@ performance and resilience for local and remote transfers through a variety of t toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TGZ] -source_urls = [('http://sourceforge.net/projects/shiftc/files', 'download')] +source_urls = [SOURCEFORGE_SOURCE] dependencies = [ ('Perl', '5.22.1'), -- GitLab From 753e200d5c6fac3ef8f3f243fed29ce9ec81b918 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 15:23:06 +0100 Subject: [PATCH 0896/2133] {vis}[intel-2016a] GL2PS 1.3.9 (REVIEW) --- .../f/freeglut/freeglut-3.0.0-intel-2016a.eb | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb index 50285c0962..095b105fda 100644 --- a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb @@ -14,10 +14,21 @@ source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] builddependencies = [('CMake', '3.4.3')] dependencies = [ - ('libXi', '1.7.6'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', '11.1.2'), ] +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' + sanity_check_paths = { 'files': ['lib64/libglut.a', 'lib64/libglut.%s' % SHLIB_EXT], 'dirs': ['include/GL'], -- GitLab From 8669cc78fb308a53a24225f9fbb9c6cb0862ff82 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 8 Mar 2016 15:36:52 +0100 Subject: [PATCH 0897/2133] Fix shift download url --- easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb index 14d911f6fc..62fb0dbd9d 100644 --- a/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb @@ -12,7 +12,7 @@ performance and resilience for local and remote transfers through a variety of t toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TGZ] -source_urls = [SOURCEFORGE_SOURCE] +source_urls = [('http://sourceforge.net/projects/shiftc/files', 'download')] dependencies = [ ('Perl', '5.22.1'), -- GitLab From c4a331b38985bf7c412ad788b2e519ed8b3abf12 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 8 Mar 2016 14:50:41 +0000 Subject: [PATCH 0898/2133] Fix download location --- .../Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb | 2 +- .../Xerces-C++-3.1.1-intel-2015a.eb | 3 ++- .../Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb | 2 +- .../Xerces-C++/Xerces-C++-3.1.2-foss-2015b.eb | 25 +++++++++++++++++++ .../Xerces-C++-3.1.2-goolf-1.7.20.eb | 2 +- .../Xerces-C++-3.1.2-intel-2015a.eb | 2 +- 6 files changed, 31 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015b.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb index 443076c83e..031a0f54b9 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['xerces-c-%(version)s.tar.gz'] source_urls = [ - 'http://apache.belnet.be/xerces/c/3/sources/' + 'http://archive.apache.org/dist/xerces/c/%(version_major)s/sources/' ] dependencies = [ diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb index 9437987e64..2dd8450711 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb @@ -10,9 +10,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = ['xerces-c-%(version)s.tar.gz'] source_urls = [ - 'http://apache.belnet.be/xerces/c/3/sources/' + 'http://archive.apache.org/dist/xerces/c/%(version_major)s/sources/' ] + dependencies = [ ('cURL', '7.40.0'), ] diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb index e2bfd14b2a..b0abf7e5eb 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['xerces-c-%(version)s.tar.gz'] source_urls = [ - 'http://apache.belnet.be/xerces/c/%(version_major)s/sources/' + 'http://archive.apache.org/dist/xerces/c/%(version_major)s/sources/' ] dependencies = [ diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015b.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015b.eb new file mode 100644 index 0000000000..087db393ee --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.1.2' + +homepage = 'http://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['xerces-c-%(version)s.tar.gz'] +source_urls = [ + 'http://archive.apache.org/dist/xerces/c/%(version_major)s/sources/' +] + +dependencies = [ + ('cURL', '7.44.0'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb index 258f78b64a..64c371a561 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} sources = ['xerces-c-%(version)s.tar.gz'] source_urls = [ - 'http://apache.belnet.be/xerces/c/%(version_major)s/sources/' + 'http://archive.apache.org/dist/xerces/c/%(version_major)s/sources/' ] dependencies = [ diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb index 78f997327e..1ddefd9f96 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = ['xerces-c-%(version)s.tar.gz'] source_urls = [ - 'http://apache.belnet.be/xerces/c/%(version_major)s/sources/' + 'http://archive.apache.org/dist/xerces/c/%(version_major)s/sources/' ] dependencies = [ -- GitLab From 9563423f78b19d1f50b77580721e630b7ea83364 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 16:07:46 +0100 Subject: [PATCH 0899/2133] {numlib}[intel-2016a] SuiteSparse 4.5.1 with external METIS (REVIEW) --- .../m/METIS/METIS-5.1.0-intel-2016a.eb | 22 +++++++++++++++++ ...iteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb | 24 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a.eb new file mode 100644 index 0000000000..b79e95dce7 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, + and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the + multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.4.3')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000..f6beb0e31f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb @@ -0,0 +1,24 @@ +name = 'SuiteSparse' +version = '4.5.1' + +homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' + +maxparallel = 1 + +moduleclass = 'numlib' -- GitLab From 7d7e21cc3c7cdeee99070768396013a48476d580 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 8 Mar 2016 16:18:14 +0100 Subject: [PATCH 0900/2133] Do extensions update in other PR --- .../p/Perl/Perl-5.22.1-intel-2016a.eb | 108 +++++++++--------- 1 file changed, 54 insertions(+), 54 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index 2729eb6536..53fd47ad2d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -11,7 +11,7 @@ source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] exts_list = [ - ('Config::General', '2.60', { + ('Config::General', '2.58', { 'source_tmpl': 'Config-General-2.58.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], }), @@ -27,7 +27,7 @@ exts_list = [ 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), - ('TAP::Harness::Env', '3.36', { + ('TAP::Harness::Env', '3.35', { 'source_tmpl': 'Test-Harness-3.35.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), @@ -47,7 +47,7 @@ exts_list = [ 'source_tmpl': 'Text-Glob-0.09.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], }), - ('Regexp::Common', '2016020301', { + ('Regexp::Common', '2013031301', { 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], }), @@ -63,15 +63,15 @@ exts_list = [ 'source_tmpl': 'Test-Fatal-0.014.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), - ('Test::Warnings', '0.026', { + ('Test::Warnings', '0.021', { 'source_tmpl': 'Test-Warnings-0.021.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('DateTime::Locale', '1.02', { + ('DateTime::Locale', '0.46', { 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), - ('DateTime::TimeZone', '1.95', { + ('DateTime::TimeZone', '1.93', { 'source_tmpl': 'DateTime-TimeZone-1.93.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -87,11 +87,11 @@ exts_list = [ 'source_tmpl': 'Module-Runtime-0.014.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], }), - ('Try::Tiny', '0.24', { + ('Try::Tiny', '0.22', { 'source_tmpl': 'Try-Tiny-0.22.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], }), - ('Params::Validate', '1.22', { + ('Params::Validate', '1.21', { 'source_tmpl': 'Params-Validate-1.21.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -107,7 +107,7 @@ exts_list = [ 'source_tmpl': 'Class-Singleton-1.5.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], }), - ('DateTime', '1.25', { + ('DateTime', '1.20', { 'source_tmpl': 'DateTime-1.20.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -115,11 +115,11 @@ exts_list = [ 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('Module::Build', '0.4216', { + ('Module::Build', '0.4214', { 'source_tmpl': 'Module-Build-0.4214.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), - ('Readonly', '2.01', { + ('Readonly', '2.00', { 'source_tmpl': 'Readonly-2.00.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO'], }), @@ -127,7 +127,7 @@ exts_list = [ 'source_tmpl': 'Git-0.41.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], }), - ('Tree::DAG_Node', '1.29', { + ('Tree::DAG_Node', '1.27', { 'source_tmpl': 'Tree-DAG_Node-1.27.tgz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], }), @@ -143,7 +143,7 @@ exts_list = [ 'source_tmpl': 'DBI-1.634.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], }), - ('DBD::SQLite', '1.50', { + ('DBD::SQLite', '1.48', { 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], }), @@ -159,11 +159,11 @@ exts_list = [ 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD'], }), - ('Shell', '0.73', { + ('Shell', '0.72', { 'source_tmpl': 'Shell-0.72.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], }), - ('File::Spec', '3.62', { + ('File::Spec', '3.47', { 'source_tmpl': 'PathTools-3.47.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], }), @@ -203,7 +203,7 @@ exts_list = [ 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], }), - ('Test::Exception', '0.43', { + ('Test::Exception', '0.40', { 'source_tmpl': 'Test-Exception-0.40.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], }), @@ -211,7 +211,7 @@ exts_list = [ 'source_tmpl': 'Text-Table-1.130.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], }), - ('MIME::Types', '2.13', { + ('MIME::Types', '2.11', { 'source_tmpl': 'MIME-Types-2.11.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), @@ -227,7 +227,7 @@ exts_list = [ 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], }), - ('HTML::Parser', '3.72', { + ('HTML::Parser', '3.71', { 'source_tmpl': 'HTML-Parser-3.71.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], }), @@ -251,7 +251,7 @@ exts_list = [ 'source_tmpl': 'Class-ISA-0.36.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], }), - ('URI', '1.71', { + ('URI', '1.69', { 'source_tmpl': 'URI-1.69.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), @@ -271,7 +271,7 @@ exts_list = [ 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], }), - ('Pod::POM', '2.01', { + ('Pod::POM', '2.00', { 'source_tmpl': 'Pod-POM-2.00.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], }), @@ -279,7 +279,7 @@ exts_list = [ 'source_tmpl': 'Math-Round-0.07.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], }), - ('Text::Diff', '1.44', { + ('Text::Diff', '1.43', { 'source_tmpl': 'Text-Diff-1.43.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], }), @@ -287,7 +287,7 @@ exts_list = [ 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), - ('IO::Socket::SSL', '2.024', { + ('IO::Socket::SSL', '2.020', { 'source_tmpl': 'IO-Socket-SSL-2.020.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], }), @@ -311,7 +311,7 @@ exts_list = [ 'source_tmpl': 'IO-stringy-2.111.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], }), - ('Getopt::Long', '2.48', { + ('Getopt::Long', '2.47', { 'source_tmpl': 'Getopt-Long-2.47.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], }), @@ -335,7 +335,7 @@ exts_list = [ 'source_tmpl': 'Net-HTTP-6.09.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('Test::Deep', '1.120', { + ('Test::Deep', '0.117', { 'source_tmpl': 'Test-Deep-0.117.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), @@ -347,7 +347,7 @@ exts_list = [ 'source_tmpl': 'MRO-Compat-0.12.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], }), - ('Moo', '2.001001', { + ('Moo', '2.000002', { 'source_tmpl': 'Moo-2.000002.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], }), @@ -375,7 +375,7 @@ exts_list = [ 'source_tmpl': 'IPC-Run-0.94.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], }), - ('HTML::Entities::Interpolate', '1.09', { + ('HTML::Entities::Interpolate', '1.05', { 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], }), @@ -391,7 +391,7 @@ exts_list = [ 'source_tmpl': 'Class-Accessor-0.34.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], }), - ('Test::Differences', '0.64', { + ('Test::Differences', '0.63', { 'source_tmpl': 'Test-Differences-0.63.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], }), @@ -399,7 +399,7 @@ exts_list = [ 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], }), - ('Package::DeprecationManager', '0.15', { + ('Package::DeprecationManager', '0.14', { 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -411,7 +411,7 @@ exts_list = [ 'source_tmpl': 'TimeDate-2.30.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], }), - ('version', '0.9915', { + ('version', '0.9912', { 'source_tmpl': 'version-0.9912.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], }), @@ -432,7 +432,7 @@ exts_list = [ 'source_tmpl': 'Sub-Name-0.14.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('Time::Piece', '1.31', { + ('Time::Piece', '1.30', { 'source_tmpl': 'Time-Piece-1.30.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), @@ -460,7 +460,7 @@ exts_list = [ 'source_tmpl': 'Canary-Stability-2006.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], }), - ('AnyEvent', '7.12', { + ('AnyEvent', '7.11', { 'source_tmpl': 'AnyEvent-7.11.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], }), @@ -520,7 +520,7 @@ exts_list = [ 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], }), - ('Statistics::Descriptive', '3.0612', { + ('Statistics::Descriptive', '3.0609', { 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], }), @@ -528,7 +528,7 @@ exts_list = [ 'source_tmpl': 'Class-Load-0.23.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('LWP::Simple', '6.15', { + ('LWP::Simple', '6.13', { 'source_tmpl': 'libwww-perl-6.13.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), @@ -540,7 +540,7 @@ exts_list = [ 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], }), - ('GD::Graph', '1.52', { + ('GD::Graph', '1.49', { 'source_tmpl': 'GDGraph-1.49.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], }), @@ -580,19 +580,19 @@ exts_list = [ 'source_tmpl': 'Class-Inspector-1.28.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], }), - ('Parse::RecDescent', '1.967013', { + ('Parse::RecDescent', '1.967012', { 'source_tmpl': 'Parse-RecDescent-1.967012.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], }), - ('Carp', '1.38', { + ('Carp', '1.36', { 'source_tmpl': 'Carp-1.36.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), - ('XML::XPath', '1.33', { + ('XML::XPath', '1.13', { 'source_tmpl': 'XML-XPath-1.13.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT'], }), - ('Capture::Tiny', '0.36', { + ('Capture::Tiny', '0.30', { 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], }), @@ -616,7 +616,7 @@ exts_list = [ 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], }), - ('LWP', '6.15', { + ('LWP', '6.13', { 'source_tmpl': 'libwww-perl-6.13.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), @@ -648,7 +648,7 @@ exts_list = [ 'source_tmpl': 'Text-Balanced-2.03.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], }), - ('strictures', '2.000002', { + ('strictures', '2.000001', { 'source_tmpl': 'strictures-2.000001.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], }), @@ -656,7 +656,7 @@ exts_list = [ 'source_tmpl': 'Switch-2.17.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], }), - ('File::Which', '1.21', { + ('File::Which', '1.19', { 'source_tmpl': 'File-Which-1.19.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], }), @@ -692,7 +692,7 @@ exts_list = [ 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], }), - ('Exception::Class', '1.40', { + ('Exception::Class', '1.39', { 'source_tmpl': 'Exception-Class-1.39.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -724,7 +724,7 @@ exts_list = [ 'source_tmpl': 'IO-String-1.08.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], }), - ('XML::Simple', '2.22', { + ('XML::Simple', '2.20', { 'source_tmpl': 'XML-Simple-2.20.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], }), @@ -748,7 +748,7 @@ exts_list = [ 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], }), - ('Scalar::Util', '1.43', { + ('Scalar::Util', '1.42', { 'source_tmpl': 'Scalar-List-Utils-1.42.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], }), @@ -808,7 +808,7 @@ exts_list = [ 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], }), - ('Log::Handler', '0.84', { + ('Log::Handler', '0.87', { 'source_tmpl': 'Log-Handler-0.87.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], }), @@ -816,11 +816,11 @@ exts_list = [ 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], }), - ('HTML::Entities', '3.72', { + ('HTML::Entities', '3.71', { 'source_tmpl': 'HTML-Parser-3.71.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], }), - ('Devel::StackTrace', '2.01', { + ('Devel::StackTrace', '2.00', { 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], }), @@ -832,7 +832,7 @@ exts_list = [ 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], }), - ('Moose', '2.1605', { + ('Moose', '2.1603', { 'source_tmpl': 'Moose-2.1603.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), @@ -848,7 +848,7 @@ exts_list = [ 'source_tmpl': 'IPC-Run3-0.048.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), - ('File::Find::Rule', '0.34', { + ('File::Find::Rule', '0.33', { 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], }), @@ -868,11 +868,11 @@ exts_list = [ 'source_tmpl': 'Data-OptList-0.109.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), - ('CPANPLUS', '0.9156', { + ('CPANPLUS', '0.9154', { 'source_tmpl': 'CPANPLUS-0.9154.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), - ('Test::Harness', '3.36', { + ('Test::Harness', '3.35', { 'source_tmpl': 'Test-Harness-3.35.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), @@ -880,15 +880,15 @@ exts_list = [ 'source_tmpl': 'IO-Tty-1.12.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], }), - ('Text::Soundex', '3.05', { + ('Text::Soundex', '3.04', { 'source_tmpl': 'Text-Soundex-3.04.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], }), - ('Lingua::EN::PluralToSingular', '0.18', { + ('Lingua::EN::PluralToSingular', '0.14', { 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB'], }), - ('Want', '0.29', { + ('Want', '0.26', { 'source_tmpl': 'Want-0.26.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], }), -- GitLab From e04cfd11177a408dfa72ad11898829595a38bc57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 16:46:53 +0100 Subject: [PATCH 0901/2133] {lang}[intel/2016a] Perl 5.22.1 --- .../p/Perl/Perl-5.22.1-intel-2016a.eb | 886 ++++++++++++++++++ 1 file changed, 886 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb new file mode 100644 index 0000000000..ae84220ef2 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -0,0 +1,886 @@ +name = 'Perl' +version = '5.22.1' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.60', { + 'source_tmpl': 'Config-General-2.60.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.36', { + 'source_tmpl': 'Test-Harness-3.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016020301', { + 'source_tmpl': 'Regexp-Common-2016020301.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-0.026.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.02', { + 'source_tmpl': 'DateTime-Locale-1.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.95', { + 'source_tmpl': 'DateTime-TimeZone-1.95.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4216', { + 'source_tmpl': 'Module-Build-0.4216.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.24', { + 'source_tmpl': 'Try-Tiny-0.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.22', { + 'source_tmpl': 'Params-Validate-1.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.25', { + 'source_tmpl': 'DateTime-1.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.01', { + 'source_tmpl': 'Readonly-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-1.29.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "BINGOS"'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-0.73.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-0.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-3.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.71', { + 'source_tmpl': 'URI-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.44', { + 'source_tmpl': 'Text-Diff-1.44.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.024', { + 'source_tmpl': 'IO-Socket-SSL-2.024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '1.120', { + 'source_tmpl': 'Test-Deep-1.120.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.001001', { + 'source_tmpl': 'Moo-2.001001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.09', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.09.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-0.64.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.15', { + 'source_tmpl': 'Package-DeprecationManager-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "GBARR"'], + }), + ('version', '0.9915', { + 'source_tmpl': 'version-0.9915.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + # fails: uses 'gcc' + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.31', { + 'source_tmpl': 'Time-Piece-1.31.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.12', { + 'source_tmpl': 'AnyEvent-7.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-3.0612.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.15', { + 'source_tmpl': 'libwww-perl-6.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.52', { + 'source_tmpl': 'GDGraph-1.52.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "INGY"'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967013', { + 'source_tmpl': 'Parse-RecDescent-1.967013.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-1.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.33', { + 'source_tmpl': 'XML-XPath-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.36', { + 'source_tmpl': 'Capture-Tiny-0.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000002', { + 'source_tmpl': 'strictures-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.40', { + 'source_tmpl': 'Exception-Class-1.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-2.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.43', { + 'source_tmpl': 'Scalar-List-Utils-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.84', { + 'source_tmpl': 'Log-Handler-0.84.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.01', { + 'source_tmpl': 'Devel-StackTrace-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1605', { + 'source_tmpl': 'Moose-2.1605.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9156', { + 'source_tmpl': 'CPANPLUS-0.9156.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-3.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.18', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-0.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' -- GitLab From bd08387aa585149739945ec279d4f81b23ce426f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 16:49:30 +0100 Subject: [PATCH 0902/2133] enable XML::Bare in all Perl easyconfigs --- easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2015b.eb | 9 ++++----- easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2016a.eb | 9 ++++----- .../easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb | 10 +++++----- .../easyconfigs/p/Perl/Perl-5.20.3-intel-2016a.eb | 10 +++++----- 4 files changed, 18 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2015b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2015b.eb index 35f20adfa3..6c8f5e608f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2015b.eb @@ -419,11 +419,10 @@ exts_list = [ 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], }), - # fails: uses 'gcc' - #('XML::Bare', '0.53', { - # 'source_tmpl': 'XML-Bare-0.53.tar.gz', - # 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], - #}), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD/'], + }), ('Dist::CheckConflicts', '0.11', { 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2016a.eb index 0dbde8ec2c..c82d048099 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-foss-2016a.eb @@ -419,11 +419,10 @@ exts_list = [ 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], }), - # fails: uses 'gcc' - #('XML::Bare', '0.53', { - # 'source_tmpl': 'XML-Bare-0.53.tar.gz', - # 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], - #}), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD/'], + }), ('Dist::CheckConflicts', '0.11', { 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb index ab7a8379bf..2447ac9616 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb @@ -419,11 +419,11 @@ exts_list = [ 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], }), - # fails: uses 'gcc' - #('XML::Bare', '0.53', { - # 'source_tmpl': 'XML-Bare-0.53.tar.gz', - # 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], - #}), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD/'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), ('Dist::CheckConflicts', '0.11', { 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2016a.eb index 146a854c21..e8b65cc525 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2016a.eb @@ -419,11 +419,11 @@ exts_list = [ 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], }), - # fails: uses 'gcc' - #('XML::Bare', '0.53', { - # 'source_tmpl': 'XML-Bare-0.53.tar.gz', - # 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], - #}), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD/'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), ('Dist::CheckConflicts', '0.11', { 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], -- GitLab From 41026ced1cf46f65783212b2baa731f6bffa1fd3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 18:27:17 +0200 Subject: [PATCH 0903/2133] add easyconfig LLVM-3.7.1-gimkl-2.11.5.eb, add easyconfig Mesa-11.1.2-gimkl-2.11.5.eb, add easyconfig eudev-3.1.5-gimkl-2.11.5.eb, add easyconfig flex-2.6.0-gimkl-2.11.5.eb, add easyconfig glproto-1.4.17-gimkl-2.11.5.eb, add easyconfig gperf-3.0.4-gimkl-2.11.5.eb, add easyconfig libdrm-2.4.67-gimkl-2.11.5.eb, add easyconfig libpciaccess-0.13.4-gimkl-2.11.5.eb, add easyconfig libxml2-2.9.3-gimkl-2.11.5.eb, add easyconfig makedepend-1.0.5-gimkl-2.11.5.eb, add easyconfig pkg-config-0.29-gimkl-2.11.5.eb --- .../e/eudev/eudev-3.1.5-gimkl-2.11.5.eb | 33 +++++++++ .../f/flex/flex-2.6.0-gimkl-2.11.5.eb | 16 +++++ .../g/glproto/glproto-1.4.17-gimkl-2.11.5.eb | 20 ++++++ .../g/gperf/gperf-3.0.4-gimkl-2.11.5.eb | 22 ++++++ .../l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb | 39 +++++++++++ .../l/libdrm/libdrm-2.4.67-gimkl-2.11.5.eb | 28 ++++++++ .../libpciaccess-0.13.4-gimkl-2.11.5.eb | 26 +++++++ .../l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb | 29 ++++++++ .../m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 68 +++++++++++++++++++ .../makedepend-1.0.5-gimkl-2.11.5.eb | 20 ++++++ .../pkg-config-0.29-gimkl-2.11.5.eb | 27 ++++++++ 11 files changed, 328 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-gimkl-2.11.5.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.eb new file mode 100644 index 0000000000..217a49f901 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.1.5' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-3.1.2_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb new file mode 100644 index 0000000000..c2677565b5 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb new file mode 100644 index 0000000000..46b9bdb324 --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'glproto' +version = '1.4.17' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-gimkl-2.11.5.eb new file mode 100644 index 0000000000..53134ddab6 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-gimkl-2.11.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000..edbbaa6b61 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.7.1' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.4.3'), + ('Python', '2.7.11'), +] + +dependencies = [ + ('ncurses', '5.9'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-gimkl-2.11.5.eb new file mode 100644 index 0000000000..caf76a0cf5 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-gimkl-2.11.5.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.67' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb new file mode 100644 index 0000000000..2a5e9c8d05 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.4' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +builddependencies = [ + ('Autotools', '20150215'), + ('xorg-macros', '1.19.0'), +] + +preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb new file mode 100644 index 0000000000..1f39ac3f7d --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb new file mode 100644 index 0000000000..72d772f450 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.1.2' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.67'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1'), + ('LLVM', '3.7.1'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb new file mode 100644 index 0000000000..c92d8634e2 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-gimkl-2.11.5.eb new file mode 100644 index 0000000000..c593a8d395 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-gimkl-2.11.5.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 5fb626f666ca2bf5f44367857f05d999ffac3f96 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 8 Mar 2016 17:03:32 +0000 Subject: [PATCH 0904/2133] Use latest available cURL for foss-2015b --- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015b.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015b.eb index 087db393ee..ae3ef1e8c2 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015b.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015b.eb @@ -19,7 +19,7 @@ source_urls = [ ] dependencies = [ - ('cURL', '7.44.0'), + ('cURL', '7.45.0'), ] moduleclass = 'lib' -- GitLab From 15ad050da351d4224417d2882ec31477e9dc24b5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 8 Mar 2016 17:29:35 +0000 Subject: [PATCH 0905/2133] Remove versionsuffix and rename file --- ...atGen-1.0.13-foss-2015b.eb => BamUtil-1.0.13-foss-2015b.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/b/BamUtil/{BamUtil-libStatGen-1.0.13-foss-2015b.eb => BamUtil-1.0.13-foss-2015b.eb} (89%) diff --git a/easybuild/easyconfigs/b/BamUtil/BamUtil-libStatGen-1.0.13-foss-2015b.eb b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb similarity index 89% rename from easybuild/easyconfigs/b/BamUtil/BamUtil-libStatGen-1.0.13-foss-2015b.eb rename to easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb index ceee101f27..66b054cceb 100644 --- a/easybuild/easyconfigs/b/BamUtil/BamUtil-libStatGen-1.0.13-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb @@ -4,11 +4,10 @@ # adam.huffman@crick.ac.uk # The Francis Crick Institute # -# This is the version bundled with the libStatGen library +# This is the version with the bundled libStatGen library name = 'BamUtil' version = '1.0.13' -versionsuffix = 'libStatGen' easyblock = 'MakeCp' -- GitLab From 5cfd3869361d6cccf6c4ada8c54de1bd0d974f19 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 19:50:01 +0200 Subject: [PATCH 0906/2133] modify easyconfig eudev-3.1.5-gimkl-2.11.5.eb, modify easyconfig LLVM-3.7.1-gimkl-2.11.5.eb --- easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.eb | 1 - easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.eb index 217a49f901..2d6463fa7e 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-gimkl-2.11.5.eb @@ -10,7 +10,6 @@ description = """eudev is a fork of systemd-udev with the goal of obtaining and anything else required by users and various distributions.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} -toolchainopts = {'cstd': 'c99'} sources = [SOURCE_TAR_GZ] source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb index edbbaa6b61..6ad7225296 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-gimkl-2.11.5.eb @@ -27,7 +27,7 @@ dependencies = [ ('ncurses', '5.9'), ] -configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +configopts = '-DBUILD_SHARED_LIBS=ON' sanity_check_paths = { 'files': ['bin/llvm-ar'], -- GitLab From b2e2dd698e6d46d333670b9ead5dad39b7eafe02 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 8 Mar 2016 19:00:42 +0100 Subject: [PATCH 0907/2133] Simplify SuperLU easyconfigs to use the new easyblock --- .../s/SuperLU/SuperLU-5.1.1-foss-2016a.eb | 26 ------------------- .../s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb | 24 ----------------- 2 files changed, 50 deletions(-) diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb index 7f7793d488..d58d7f4d85 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb @@ -1,5 +1,3 @@ -easyblock = 'CMakeMake' - name = 'SuperLU' version = '5.1.1' @@ -7,7 +5,6 @@ homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'opt': True, 'pic': True} source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] sources = ["superlu_%(version)s.tar.gz"] @@ -15,29 +12,6 @@ sources = ["superlu_%(version)s.tar.gz"] # Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['260a3cd90b2100122abff38587a8290a'] -# Set to ON to generate shared library -configopts = "-DBUILD_SHARED_LIBS=OFF" - -# Make sure not to build the slow BLAS library included in the package -configopts += " -Denable_blaslib=OFF" - -# Set the BLAS library to use -# cf https://cmake.org/cmake/help/latest/module/FindBLAS.html -# Unfortunately, OpenBLAS is not recognized by FindBLAS from CMake, -# we have to specify the OpenBLAS library manually -configopts += ' -DBLAS_LIBRARIES="${EBROOTOPENBLAS}/lib/libopenblas.a;-pthread"' - -# Make symlink to version-numbered library filename -installopts = ' && cd %(installdir)s/lib && ln -s libsuperlu_%(version)s.a libsuperlu.a' - builddependencies = [('CMake', '3.4.3')] -separate_build_dir = True - -runtest = "test" - -sanity_check_paths = { - 'files': ["include/supermatrix.h", "lib/libsuperlu.a"], - 'dirs': [], -} moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb index 514dd74cfa..4640b8c826 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb @@ -1,5 +1,3 @@ -easyblock = 'CMakeMake' - name = 'SuperLU' version = '5.1.1' @@ -7,7 +5,6 @@ homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" toolchain = {'name': 'ictce', 'version': '7.3.5'} -toolchainopts = {'opt': True, 'pic': True} source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] sources = ["superlu_%(version)s.tar.gz"] @@ -15,27 +12,6 @@ sources = ["superlu_%(version)s.tar.gz"] # Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['260a3cd90b2100122abff38587a8290a'] -# Set to ON to generate shared library -configopts = "-DBUILD_SHARED_LIBS=OFF" - -# Make sure not to build the slow BLAS library included in the package -configopts += " -Denable_blaslib=OFF" - -# Set the BLAS library to use -# cf https://cmake.org/cmake/help/latest/module/FindBLAS.html -configopts += " -DBLA_VENDOR=Intel10_64lp" - -# Make symlink to version-numbered library filename -installopts = ' && cd %(installdir)s/lib && ln -s libsuperlu_%(version)s.a libsuperlu.a' - builddependencies = [('CMake', '3.2.3')] -separate_build_dir = True - -runtest = "test" - -sanity_check_paths = { - 'files': ["include/supermatrix.h", "lib/libsuperlu.a"], - 'dirs': [], -} moduleclass = 'numlib' -- GitLab From 2233e6b571ca238397374a46799cdc4434718d19 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 20:02:35 +0100 Subject: [PATCH 0908/2133] {devel}[gimkl/2.11.5] Qt 4.8.7 --- .../g/GLib/GLib-2.47.5-gimkl-2.11.5.eb | 33 ++++++++++++++++ .../g/gettext/gettext-0.19.6-gimkl-2.11.5.eb | 18 +++++++++ .../l/libICE/libICE-1.0.9-gimkl-2.11.5.eb | 27 +++++++++++++ .../l/libSM/libSM-1.2.2-gimkl-2.11.5.eb | 28 +++++++++++++ .../libXrender-0.9.9-gimkl-2.11.5.eb | 28 +++++++++++++ .../l/libXt/libXt-1.1.5-gimkl-2.11.5.eb | 39 +++++++++++++++++++ .../l/libffi/libffi-3.2.1-gimkl-2.11.5.eb | 23 +++++++++++ .../p/PCRE/PCRE-8.38-gimkl-2.11.5.eb | 20 ++++++++++ .../easyconfigs/q/Qt/Qt-4.8.7-gimkl-2.11.5.eb | 24 ++++++++++++ .../renderproto-0.11-gimkl-2.11.5.eb | 20 ++++++++++ 10 files changed, 260 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libXt/libXt-1.1.5-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.38-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-gimkl-2.11.5.eb new file mode 100644 index 0000000000..8580a33ef1 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-gimkl-2.11.5.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb new file mode 100644 index 0000000000..4aed92d350 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.6' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb new file mode 100644 index 0000000000..407ce4845d --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libICE' +version = '1.0.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xtrans', '1.3.5'), +] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb new file mode 100644 index 0000000000..580ce7f28a --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libSM' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Session Management library, which allows for applications to both manage sessions, + and make use of session managers to save and restore their state for later use.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libICE', '1.0.9'), +] +builddependencies = [ + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-gimkl-2.11.5.eb new file mode 100644 index 0000000000..ba222c9ba7 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-gimkl-2.11.5.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-gimkl-2.11.5.eb new file mode 100644 index 0000000000..79ad76f252 --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-gimkl-2.11.5.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'libXt' +version = '1.1.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are + based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('kbproto', '1.0.7'), +] + +dependencies = [ + ('libSM', '1.2.2'), + ('libICE', '1.0.9'), + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', + 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', + 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', + 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', + 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-gimkl-2.11.5.eb new file mode 100644 index 0000000000..7436f22a76 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-gimkl-2.11.5.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-gimkl-2.11.5.eb new file mode 100644 index 0000000000..98509a1b4e --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-gimkl-2.11.5.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.38' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-gimkl-2.11.5.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-gimkl-2.11.5.eb new file mode 100644 index 0000000000..607058cfe3 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-gimkl-2.11.5.eb @@ -0,0 +1,24 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +dependencies = [ + ('GLib', '2.47.5'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXrender', '0.9.9'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb new file mode 100644 index 0000000000..c363620cb6 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 0a4d487219fb40608f605ebcdc55e342d2b7d8b9 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 9 Mar 2016 06:16:59 +1030 Subject: [PATCH 0909/2133] Whitespace fixes --- .../c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb index 1b0f60b271..87ecf8bccd 100644 --- a/easybuild/easyconfigs/c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/csvkit/csvkit-0.9.1-foss-2015b-Python-2.7.10.eb @@ -26,11 +26,11 @@ postinstallcmds = ["chmod -R +r %(installdir)s/lib/"] sanity_check_paths = { 'files': ['bin/in2csv', 'bin/sql2csv', 'bin/csvclean', 'bin/csvcut', 'bin/csvgrep', 'bin/csvjoin', - 'bin/csvsort', 'bin/csvstack', 'bin/csvformat', 'bin/csvjson', 'bin/csvlook', 'bin/csvpy', - 'bin/csvsql', 'bin/csvstat'], + 'bin/csvsort', 'bin/csvstack', 'bin/csvformat', 'bin/csvjson', 'bin/csvlook', 'bin/csvpy', + 'bin/csvsql', 'bin/csvstat'], 'dirs': [], } -sanity_check_commands = [('csvlook','-h')] +sanity_check_commands = [('csvlook', '-h')] moduleclass = 'tools' -- GitLab From f053247b9a41764861442340aa52fee95462193b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 20:56:57 +0100 Subject: [PATCH 0910/2133] {numlib}[intel-2016a] qrupdate 1.1.2 (REVIEW) --- .../q/qrupdate/qrupdate-1.1.2-intel-2016a.eb | 28 +++++++++++++++++++ .../q/qrupdate/qrupdate-1.1.2_makeconf.patch | 17 +++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2_makeconf.patch diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016a.eb new file mode 100644 index 0000000000..2829bff70e --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'http://freeglut.sourceforge.net/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['%(name)s-%(version)s_makeconf.patch'] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2_makeconf.patch b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2_makeconf.patch new file mode 100644 index 0000000000..8e0f5c03c6 --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2_makeconf.patch @@ -0,0 +1,17 @@ +# Pick FC and FFLAGS from environmental variables +# March 8th 2016 B. Hajgato (Free Uviveristy Brussels - VUB) +--- qrupdate-1.1.2/Makeconf.old 2010-01-19 12:35:49.000000000 +0100 ++++ qrupdate-1.1.2/Makeconf 2016-03-08 20:51:11.662603099 +0100 +@@ -1,9 +1,9 @@ + # set this to your compiler's executable name (e.g. gfortran, g77) +-FC=gfortran ++FC?=gfortran + # requested flags +-FFLAGS=-fimplicit-none -O3 -funroll-loops ++FFLAGS?=-fimplicit-none -O3 -funroll-loops + # set if you need shared library +-FPICFLAGS=-fPIC ++FPICFLAGS= + + # BLAS library (only required for tests) + BLAS=-lblas -- GitLab From ffad529c31ea9063db8f1c77be441b4ff544589b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 21:04:16 +0100 Subject: [PATCH 0911/2133] diSNOW added --- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index 60dfecc0d6..49fadf4c1f 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -449,6 +449,7 @@ exts_list = [ ('ggm', '2.3', ext_options), ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), ] moduleclass = 'lang' -- GitLab From 511bdfee7d1f3956cc5a711acbafc71fc5d0ff31 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 21:18:56 +0100 Subject: [PATCH 0912/2133] homepage corrected --- easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016a.eb index 2829bff70e..eaa4c88212 100644 --- a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'MakeCp' name = 'qrupdate' version = '1.1.2' -homepage = 'http://freeglut.sourceforge.net/' +homepage = 'https://sourceforge.net/projects/qrupdate/' description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" toolchain = {'name': 'intel', 'version': '2016a'} -- GitLab From 94471da2337738e879ded434c6a7abfa346bcc46 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2016 22:20:43 +0200 Subject: [PATCH 0913/2133] add easyconfig ParaView-4.4.0-gimkl-2.11.5-mpi.eb, add easyconfig libGLU-9.0.0-gimkl-2.11.5.eb --- .../l/libGLU/libGLU-9.0.0-gimkl-2.11.5.eb | 24 +++++++++ .../ParaView-4.4.0-gimkl-2.11.5-mpi.eb | 52 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-gimkl-2.11.5.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-gimkl-2.11.5.eb new file mode 100644 index 0000000000..2efc0a1d43 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-gimkl-2.11.5.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '11.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb new file mode 100644 index 0000000000..a0d908d3d5 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '4.4.0' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s-source.tar.gz"] + +patches = ['%(name)s-%(version)s_missingheader.patch'] + +python = 'Python' +pyver = '2.7.10' +pysuff = '-%s-%s' % (python, pyver) +dependencies = [ + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('libXt', '1.1.5'), + ('Qt', '4.8.7'), + ('libXext', '1.3.3'), + ('libX11', '1.6.3'), + ('zlib', '1.2.8'), +] + +builddependencies = [('CMake', '3.4.3')] + +separate_build_dir = True + +maxparallel = 4 + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +# Without internet connection turn off testing (uncomment the following line) +#configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From 3defaa7cb4280d0ea6fc193622fa93b4eadafe75 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 21:56:34 +0100 Subject: [PATCH 0914/2133] CMake builddep added --- easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a.eb index 640e02a1af..9b004cefef 100644 --- a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a.eb @@ -11,6 +11,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://geuz.org/gl2ps/src/'] sources = [SOURCELOWER_TGZ] +builddependencies = [ + ('CMake', '3.4.3'), +] + dependencies = [ ('libX11', '1.6.3'), ('libXi', '1.7.6'), -- GitLab From 24b0a15e15d6580b506442a6c75e0e276c493fad Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 8 Mar 2016 22:06:15 +0100 Subject: [PATCH 0915/2133] Add toolchainopts --- easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb | 1 + easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb index d58d7f4d85..18ef21e40a 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb @@ -5,6 +5,7 @@ homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True} source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] sources = ["superlu_%(version)s.tar.gz"] diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb index 4640b8c826..36729b6f64 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb @@ -5,6 +5,7 @@ homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'opt': True, 'pic': True} source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] sources = ["superlu_%(version)s.tar.gz"] -- GitLab From 609b7695965f5d75bb9aa0a357f134fbb3115049 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Mar 2016 22:17:33 +0100 Subject: [PATCH 0916/2133] check both lib/lib64 for freeglut --- easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb index 095b105fda..fe4a731eff 100644 --- a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb @@ -30,7 +30,7 @@ configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' sanity_check_paths = { - 'files': ['lib64/libglut.a', 'lib64/libglut.%s' % SHLIB_EXT], + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], 'dirs': ['include/GL'], } -- GitLab From 3a76e163287326199ecf8991a89a77ed3713774a Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 9 Mar 2016 09:21:56 +0100 Subject: [PATCH 0917/2133] fix remarks --- .../easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb index c7ee77bd84..6caf9a9b85 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb @@ -9,13 +9,11 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'optarch': True, 'shared': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-%(version)s_configure_darwin.patch'] - configopts = [ # default build '--with-shared --enable-overwrite', -- GitLab From 1cc16cf822933f32f1ed962b912e7cb6e8d02f11 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 9 Mar 2016 09:23:28 +0100 Subject: [PATCH 0918/2133] clean up --- .../easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb | 4 +--- .../easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb index 39a02a2b9d..f11ad3873e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb @@ -9,13 +9,11 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'optarch': True, 'shared': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-%(version)s_configure_darwin.patch'] - configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb index a3d14a3a11..0c15e725f4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb @@ -9,13 +9,11 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'optarch': True, 'shared': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-%(version)s_configure_darwin.patch'] - configopts = [ # default build '--with-shared --enable-overwrite', -- GitLab From a7b15e1944e1d14979c38e30214b6fb8480283f6 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 9 Mar 2016 09:33:07 +0100 Subject: [PATCH 0919/2133] removed ncurses (as it should come from PR#2606) --- .../ncurses-5.9-CrayIntel-2015.11-XC.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb deleted file mode 100644 index c7ee77bd84..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'optarch': True, 'shared': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['ncurses-%(version)s_configure_darwin.patch'] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' -- GitLab From 383ff3305b9b3435edf0c8b6c36fdd66cac9cdcc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 9 Mar 2016 09:36:24 +0100 Subject: [PATCH 0920/2133] {vis}[intel-2016a] GraphicsMagick 1.3.23 (REVIEW) --- .../GraphicsMagick-1.3.23-intel-2016a.eb | 34 +++++++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb | 30 ++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb new file mode 100644 index 0000000000..755ecbe16c --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.23' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('libtool', '2.4.6'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('bzip2', '1.0.6'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libxml2', '2.9.3'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb new file mode 100644 index 0000000000..b717af018a --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('gettext', '0.19.6'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From c5a2f52c1c9e836dedc7649a8ddc2551bf6f4bb9 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Wed, 9 Mar 2016 10:57:15 +0100 Subject: [PATCH 0921/2133] Update dead link for SuiteSparse --- .../SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb | 4 ++-- .../SuiteSparse-3.7.0-goalf-1.1.0-no-OFED-withparmetis.eb | 4 ++-- .../SuiteSparse-3.7.0-goolf-1.4.10-withparmetis.eb | 4 ++-- .../SuiteSparse/SuiteSparse-3.7.0-ictce-4.0.6-withparmetis.eb | 4 ++-- .../SuiteSparse/SuiteSparse-3.7.0-ictce-5.3.0-withparmetis.eb | 4 ++-- .../SuiteSparse-3.7.1-goolf-1.4.10-ParMETIS-4.0.3.eb | 4 ++-- .../SuiteSparse-3.7.1-ictce-5.5.0-ParMETIS-4.0.3.eb | 4 ++-- .../SuiteSparse-4.2.1-goolf-1.4.10-ParMETIS-4.0.3.eb | 4 ++-- .../SuiteSparse-4.2.1-ictce-5.5.0-ParMETIS-4.0.3.eb | 4 ++-- .../SuiteSparse-4.2.1-intel-2014b-ParMETIS-4.0.3.eb | 4 ++-- .../SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb | 2 +- .../SuiteSparse/SuiteSparse-4.4.5-intel-2015b-METIS-5.1.0.eb | 2 +- .../SuiteSparse-4.4.6-intel-2015b-ParMETIS-4.0.3.eb | 2 +- .../SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb | 2 +- 14 files changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb index 2776109eda..d45fed3224 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb @@ -2,13 +2,13 @@ name = 'SuiteSparse' version = '3.7.0' versionsuffix = '-withparmetis' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'gmpolf', 'version': '1.4.8'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] dependencies = [('ParMETIS', '4.0.2')] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-goalf-1.1.0-no-OFED-withparmetis.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-goalf-1.1.0-no-OFED-withparmetis.eb index 2af57df4b1..be453ea4e0 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-goalf-1.1.0-no-OFED-withparmetis.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-goalf-1.1.0-no-OFED-withparmetis.eb @@ -2,13 +2,13 @@ name = 'SuiteSparse' version = '3.7.0' versionsuffix = '-withparmetis' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] dependencies = [('ParMETIS', '4.0.2')] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-goolf-1.4.10-withparmetis.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-goolf-1.4.10-withparmetis.eb index 4a43a48137..b237096229 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-goolf-1.4.10-withparmetis.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-goolf-1.4.10-withparmetis.eb @@ -2,13 +2,13 @@ name = 'SuiteSparse' version = '3.7.0' versionsuffix = '-withparmetis' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] dependencies = [('ParMETIS', '4.0.2')] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-ictce-4.0.6-withparmetis.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-ictce-4.0.6-withparmetis.eb index 73e75a56ff..31eaab67de 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-ictce-4.0.6-withparmetis.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-ictce-4.0.6-withparmetis.eb @@ -2,13 +2,13 @@ name = 'SuiteSparse' version = '3.7.0' versionsuffix = '-withparmetis' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] dependencies = [('ParMETIS', '4.0.2')] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-ictce-5.3.0-withparmetis.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-ictce-5.3.0-withparmetis.eb index 6cd219c100..1f9476f389 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-ictce-5.3.0-withparmetis.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-ictce-5.3.0-withparmetis.eb @@ -2,14 +2,14 @@ name = 'SuiteSparse' version = '3.7.0' versionsuffix = '-withparmetis' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] dependencies = [('ParMETIS', '4.0.2')] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-goolf-1.4.10-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-goolf-1.4.10-ParMETIS-4.0.3.eb index 62896760f1..7e5f7e0b83 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-goolf-1.4.10-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-goolf-1.4.10-ParMETIS-4.0.3.eb @@ -1,13 +1,13 @@ name = 'SuiteSparse' version = '3.7.1' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] parmetis = 'ParMETIS' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-ictce-5.5.0-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-ictce-5.5.0-ParMETIS-4.0.3.eb index 02396e3728..7977eac7fc 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-ictce-5.5.0-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-ictce-5.5.0-ParMETIS-4.0.3.eb @@ -1,13 +1,13 @@ name = 'SuiteSparse' version = '3.7.1' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] parmetis = 'ParMETIS' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.4.10-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.4.10-ParMETIS-4.0.3.eb index 1193a31b09..e1b3ef8d57 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.4.10-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.4.10-ParMETIS-4.0.3.eb @@ -1,13 +1,13 @@ name = 'SuiteSparse' version = '4.2.1' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] parmetis = 'ParMETIS' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-ictce-5.5.0-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-ictce-5.5.0-ParMETIS-4.0.3.eb index c537c65755..a4f5ba5d15 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-ictce-5.5.0-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-ictce-5.5.0-ParMETIS-4.0.3.eb @@ -1,13 +1,13 @@ name = 'SuiteSparse' version = '4.2.1' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] parmetis = 'ParMETIS' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-intel-2014b-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-intel-2014b-ParMETIS-4.0.3.eb index eb9d92e5d5..bb01d5bbb6 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-intel-2014b-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-intel-2014b-ParMETIS-4.0.3.eb @@ -1,13 +1,13 @@ name = 'SuiteSparse' version = '4.2.1' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] parmetis = 'ParMETIS' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb index ace5e25985..3d9532a033 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb @@ -1,7 +1,7 @@ name = 'SuiteSparse' version = '4.4.3' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.5-intel-2015b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.5-intel-2015b-METIS-5.1.0.eb index 36dee081ed..cce45a4f26 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.5-intel-2015b-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.5-intel-2015b-METIS-5.1.0.eb @@ -1,7 +1,7 @@ name = 'SuiteSparse' version = '4.4.5' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.6-intel-2015b-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.6-intel-2015b-ParMETIS-4.0.3.eb index f139f365f0..3136cae63d 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.6-intel-2015b-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.6-intel-2015b-ParMETIS-4.0.3.eb @@ -1,7 +1,7 @@ name = 'SuiteSparse' version = '4.4.6' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb index f6beb0e31f..ac231b59ef 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb @@ -1,7 +1,7 @@ name = 'SuiteSparse' version = '4.5.1' -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'intel', 'version': '2016a'} -- GitLab From 7f7b81153e1f8356f2cc137617703c6e2d378afd Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Wed, 9 Mar 2016 11:44:05 +0100 Subject: [PATCH 0922/2133] Use CMake 3.4.3 for SuperLU-5.1.1-ictce-7.3.5 --- .../{CMake-3.2.3-ictce-7.3.5.eb => CMake-3.4.3-ictce-7.3.5.eb} | 2 +- easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/CMake/{CMake-3.2.3-ictce-7.3.5.eb => CMake-3.4.3-ictce-7.3.5.eb} (97%) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb similarity index 97% rename from easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb rename to easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb index 5ae7415b1c..7deb175b91 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'CMake' -version = '3.2.3' +version = '3.4.3' homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb index 36729b6f64..411ef70cfb 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb @@ -13,6 +13,6 @@ sources = ["superlu_%(version)s.tar.gz"] # Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['260a3cd90b2100122abff38587a8290a'] -builddependencies = [('CMake', '3.2.3')] +builddependencies = [('CMake', '3.4.3')] moduleclass = 'numlib' -- GitLab From 004d3d32eab2707b3c8111d05e1601944a309008 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 9 Mar 2016 14:24:22 +0100 Subject: [PATCH 0923/2133] Fix remark --- easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb | 7 +++---- easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb | 4 ++-- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb index 363a280e90..d474edee9b 100644 --- a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb +++ b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb @@ -1,4 +1,7 @@ name = 'mutil' +coreutils_maj = '8' +coreutils_min = '22' +version = '1.%s%s.3' % (coreutils_maj, coreutils_min) homepage = 'http://people.nas.nasa.gov/~kolano/projects/mutil.html' description = """Mutil is a set of standard utilities that have been parallelized to maximize performance on @@ -8,10 +11,6 @@ GNU coreutils, which have achieved 10/30x rates on one/many nodes. toolchain = {'name': 'intel', 'version': '2016a'} -coreutils_maj = '8' -coreutils_min = '22' -version = '1.%s%s.3' % (coreutils_maj, coreutils_min) - sources = [ "coreutils-%s.%s.tar.xz" % (coreutils_maj, coreutils_min), # must be first SOURCE_TGZ, diff --git a/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb index 62fb0dbd9d..e47d185932 100644 --- a/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/s/shift/shift-4.0-intel-2016a.eb @@ -24,8 +24,8 @@ skipsteps = ['build'] files_to_copy = [(['perl/shiftc', 'perl/shift-mgr', 'perl/shift-aux'], 'bin'), 'etc', (['doc/shiftc.1'], 'man/man1')] sanity_check_paths = { - 'files': ['bin/shiftc'], - 'dirs': ['etc'] + 'files': ['bin/%s' % x for x in ['shiftc', 'shift-mgr', 'shift-aux']], + 'dirs': ['etc', 'man/man1'] } moduleclass = 'tools' -- GitLab From d783767305fed790377296e4b1695ed98a5f308d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Mar 2016 14:46:02 +0100 Subject: [PATCH 0924/2133] fix style issues: no tabs --- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 246106ec92..40e3ccc1a8 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -12,7 +12,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] builddependencies = [ - ('M4', '1.4.17'), + ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), # zlib required, but being linked instatically, so not a runtime dep diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb index ce96075acd..32dffb057f 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb @@ -12,8 +12,8 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('M4', '1.4.17'), - ('binutils', '2.25', '', True) + ('M4', '1.4.17'), + ('binutils', '2.25', '', True) ] moduleclass = 'lang' -- GitLab From 7b57c9254a2b71bc6443b575a862831b6e0de888 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Mar 2016 15:23:10 +0100 Subject: [PATCH 0925/2133] remove custom exts_filter in GC3Pie easyconfigs, since PythonPackage will use right filter by default --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 1 - easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 1 - easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 1 - easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 1 - easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 1 - 5 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index 3b725d6c3c..a6eca83b67 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 662fb134c2..84677a5142 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index b08b112eb7..55217f87b7 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 92f6d885db..dbc732d179 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index e5720c5610..0e7690c9c0 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] -- GitLab From 08a1f1630b4a92d877a3bc279622d8cc3e7cf102 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Mar 2016 15:56:32 +0100 Subject: [PATCH 0926/2133] remove custom exts_filter in various easyconfigs for (bundles of) Python packages --- .../i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb | 1 - .../i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb | 1 - .../i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb | 1 - .../m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb | 1 - .../m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb | 1 - .../m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb | 1 - .../n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb | 1 - .../s/Sphinx/Sphinx-1.3.3-intel-2015b-Python-2.7.11.eb | 1 - 8 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb index 4c966b0d8a..92dcaa700c 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb @@ -25,7 +25,6 @@ dependencies = [ # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('pysqlite', '2.7.0', { diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb index 6a2901ff52..693b2889a6 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb @@ -25,7 +25,6 @@ dependencies = [ # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('pysqlite', '2.8.1', { diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb index fd3e839da8..e3341fcf31 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb @@ -25,7 +25,6 @@ dependencies = [ # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('pysqlite', '2.8.1', { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb index 207a23ff90..712519a60c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'foss', 'version': '2015b'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') dependencies = [ ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb index 1364208cee..8b047bb737 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'intel', 'version': '2015b'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') dependencies = [ ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb index c62d74a1eb..551c06ecef 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'intel', 'version': '2016a'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') dependencies = [ ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb index 402bb7ef96..6456ccb4fb 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'intel', 'version': '2015b'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') pyver = '2.7.11' versionsuffix = '-Python-%s' % pyver diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.3.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.3.3-intel-2015b-Python-2.7.11.eb index 3813e03737..be559f9b42 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.3.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.3.3-intel-2015b-Python-2.7.11.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'intel', 'version': '2015b'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[0:2]) -- GitLab From 63bb41c84a63bb99714ee6c70e633e6453074961 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 09:35:23 +0100 Subject: [PATCH 0927/2133] {bio}[intel/2016a] npstat 0.99 --- .../npstat-0.99_fix-hardcoding-Makefile.patch | 16 +++++++++ easybuild/easyconfigs/n/npstat/npstat.eb | 33 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch create mode 100644 easybuild/easyconfigs/n/npstat/npstat.eb diff --git a/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch b/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch new file mode 100644 index 0000000000..b9cdbe3811 --- /dev/null +++ b/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch @@ -0,0 +1,16 @@ +fix hardcoding of 'gcc' +author: Kenneth Hoste (HPC-UGent) +--- npstat/trunk/Makefile.orig 2016-02-15 01:16:51.000000000 +0100 ++++ npstat/trunk/Makefile 2016-03-10 09:25:46.000000000 +0100 +@@ -1,8 +1,7 @@ + all: npstat + +- + npstat: +- gcc -o npstat NPStat-v0.99.c -lgsl -lgslcblas -lm ++ ${CC} -o npstat NPStat-v0.99.c -lgsl -lgslcblas -lm + + clean: +- rm npstat +\ No newline at end of file ++ rm npstat diff --git a/easybuild/easyconfigs/n/npstat/npstat.eb b/easybuild/easyconfigs/n/npstat/npstat.eb new file mode 100644 index 0000000000..b8f9940b59 --- /dev/null +++ b/easybuild/easyconfigs/n/npstat/npstat.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'npstat' +version = '0.99' + +homepage = 'https://code.google.com/archive/p/npstat/' +description = """npstat implements some population genetics tests and estimators that can be applied + to pooled sequences from Next Generation Sequencing experiments.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://storage.googleapis.com/google-code-archive-source/v2/code.google.com/npstat/'] +sources = ['source-archive.zip'] + +patches = ['npstat-%(version)s_fix-hardcoding-Makefile.patch'] + +# commit 14, Oct 31st 2013 +checksums = ['a1595b7c46312d0f51b8b68987289337'] + +dependencies = [ + ('GSL', '1.16'), +] + +start_dir = 'trunk' + +files_to_copy = [(['npstat'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/npstat'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a9cd29fdaa6c1bc62c65738484548ab0dfad6d11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 09:58:56 +0100 Subject: [PATCH 0928/2133] switch to foss/2016a (& fix easyconfig filename) + fix remarks w.r.t. $CFLAGS in patch --- .../n/npstat/{npstat.eb => npstat-0.99-foss-2016a.eb} | 2 +- .../n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/n/npstat/{npstat.eb => npstat-0.99-foss-2016a.eb} (93%) diff --git a/easybuild/easyconfigs/n/npstat/npstat.eb b/easybuild/easyconfigs/n/npstat/npstat-0.99-foss-2016a.eb similarity index 93% rename from easybuild/easyconfigs/n/npstat/npstat.eb rename to easybuild/easyconfigs/n/npstat/npstat-0.99-foss-2016a.eb index b8f9940b59..b72652fe93 100644 --- a/easybuild/easyconfigs/n/npstat/npstat.eb +++ b/easybuild/easyconfigs/n/npstat/npstat-0.99-foss-2016a.eb @@ -7,7 +7,7 @@ homepage = 'https://code.google.com/archive/p/npstat/' description = """npstat implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments.""" -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://storage.googleapis.com/google-code-archive-source/v2/code.google.com/npstat/'] sources = ['source-archive.zip'] diff --git a/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch b/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch index b9cdbe3811..54420af1c1 100644 --- a/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch +++ b/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch @@ -1,4 +1,4 @@ -fix hardcoding of 'gcc' +fix hardcoding of 'gcc', add optimization flags defined in $CFLAGS author: Kenneth Hoste (HPC-UGent) --- npstat/trunk/Makefile.orig 2016-02-15 01:16:51.000000000 +0100 +++ npstat/trunk/Makefile 2016-03-10 09:25:46.000000000 +0100 @@ -8,7 +8,7 @@ author: Kenneth Hoste (HPC-UGent) - npstat: - gcc -o npstat NPStat-v0.99.c -lgsl -lgslcblas -lm -+ ${CC} -o npstat NPStat-v0.99.c -lgsl -lgslcblas -lm ++ ${CC} ${CFLAGS} -o npstat NPStat-v0.99.c -lgsl -lgslcblas -lm clean: - rm npstat -- GitLab From fe62c93d7d5080fcfa7782a71bd8399c207e47f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 10:00:01 +0100 Subject: [PATCH 0929/2133] {lang,numlib}[foss/2016a] OCaml 4.02.3 + GSL 1.16 --- .../easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb | 19 ++++++++ .../o/OCaml/OCaml-4.02.3-foss-2016a.eb | 48 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb create mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb new file mode 100644 index 0000000000..2cce073a65 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2016a.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2016a.eb new file mode 100644 index 0000000000..ee452fb08e --- /dev/null +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2016a.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## +name = 'OCaml' +version = '4.02.3' + +homepage = 'http://ocaml.org/' +description = """OCaml is a general purpose industrial-strength programming language + with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria + it benefits from one of the most advanced type systems and supports functional, + imperative and object-oriented styles of programming.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +opam_ver = '1.2.2' +source_urls = [ + 'http://caml.inria.fr/pub/distrib/ocaml-%s' % '.'.join(version.split('.')[:2]), + 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, +] +sources = [ + SOURCELOWER_TAR_GZ, + 'opam-full-%s.tar.gz' % opam_ver, +] + +builddependencies = [('Autotools', '20150215')] +dependencies = [ + ('ncurses', '6.0'), + ('libreadline', '6.3'), + ('GSL', '1.16'), +] + +# parallel build tends to break +parallel = 1 + +# handled by OPAM, order matters! +exts_list = [ + ('ocamlfind', '1.5.5'), + ('batteries', '2.3.1'), + ('ocaml+twt', '0.94.0'), + ('gsl', '1.18.5'), +] + +moduleclass = 'lang' -- GitLab From 055acbe0dec9d4bc577a6d25cf4cb95601e7144f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 10:27:18 +0100 Subject: [PATCH 0930/2133] {bio}[foss/2016a] SNAPE-pooled r32 --- .../SNAPE-pooled-r32-foss-2016a.eb | 35 +++++++++++++++++++ ...E-pooled-r32_fix-hardcoding-Makefile.patch | 12 +++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32_fix-hardcoding-Makefile.patch diff --git a/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32-foss-2016a.eb b/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32-foss-2016a.eb new file mode 100644 index 0000000000..ee4b4bad14 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'SNAPE-pooled' +version = 'r32' + +homepage = 'https://code.google.com/archive/p/snape-pooled/' +description = """SNAPE-pooled computes the probability distribution for the frequency of the minor allele + in a certain population, at a certain position in the genome.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://storage.googleapis.com/google-code-archive-source/v2/code.google.com/snape-pooled/'] +sources = ['source-archive.zip'] + +patches = ['SNAPE-pooled-%(version)s_fix-hardcoding-Makefile.patch'] + +# commit 32, Aug 12th 2013 +checksums = ['0e9741a45731a2e92d84c129125db3f1'] + +dependencies = [ + ('OCaml', '4.02.3'), +] + +start_dir = 'trunk' + +buildopts = "snape-pooled snape-pooled-fast" + +files_to_copy = [(['snape-pooled', 'snape-pooled-fast'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/snape-pooled', 'bin/snape-pooled-fast'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32_fix-hardcoding-Makefile.patch b/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32_fix-hardcoding-Makefile.patch new file mode 100644 index 0000000000..85d8d5a910 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32_fix-hardcoding-Makefile.patch @@ -0,0 +1,12 @@ +fix hardcoded 'gcc' + add optimization flags through $CFLAGS +author: Kenneth Hoste (HPC-UGent) +--- snape-pooled/trunk/Makefile.orig 2016-03-10 10:23:16.000000000 +0100 ++++ snape-pooled/trunk/Makefile 2016-03-10 10:23:32.000000000 +0100 +@@ -8,6 +8,6 @@ + latex $< + dvips -o snape-pooled-manual.ps snape-pooled-manual.dvi + snape-pooled-fast: snape-pooled.c +- gcc -g -o $@ $< -lm ++ ${CC} ${CFLAGS} -g -o $@ $< -lm + clean: + rm *.cmx *.cmi *.cmo pooled.o snape-pooled *.log *.ps *.dvi *.aux -- GitLab From 3c1a86c564c9ff99c8e7f1f6d755e98b695f2555 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 12:05:22 +0200 Subject: [PATCH 0931/2133] add easyconfig BWA-0.7.13-foss-2016a.eb, add easyconfig picard-2.1.1-Java-1.8.0_74.eb, add easyconfig GATK-3.5-Java-1.8.0_74.eb --- .../b/BWA/BWA-0.7.13-foss-2016a.eb | 32 +++++++++++++++ .../g/GATK/GATK-3.5-Java-1.8.0_74.eb | 40 +++++++++++++++++++ .../p/picard/picard-2.1.1-Java-1.8.0_74.eb | 18 +++++++++ 3 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb create mode 100644 easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb new file mode 100644 index 0000000000..419aba7bab --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.13 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.13' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb new file mode 100644 index 0000000000..c52824dc92 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '3.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] + +dependencies = [('Java', '1.8.0_74')] + +modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb new file mode 100644 index 0000000000..b7bb2304d4 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb @@ -0,0 +1,18 @@ +name = 'picard' +version = '2.1.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM + (http://samtools.github.io/hts-specs) format.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] +sources = ['%(name)s-tools-%(version)s.zip'] + +dependencies = [('Java', '1.8.0_74')] + +modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" + +moduleclass = 'bio' -- GitLab From 4b1b643f11d53d19d0c9665eac3a326eaa7d1a79 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 12:11:05 +0200 Subject: [PATCH 0932/2133] add easyconfig Python-3.5.1-foss-2016a.eb --- .../p/Python/Python-3.5.1-foss-2016a.eb | 109 ++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb new file mode 100644 index 0000000000..38309ea23d --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -0,0 +1,109 @@ +name = 'Python' +version = '3.5.1' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.4' +scipyversion = '0.17.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), +# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# order is important! +# package versions updated Feb 25th 2016 +exts_list = [ + ('setuptools', '20.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + }), + ('scipy', scipyversion, { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('decorator', '4.0.9', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' -- GitLab From c012661d8159a3f76e32fe60a4e36aa035967117 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 10 Mar 2016 11:22:40 +0100 Subject: [PATCH 0933/2133] Removed hidden deps. Added missing popt easyconfig --- easybuild/easyconfigs/p/popt/popt-1.16.eb | 23 +++++++++++++++++++ .../p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 4 ---- .../psmpi-5.1.0-1-iccifort-2015.1.133.eb | 4 ---- .../p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb | 4 ---- .../p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb | 4 ---- .../psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb | 4 ---- .../psmpi-5.1.5-1-iccifort-2015.1.133.eb | 4 ---- 7 files changed, 23 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/p/popt/popt-1.16.eb diff --git a/easybuild/easyconfigs/p/popt/popt-1.16.eb b/easybuild/easyconfigs/p/popt/popt-1.16.eb new file mode 100644 index 0000000000..4b05ae3e4e --- /dev/null +++ b/easybuild/easyconfigs/p/popt/popt-1.16.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'popt' +version = "1.16" + +homepage = "http://freecode.com/projects/popt" +description = """Popt is a C library for parsing command line parameters.""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://rpm5.org/files/popt/'] +sources = [SOURCE_TAR_GZ] + +toolchainopts = {'optarch': False} +sanity_check_paths = { + 'files': ['include/popt.h', + ('lib/libpopt.a', 'lib64/libpopt.a'), + ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], + 'dirs': [], +} + +maxparallel = 1 + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 3b8d70635f..89eb3c9f54 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -23,8 +23,4 @@ dependencies = [ ('pscom', '5.0.44-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.44-1', '', True), -] - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index a5c1e058f0..e8adea5cdd 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -23,8 +23,4 @@ dependencies = [ ('pscom', '5.0.48-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.48-1', '', True), -] - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb index c783f37b64..1bfdad4fb7 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb @@ -23,8 +23,4 @@ dependencies = [ ('pscom', '5.0.48-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.48-1', '', True), -] - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb index aac098925c..93f76f8af0 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb @@ -20,8 +20,4 @@ dependencies = [ ('pscom', '5.0.48-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.48-1', '', True), -] - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb index c33effaedb..9bf66b5728 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb @@ -23,8 +23,4 @@ dependencies = [ ('pscom', '5.0.48-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.48-1', '', True), -] - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb index 22468a4f7f..8251dde430 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb @@ -20,8 +20,4 @@ dependencies = [ ('pscom', '5.0.48-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.48-1', '', True), -] - moduleclass = 'mpi' -- GitLab From 9183d921acb0e78a46f4ba973e5ec3d4707ce945 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 12:23:12 +0200 Subject: [PATCH 0934/2133] add easyconfig Perl-5.22.1-foss-2016a.eb --- .../p/Perl/Perl-5.22.1-foss-2016a.eb | 886 ++++++++++++++++++ 1 file changed, 886 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb new file mode 100644 index 0000000000..652f0d5227 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -0,0 +1,886 @@ +name = 'Perl' +version = '5.22.1' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.60', { + 'source_tmpl': 'Config-General-2.60.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.36', { + 'source_tmpl': 'Test-Harness-3.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016020301', { + 'source_tmpl': 'Regexp-Common-2016020301.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-0.026.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.02', { + 'source_tmpl': 'DateTime-Locale-1.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.95', { + 'source_tmpl': 'DateTime-TimeZone-1.95.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4216', { + 'source_tmpl': 'Module-Build-0.4216.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.24', { + 'source_tmpl': 'Try-Tiny-0.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.22', { + 'source_tmpl': 'Params-Validate-1.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.25', { + 'source_tmpl': 'DateTime-1.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.01', { + 'source_tmpl': 'Readonly-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-1.29.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "BINGOS"'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-0.73.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-0.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-3.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.71', { + 'source_tmpl': 'URI-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.44', { + 'source_tmpl': 'Text-Diff-1.44.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.024', { + 'source_tmpl': 'IO-Socket-SSL-2.024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '1.120', { + 'source_tmpl': 'Test-Deep-1.120.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.001001', { + 'source_tmpl': 'Moo-2.001001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.09', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.09.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-0.64.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.15', { + 'source_tmpl': 'Package-DeprecationManager-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "GBARR"'], + }), + ('version', '0.9915', { + 'source_tmpl': 'version-0.9915.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + # fails: uses 'gcc' + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.31', { + 'source_tmpl': 'Time-Piece-1.31.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.12', { + 'source_tmpl': 'AnyEvent-7.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-3.0612.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.15', { + 'source_tmpl': 'libwww-perl-6.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.52', { + 'source_tmpl': 'GDGraph-1.52.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "INGY"'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967013', { + 'source_tmpl': 'Parse-RecDescent-1.967013.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-1.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.33', { + 'source_tmpl': 'XML-XPath-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.36', { + 'source_tmpl': 'Capture-Tiny-0.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000002', { + 'source_tmpl': 'strictures-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.40', { + 'source_tmpl': 'Exception-Class-1.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-2.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.43', { + 'source_tmpl': 'Scalar-List-Utils-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.84', { + 'source_tmpl': 'Log-Handler-0.84.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.01', { + 'source_tmpl': 'Devel-StackTrace-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1605', { + 'source_tmpl': 'Moose-2.1605.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9156', { + 'source_tmpl': 'CPANPLUS-0.9156.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-3.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.18', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-0.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' -- GitLab From 668864908a998ef90936acb70b3214e40a442f3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 12:49:12 +0200 Subject: [PATCH 0935/2133] add easyconfig Doxygen-1.8.11-foss-2016a.eb, add easyconfig GDAL-2.0.2-foss-2016a.eb, add easyconfig HDF5-1.8.16-foss-2016a.eb, add easyconfig NASM-2.11.08-foss-2016a.eb, add easyconfig PROJ-4.9.2-foss-2016a.eb, add easyconfig R-3.2.3-foss-2016a.eb, add easyconfig Szip-2.1-foss-2016a.eb, add easyconfig cURL-7.47.0-foss-2016a.eb, add easyconfig expat-2.1.0-foss-2016a.eb, add easyconfig libjpeg-turbo-1.4.2-foss-2016a.eb, add easyconfig libpng-1.6.21-foss-2016a.eb, add easyconfig libxml2-2.9.3-foss-2016a.eb, add easyconfig netCDF-4.3.3.1-foss-2016a.eb --- .../c/cURL/cURL-7.47.0-foss-2016a.eb | 31 ++ .../d/Doxygen/Doxygen-1.8.11-foss-2016a.eb | 19 + .../e/expat/expat-2.1.0-foss-2016a.eb | 16 + .../g/GDAL/GDAL-2.0.2-foss-2016a.eb | 29 ++ .../h/HDF5/HDF5-1.8.16-foss-2016a.eb | 26 + .../libjpeg-turbo-1.4.2-foss-2016a.eb | 30 ++ .../l/libpng/libpng-1.6.21-foss-2016a.eb | 26 + .../l/libxml2/libxml2-2.9.3-foss-2016a.eb | 29 ++ .../n/NASM/NASM-2.11.08-foss-2016a.eb | 31 ++ .../n/netCDF/netCDF-4.3.3.1-foss-2016a.eb | 34 ++ .../p/PROJ/PROJ-4.9.2-foss-2016a.eb | 30 ++ .../easyconfigs/r/R/R-3.2.3-foss-2016a.eb | 443 ++++++++++++++++++ .../easyconfigs/s/Szip/Szip-2.1-foss-2016a.eb | 23 + 13 files changed, 767 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.47.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.47.0-foss-2016a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-foss-2016a.eb new file mode 100644 index 0000000000..fa67e92bf9 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.47.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1s')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb new file mode 100644 index 0000000000..fea350b755 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.11' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.3'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2016a.eb new file mode 100644 index 0000000000..c31495ccee --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb new file mode 100644 index 0000000000..1d59b9bdac --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.2' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.3.3.1'), + ('expat', '2.1.0'), + ('libxml2', '2.9.3'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb new file mode 100644 index 0000000000..84580d9ba8 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.16' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a.eb new file mode 100644 index 0000000000..fe5eb900db --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2016a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2016a.eb new file mode 100644 index 0000000000..8cfac2c6e9 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb new file mode 100644 index 0000000000..9f21eb1b66 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016a.eb new file mode 100644 index 0000000000..691495f52f --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2016a.eb new file mode 100644 index 0000000000..921f90805c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2016a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.3.3.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.47.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.11'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016a.eb new file mode 100644 index 0000000000..8073931ffc --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.2' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb new file mode 100644 index 0000000000..bc318c4a60 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -0,0 +1,443 @@ +name = 'R' +version = '3.2.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('libpng', '1.6.21'), # for plotting in R + ('libjpeg-turbo', '1.4.2'), # for plottting in R + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.47.0'), # for RCurl + ('libxml2', '2.9.3'), # for XML + ('GDAL', '2.0.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 21st 2016 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', ext_options), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.3', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.9', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2.1', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5.1', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-22', 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'1.95-4.7', ext_options), + ('bio3d', '2.2-4', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), + ('SuperLearner', '2.0-15', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('caret', '6.0-64', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.6', ext_options), + ('ggvis', '0.4.2', ext_options), + ('mlr', '2.7', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-7', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.10', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.2', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.4.0', ext_options), + ('roxygen2', '5.0.1', ext_options), + ('git2r', '0.13.1', ext_options), + ('xml2', '0.1.2', ext_options), + ('rversions', '1.0.2', ext_options), + ('devtools', '1.9.1', ext_options), + ('Rook', '1.1-1', ext_options), + ('rjson', '0.2.15', ext_options), + ('Cairo', '1.5-9', ext_options), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.1-6', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-7', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-9', ext_options), + ('ks', '1.10.1', ext_options), + ('logcondens', '2.1.4', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-45', ext_options), + ('coin', '1.1-2', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.0.7', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.5.8', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-20', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.8-6', ext_options), + ('mi', '1.0', ext_options), + ('htmlwidgets', '0.6', ext_options), + ('visNetwork', '0.2.1', ext_options), + ('DiagrammeR', '0.8.2', ext_options), + ('sem', '3.1-6', ext_options), + ('jpeg', '0.1-8', ext_options), + ('sna', '2.3-2', ext_options), + ('glasso', '1.8', ext_options), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.3.2', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2016a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2016a.eb new file mode 100644 index 0000000000..747addc8df --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From d2f2ef45168932839ef2d2582349600c6caf64c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 11:55:56 +0100 Subject: [PATCH 0936/2133] add Szip as dep in netCDF 4.4.0 easyconfig --- easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb index 2818683dd7..719c330b9d 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb @@ -17,6 +17,7 @@ source_urls = [ dependencies = [ ('HDF5', '1.8.16'), ('cURL', '7.47.0'), + ('Szip', '2.1'), ] builddependencies = [ -- GitLab From 37a39678dd32e9226a54a1ee46a26469c71b1c43 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 10 Mar 2016 12:12:56 +0100 Subject: [PATCH 0937/2133] Added missing pscom easyconfig --- .../easyconfigs/p/pscom/pscom-5.0.44-1.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb new file mode 100644 index 0000000000..9a9312254f --- /dev/null +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'pscom' +version = '5.0.44-1' +homepage = 'http://www.par-tec.com' +description = """ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] +sources = ['%(version)s.zip'] + +dependencies = [('popt', '1.16')] + + +sanity_check_paths = { + 'files': ['include/pscom.h', ('lib/libpscom.%s' % SHLIB_EXT, 'lib64/libpscom.%s' % SHLIB_EXT)], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From ffb4b20b3c4d46fcf325dd4de71b3632c1c7bc20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 13:20:31 +0200 Subject: [PATCH 0938/2133] enable usempi in GDAL easyconfig w/ foss toolchain --- easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb index 1d59b9bdac..80039ca350 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.2-foss-2016a.eb @@ -10,6 +10,7 @@ description = """GDAL is a translator library for raster geospatial data formats data translation and processing.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] sources = [SOURCELOWER_TAR_XZ] -- GitLab From 34a2545f7c7cbf88ccbf022a40e0927c70a9cabc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 13:24:13 +0200 Subject: [PATCH 0939/2133] add easyconfig PHYLIP-3.696-foss-2016a.eb --- .../p/PHYLIP/PHYLIP-3.696-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb new file mode 100644 index 0000000000..090561e4d6 --- /dev/null +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'PHYLIP' +version = '3.696' + +homepage = 'http://evolution.genetics.washington.edu/phylip' +description = "PHYLIP is a free package of programs for inferring phylogenies." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://evolution.gs.washington.edu/phylip/download/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' + +files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.so', 'src/libdrawtree.so'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' -- GitLab From 7d860929075a959ee22e62bc90940dc349531a6b Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 10 Mar 2016 12:27:02 +0100 Subject: [PATCH 0940/2133] Minor fixed in versioning --- .../easyconfigs/p/pscom/pscom-5.0.44-1.eb | 20 ------------------- .../p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 2 +- 2 files changed, 1 insertion(+), 21 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb deleted file mode 100644 index 9a9312254f..0000000000 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pscom' -version = '5.0.44-1' -homepage = 'http://www.par-tec.com' -description = """ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] -sources = ['%(version)s.zip'] - -dependencies = [('popt', '1.16')] - - -sanity_check_paths = { - 'files': ['include/pscom.h', ('lib/libpscom.%s' % SHLIB_EXT, 'lib64/libpscom.%s' % SHLIB_EXT)], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 89eb3c9f54..dfba4ffaa8 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -20,7 +20,7 @@ source_urls = [ mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.44-1', '', True), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' -- GitLab From 0514fe5162f0f426085766ea037bc54463394c7a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 13:33:36 +0200 Subject: [PATCH 0941/2133] add easyconfig MUSCLE-3.8.31-intel-2016a.eb --- .../m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb new file mode 100644 index 0000000000..467b83b6ce --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'http://drive5.com/muscle/' +description = """ MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes—only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s%(version)s_src.tar.gz'] +source_urls = ['http://www.drive5.com/muscle/downloads%(version)s/'] + +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 862ff1060c15af3f1a43b9cb638f217bd06679ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 14:00:19 +0200 Subject: [PATCH 0942/2133] add easyconfig MUSCLE-3.8.31-foss-2016a.eb --- .../m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb new file mode 100644 index 0000000000..026425a12b --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'http://drive5.com/muscle/' +description = """ MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes—only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s%(version)s_src.tar.gz'] +source_urls = ['http://www.drive5.com/muscle/downloads%(version)s/'] + +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6ad2325b2de444cb179df604acb285eb6c980b12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 14:22:48 +0200 Subject: [PATCH 0943/2133] add easyconfig R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb --- ...dle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb | 152 ++++++++++++++++++ 1 file changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb new file mode 100644 index 0000000000..d383fdf33e --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb @@ -0,0 +1,152 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', '3.2.3')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.16.1', bioconductor_options), + ('Biobase', '2.30.0', bioconductor_options), + ('S4Vectors', '0.8.11', bioconductor_options), + ('IRanges', '2.4.8', bioconductor_options), + ('GenomeInfoDb', '1.6.3', bioconductor_options), + ('AnnotationDbi', '1.32.3', bioconductor_options), + ('XVector', '0.10.0', bioconductor_options), + ('zlibbioc', '1.16.0', bioconductor_options), + ('Biostrings', '2.38.4', bioconductor_options), + ('GenomicRanges', '1.22.4', bioconductor_options), + ('Rsamtools', '1.22.0', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('BiocParallel', '1.4.3', bioconductor_options), + ('GenomicAlignments', '1.6.3', bioconductor_options), + ('ShortRead', '1.28.0', bioconductor_options), + ('graph', '1.48.0', bioconductor_options), + ('affyio', '1.40.0', bioconductor_options), + ('BiocInstaller', '1.20.1', bioconductor_options), + ('preprocessCore', '1.32.0', bioconductor_options), + ('affy', '1.48.0', bioconductor_options), + ('GO.db', '', bioconductor_options), + ('limma', '3.26.8', bioconductor_options), + ('RBGL', '1.46.0', bioconductor_options), + ('org.Hs.eg.db', '', bioconductor_options), + ('AnnotationForge', '1.12.2', bioconductor_options), + ('KEGG.db', '', bioconductor_options), + ('annaffy', '1.42.0', bioconductor_options), + ('gcrma', '2.42.0', bioconductor_options), + ('oligoClasses', '1.32.0', bioconductor_options), + ('edgeR', '3.12.0', bioconductor_options), + ('PFAM.db', '', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.4.1', bioconductor_options), + ('qvalue', '2.2.2', bioconductor_options), + ('impute', '1.44.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.24.0', bioconductor_options), + ('hgu133plus2.db', '', bioconductor_options), + ('illuminaio', '0.12.0', bioconductor_options), + ('rtracklayer', '1.30.2', bioconductor_options), + ('biomaRt', '2.26.1', bioconductor_options), + ('GenomicFeatures', '1.22.13', bioconductor_options), + ('bumphunter', '1.10.0', bioconductor_options), + ('multtest', '2.26.0', bioconductor_options), + ('siggenes', '1.44.0', bioconductor_options), + ('DynDoc', '1.48.0', bioconductor_options), + ('genoset', '1.24.0', bioconductor_options), + ('NOISeq', '2.14.1', bioconductor_options), + ('Rgraphviz', '2.14.0', bioconductor_options), + ('RNASeqPower', '1.10.0', bioconductor_options), + ('annotate', '1.48.0', bioconductor_options), + ('GSEABase', '1.32.0', bioconductor_options), + ('genefilter', '1.52.1', bioconductor_options), + ('Category', '2.36.0', bioconductor_options), + ('GOstats', '2.36.0', bioconductor_options), + ('BSgenome', '1.38.0', bioconductor_options), + ('VariantAnnotation', '1.16.4', bioconductor_options), + ('biovizBase', '1.18.0', bioconductor_options), + ('OrganismDbi', '1.12.1', bioconductor_options), + ('ggbio', '1.18.5', bioconductor_options), + ('geneplotter', '1.48.0', bioconductor_options), + ('DESeq2', '1.10.1', bioconductor_options), + ('ReportingTools', '2.10.0', bioconductor_options), + ('affycoretools', '1.42.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '', bioconductor_options), + ('Homo.sapiens', '', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '', bioconductor_options), + ('AgiMicroRna', '2.20.0', bioconductor_options), + ('GenomeGraphs', '1.30.0', bioconductor_options), + ('geneLenDataBase', '', bioconductor_options), + ('goseq', '1.22.0', bioconductor_options), + ('KEGGREST', '1.10.1', bioconductor_options), + ('KEGGgraph', '1.28.0', bioconductor_options), + ('KEGGprofile', '1.12.0', bioconductor_options), + ('GEOquery', '2.36.0', bioconductor_options), + ('minfi', '1.16.1', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '', bioconductor_options), + ('methylumi', '2.16.0', bioconductor_options), + ('lumi', '2.22.1', bioconductor_options), + ('widgetTools', '1.48.0', bioconductor_options), + ('tkWidgets', '1.48.0', bioconductor_options), + ('Mfuzz', '2.30.0', bioconductor_options), + ('maSigPro', '1.42.0', bioconductor_options), + ('SPIA', '2.22.0', bioconductor_options), + ('Gviz', '1.14.4', bioconductor_options), + ('cummeRbund', '2.12.1', bioconductor_options), + ('GenomicFiles', '1.6.2', bioconductor_options), + ('derfinderHelper', '1.4.1', bioconductor_options), + ('derfinder', '1.4.4', bioconductor_options), + ('polyester', '1.6.0', bioconductor_options), + ('Rsubread', '1.20.3', bioconductor_options), + ('pcaMethods', '1.60.0', bioconductor_options), + ('marray', '1.48.0', bioconductor_options), + ('CGHbase', '1.30.0', bioconductor_options), + ('sigaR', '1.14.0', bioconductor_options), + ('HCsnip', '1.10.0', bioconductor_options), + ('metagenomeSeq', '1.12.0', bioconductor_options), + ('gdsfmt', '1.6.2', bioconductor_options), + ('SNPRelate', '1.4.2', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From 60ac2c471e4c75e930f78b85fc9315806f75072d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 14:25:56 +0200 Subject: [PATCH 0944/2133] add easyconfig R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb --- ...dle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 152 ++++++++++++++++++ 1 file changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb new file mode 100644 index 0000000000..43d2df9a2e --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -0,0 +1,152 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', '3.2.3')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.16.1', bioconductor_options), + ('Biobase', '2.30.0', bioconductor_options), + ('S4Vectors', '0.8.11', bioconductor_options), + ('IRanges', '2.4.8', bioconductor_options), + ('GenomeInfoDb', '1.6.3', bioconductor_options), + ('AnnotationDbi', '1.32.3', bioconductor_options), + ('XVector', '0.10.0', bioconductor_options), + ('zlibbioc', '1.16.0', bioconductor_options), + ('Biostrings', '2.38.4', bioconductor_options), + ('GenomicRanges', '1.22.4', bioconductor_options), + ('Rsamtools', '1.22.0', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('BiocParallel', '1.4.3', bioconductor_options), + ('GenomicAlignments', '1.6.3', bioconductor_options), + ('ShortRead', '1.28.0', bioconductor_options), + ('graph', '1.48.0', bioconductor_options), + ('affyio', '1.40.0', bioconductor_options), + ('BiocInstaller', '1.20.1', bioconductor_options), + ('preprocessCore', '1.32.0', bioconductor_options), + ('affy', '1.48.0', bioconductor_options), + ('GO.db', '', bioconductor_options), + ('limma', '3.26.8', bioconductor_options), + ('RBGL', '1.46.0', bioconductor_options), + ('org.Hs.eg.db', '', bioconductor_options), + ('AnnotationForge', '1.12.2', bioconductor_options), + ('KEGG.db', '', bioconductor_options), + ('annaffy', '1.42.0', bioconductor_options), + ('gcrma', '2.42.0', bioconductor_options), + ('oligoClasses', '1.32.0', bioconductor_options), + ('edgeR', '3.12.0', bioconductor_options), + ('PFAM.db', '', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.4.1', bioconductor_options), + ('qvalue', '2.2.2', bioconductor_options), + ('impute', '1.44.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.24.0', bioconductor_options), + ('hgu133plus2.db', '', bioconductor_options), + ('illuminaio', '0.12.0', bioconductor_options), + ('rtracklayer', '1.30.2', bioconductor_options), + ('biomaRt', '2.26.1', bioconductor_options), + ('GenomicFeatures', '1.22.13', bioconductor_options), + ('bumphunter', '1.10.0', bioconductor_options), + ('multtest', '2.26.0', bioconductor_options), + ('siggenes', '1.44.0', bioconductor_options), + ('DynDoc', '1.48.0', bioconductor_options), + ('genoset', '1.24.0', bioconductor_options), + ('NOISeq', '2.14.1', bioconductor_options), + ('Rgraphviz', '2.14.0', bioconductor_options), + ('RNASeqPower', '1.10.0', bioconductor_options), + ('annotate', '1.48.0', bioconductor_options), + ('GSEABase', '1.32.0', bioconductor_options), + ('genefilter', '1.52.1', bioconductor_options), + ('Category', '2.36.0', bioconductor_options), + ('GOstats', '2.36.0', bioconductor_options), + ('BSgenome', '1.38.0', bioconductor_options), + ('VariantAnnotation', '1.16.4', bioconductor_options), + ('biovizBase', '1.18.0', bioconductor_options), + ('OrganismDbi', '1.12.1', bioconductor_options), + ('ggbio', '1.18.5', bioconductor_options), + ('geneplotter', '1.48.0', bioconductor_options), + ('DESeq2', '1.10.1', bioconductor_options), + ('ReportingTools', '2.10.0', bioconductor_options), + ('affycoretools', '1.42.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '', bioconductor_options), + ('Homo.sapiens', '', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '', bioconductor_options), + ('AgiMicroRna', '2.20.0', bioconductor_options), + ('GenomeGraphs', '1.30.0', bioconductor_options), + ('geneLenDataBase', '', bioconductor_options), + ('goseq', '1.22.0', bioconductor_options), + ('KEGGREST', '1.10.1', bioconductor_options), + ('KEGGgraph', '1.28.0', bioconductor_options), + ('KEGGprofile', '1.12.0', bioconductor_options), + ('GEOquery', '2.36.0', bioconductor_options), + ('minfi', '1.16.1', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '', bioconductor_options), + ('methylumi', '2.16.0', bioconductor_options), + ('lumi', '2.22.1', bioconductor_options), + ('widgetTools', '1.48.0', bioconductor_options), + ('tkWidgets', '1.48.0', bioconductor_options), + ('Mfuzz', '2.30.0', bioconductor_options), + ('maSigPro', '1.42.0', bioconductor_options), + ('SPIA', '2.22.0', bioconductor_options), + ('Gviz', '1.14.4', bioconductor_options), + ('cummeRbund', '2.12.1', bioconductor_options), + ('GenomicFiles', '1.6.2', bioconductor_options), + ('derfinderHelper', '1.4.1', bioconductor_options), + ('derfinder', '1.4.4', bioconductor_options), + ('polyester', '1.6.0', bioconductor_options), + ('Rsubread', '1.20.3', bioconductor_options), + ('pcaMethods', '1.60.0', bioconductor_options), + ('marray', '1.48.0', bioconductor_options), + ('CGHbase', '1.30.0', bioconductor_options), + ('sigaR', '1.14.0', bioconductor_options), + ('HCsnip', '1.10.0', bioconductor_options), + ('metagenomeSeq', '1.12.0', bioconductor_options), + ('gdsfmt', '1.6.2', bioconductor_options), + ('SNPRelate', '1.4.2', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From b66998ce4164d27da3f9e01567ec7e5dabffb228 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 14:40:58 +0200 Subject: [PATCH 0945/2133] modify easyconfig R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb --- ...dle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 43d2df9a2e..47a6df9dac 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -29,9 +29,9 @@ bioconductor_options = { 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', ], 'source_tmpl': name_tmpl, } @@ -61,24 +61,24 @@ exts_list = [ ('BiocInstaller', '1.20.1', bioconductor_options), ('preprocessCore', '1.32.0', bioconductor_options), ('affy', '1.48.0', bioconductor_options), - ('GO.db', '', bioconductor_options), + ('GO.db', '3.2.2', bioconductor_options), ('limma', '3.26.8', bioconductor_options), ('RBGL', '1.46.0', bioconductor_options), - ('org.Hs.eg.db', '', bioconductor_options), + ('org.Hs.eg.db', '3.2.3', bioconductor_options), ('AnnotationForge', '1.12.2', bioconductor_options), - ('KEGG.db', '', bioconductor_options), + ('KEGG.db', '3.2.2', bioconductor_options), ('annaffy', '1.42.0', bioconductor_options), ('gcrma', '2.42.0', bioconductor_options), ('oligoClasses', '1.32.0', bioconductor_options), ('edgeR', '3.12.0', bioconductor_options), - ('PFAM.db', '', bioconductor_options), + ('PFAM.db', '3.2.2', bioconductor_options), ('perm', '1.0-0.0', ext_options), ('baySeq', '2.4.1', bioconductor_options), ('qvalue', '2.2.2', bioconductor_options), ('impute', '1.44.0', bioconductor_options), ('samr', '2.0', ext_options), ('DEGseq', '1.24.0', bioconductor_options), - ('hgu133plus2.db', '', bioconductor_options), + ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), ('rtracklayer', '1.30.2', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), @@ -105,19 +105,19 @@ exts_list = [ ('DESeq2', '1.10.1', bioconductor_options), ('ReportingTools', '2.10.0', bioconductor_options), ('affycoretools', '1.42.0', bioconductor_options), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '', bioconductor_options), - ('Homo.sapiens', '', bioconductor_options), - ('BSgenome.Hsapiens.UCSC.hg19', '', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', bioconductor_options), + ('Homo.sapiens', '1.3.1', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), ('AgiMicroRna', '2.20.0', bioconductor_options), ('GenomeGraphs', '1.30.0', bioconductor_options), - ('geneLenDataBase', '', bioconductor_options), + ('geneLenDataBase', '1.6.0', bioconductor_options), ('goseq', '1.22.0', bioconductor_options), ('KEGGREST', '1.10.1', bioconductor_options), ('KEGGgraph', '1.28.0', bioconductor_options), ('KEGGprofile', '1.12.0', bioconductor_options), ('GEOquery', '2.36.0', bioconductor_options), ('minfi', '1.16.1', bioconductor_options), - ('FDb.InfiniumMethylation.hg19', '', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), ('methylumi', '2.16.0', bioconductor_options), ('lumi', '2.22.1', bioconductor_options), ('widgetTools', '1.48.0', bioconductor_options), -- GitLab From 3240a23cad4ea79d6fcc1695fb8db8f4489a07ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 13:48:50 +0100 Subject: [PATCH 0946/2133] add phangorn extension in R 3.2.3 easyconfigs --- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 1 + easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb | 1 + easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 1 + easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index dcabcfedb0..966d48e3c9 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -438,6 +438,7 @@ exts_list = [ ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.2', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb index bc318c4a60..323a1f2507 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -438,6 +438,7 @@ exts_list = [ ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.2', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index 49fadf4c1f..2fead5c720 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -450,6 +450,7 @@ exts_list = [ ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.2', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index ddf0479c12..91dc12b964 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -438,6 +438,7 @@ exts_list = [ ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.2', ext_options), ] moduleclass = 'lang' -- GitLab From 18427a87b82e5d144a995851376c100da8b2389f Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 10 Mar 2016 15:22:31 +0100 Subject: [PATCH 0947/2133] Fix OS dependencies for MVAPICH2 with BLCR checkpoint/restart support --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index cee59253ac..6cd874bb9a 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -23,7 +23,10 @@ dependencies = [('hwloc', '1.5.1')] # enable checkpointing support withchkpt = True -osdependencies = ['blcr-libs', 'blcr-devel'] +osdependencies = [ + ('libcr-dev', 'blcr-devel'), + ('libattr1-dev', 'libattr-devel'), +] builddependencies = [('Bison', '2.5')] -- GitLab From cd6eed7dbf4cde9809f8c0dadfa96317fc62934c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 17:01:20 +0200 Subject: [PATCH 0948/2133] modify easyconfig R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb, add easyconfig R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb --- ...dle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 6 +- ...le-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 154 ++++++++++++++++++ 2 files changed, 158 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 47a6df9dac..747435a5bf 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -45,15 +45,16 @@ exts_list = [ ('IRanges', '2.4.8', bioconductor_options), ('GenomeInfoDb', '1.6.3', bioconductor_options), ('AnnotationDbi', '1.32.3', bioconductor_options), - ('XVector', '0.10.0', bioconductor_options), ('zlibbioc', '1.16.0', bioconductor_options), + ('XVector', '0.10.0', bioconductor_options), ('Biostrings', '2.38.4', bioconductor_options), ('GenomicRanges', '1.22.4', bioconductor_options), + ('BiocParallel', '1.4.3', bioconductor_options), ('Rsamtools', '1.22.0', bioconductor_options), ('lambda.r', '1.1.7', ext_options), ('futile.options', '1.0.0', ext_options), ('futile.logger', '1.4.1', ext_options), - ('BiocParallel', '1.4.3', bioconductor_options), + ('SummarizedExperiment', '1.0.2', bioconductor_options), ('GenomicAlignments', '1.6.3', bioconductor_options), ('ShortRead', '1.28.0', bioconductor_options), ('graph', '1.48.0', bioconductor_options), @@ -116,6 +117,7 @@ exts_list = [ ('KEGGgraph', '1.28.0', bioconductor_options), ('KEGGprofile', '1.12.0', bioconductor_options), ('GEOquery', '2.36.0', bioconductor_options), + ('mixOmics', '5.2.0', ext_options), ('minfi', '1.16.1', bioconductor_options), ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), ('methylumi', '2.16.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb new file mode 100644 index 0000000000..f4c9219e9d --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -0,0 +1,154 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', '3.2.3')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.16.1', bioconductor_options), + ('Biobase', '2.30.0', bioconductor_options), + ('S4Vectors', '0.8.11', bioconductor_options), + ('IRanges', '2.4.8', bioconductor_options), + ('GenomeInfoDb', '1.6.3', bioconductor_options), + ('AnnotationDbi', '1.32.3', bioconductor_options), + ('zlibbioc', '1.16.0', bioconductor_options), + ('XVector', '0.10.0', bioconductor_options), + ('Biostrings', '2.38.4', bioconductor_options), + ('GenomicRanges', '1.22.4', bioconductor_options), + ('BiocParallel', '1.4.3', bioconductor_options), + ('Rsamtools', '1.22.0', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('SummarizedExperiment', '1.0.2', bioconductor_options), + ('GenomicAlignments', '1.6.3', bioconductor_options), + ('ShortRead', '1.28.0', bioconductor_options), + ('graph', '1.48.0', bioconductor_options), + ('affyio', '1.40.0', bioconductor_options), + ('BiocInstaller', '1.20.1', bioconductor_options), + ('preprocessCore', '1.32.0', bioconductor_options), + ('affy', '1.48.0', bioconductor_options), + ('GO.db', '3.2.2', bioconductor_options), + ('limma', '3.26.8', bioconductor_options), + ('RBGL', '1.46.0', bioconductor_options), + ('org.Hs.eg.db', '3.2.3', bioconductor_options), + ('AnnotationForge', '1.12.2', bioconductor_options), + ('KEGG.db', '3.2.2', bioconductor_options), + ('annaffy', '1.42.0', bioconductor_options), + ('gcrma', '2.42.0', bioconductor_options), + ('oligoClasses', '1.32.0', bioconductor_options), + ('edgeR', '3.12.0', bioconductor_options), + ('PFAM.db', '3.2.2', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.4.1', bioconductor_options), + ('qvalue', '2.2.2', bioconductor_options), + ('impute', '1.44.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.24.0', bioconductor_options), + ('hgu133plus2.db', '3.2.2', bioconductor_options), + ('illuminaio', '0.12.0', bioconductor_options), + ('rtracklayer', '1.30.2', bioconductor_options), + ('biomaRt', '2.26.1', bioconductor_options), + ('GenomicFeatures', '1.22.13', bioconductor_options), + ('bumphunter', '1.10.0', bioconductor_options), + ('multtest', '2.26.0', bioconductor_options), + ('siggenes', '1.44.0', bioconductor_options), + ('DynDoc', '1.48.0', bioconductor_options), + ('genoset', '1.24.0', bioconductor_options), + ('NOISeq', '2.14.1', bioconductor_options), + ('Rgraphviz', '2.14.0', bioconductor_options), + ('RNASeqPower', '1.10.0', bioconductor_options), + ('annotate', '1.48.0', bioconductor_options), + ('GSEABase', '1.32.0', bioconductor_options), + ('genefilter', '1.52.1', bioconductor_options), + ('Category', '2.36.0', bioconductor_options), + ('GOstats', '2.36.0', bioconductor_options), + ('BSgenome', '1.38.0', bioconductor_options), + ('VariantAnnotation', '1.16.4', bioconductor_options), + ('biovizBase', '1.18.0', bioconductor_options), + ('OrganismDbi', '1.12.1', bioconductor_options), + ('ggbio', '1.18.5', bioconductor_options), + ('geneplotter', '1.48.0', bioconductor_options), + ('DESeq2', '1.10.1', bioconductor_options), + ('ReportingTools', '2.10.0', bioconductor_options), + ('affycoretools', '1.42.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', bioconductor_options), + ('Homo.sapiens', '1.3.1', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.20.0', bioconductor_options), + ('GenomeGraphs', '1.30.0', bioconductor_options), + ('geneLenDataBase', '1.6.0', bioconductor_options), + ('goseq', '1.22.0', bioconductor_options), + ('KEGGREST', '1.10.1', bioconductor_options), + ('KEGGgraph', '1.28.0', bioconductor_options), + ('KEGGprofile', '1.12.0', bioconductor_options), + ('GEOquery', '2.36.0', bioconductor_options), + ('mixOmics', '5.2.0', ext_options), + ('minfi', '1.16.1', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.16.0', bioconductor_options), + ('lumi', '2.22.1', bioconductor_options), + ('widgetTools', '1.48.0', bioconductor_options), + ('tkWidgets', '1.48.0', bioconductor_options), + ('Mfuzz', '2.30.0', bioconductor_options), + ('maSigPro', '1.42.0', bioconductor_options), + ('SPIA', '2.22.0', bioconductor_options), + ('Gviz', '1.14.4', bioconductor_options), + ('cummeRbund', '2.12.1', bioconductor_options), + ('GenomicFiles', '1.6.2', bioconductor_options), + ('derfinderHelper', '1.4.1', bioconductor_options), + ('derfinder', '1.4.4', bioconductor_options), + ('polyester', '1.6.0', bioconductor_options), + ('Rsubread', '1.20.3', bioconductor_options), + ('pcaMethods', '1.60.0', bioconductor_options), + ('marray', '1.48.0', bioconductor_options), + ('CGHbase', '1.30.0', bioconductor_options), + ('sigaR', '1.14.0', bioconductor_options), + ('HCsnip', '1.10.0', bioconductor_options), + ('metagenomeSeq', '1.12.0', bioconductor_options), + ('gdsfmt', '1.6.2', bioconductor_options), + ('SNPRelate', '1.4.2', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From baf9329fdbc191d90ae2a5f392a6ef9b6c12df9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 16:52:26 +0100 Subject: [PATCH 0949/2133] remove wrong easyconfig --- ...dle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb | 152 ------------------ 1 file changed, 152 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb deleted file mode 100644 index d383fdf33e..0000000000 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb +++ /dev/null @@ -1,152 +0,0 @@ -easyblock = 'Bundle' - -name = 'R-bundle-Bioconductor' -version = '3.1' -versionsuffix = '-R-%(rver)s' - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -# these are extensions for R -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -dependencies = [('R', '3.2.3')] - -name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib/', # current version of packages - 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': name_tmpl, -} -bioconductor_options = { - 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', - ], - 'source_tmpl': name_tmpl, -} - -# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends -# !! order of packages is important !! -exts_list = [ - ('BiocGenerics', '0.16.1', bioconductor_options), - ('Biobase', '2.30.0', bioconductor_options), - ('S4Vectors', '0.8.11', bioconductor_options), - ('IRanges', '2.4.8', bioconductor_options), - ('GenomeInfoDb', '1.6.3', bioconductor_options), - ('AnnotationDbi', '1.32.3', bioconductor_options), - ('XVector', '0.10.0', bioconductor_options), - ('zlibbioc', '1.16.0', bioconductor_options), - ('Biostrings', '2.38.4', bioconductor_options), - ('GenomicRanges', '1.22.4', bioconductor_options), - ('Rsamtools', '1.22.0', bioconductor_options), - ('lambda.r', '1.1.7', ext_options), - ('futile.options', '1.0.0', ext_options), - ('futile.logger', '1.4.1', ext_options), - ('BiocParallel', '1.4.3', bioconductor_options), - ('GenomicAlignments', '1.6.3', bioconductor_options), - ('ShortRead', '1.28.0', bioconductor_options), - ('graph', '1.48.0', bioconductor_options), - ('affyio', '1.40.0', bioconductor_options), - ('BiocInstaller', '1.20.1', bioconductor_options), - ('preprocessCore', '1.32.0', bioconductor_options), - ('affy', '1.48.0', bioconductor_options), - ('GO.db', '', bioconductor_options), - ('limma', '3.26.8', bioconductor_options), - ('RBGL', '1.46.0', bioconductor_options), - ('org.Hs.eg.db', '', bioconductor_options), - ('AnnotationForge', '1.12.2', bioconductor_options), - ('KEGG.db', '', bioconductor_options), - ('annaffy', '1.42.0', bioconductor_options), - ('gcrma', '2.42.0', bioconductor_options), - ('oligoClasses', '1.32.0', bioconductor_options), - ('edgeR', '3.12.0', bioconductor_options), - ('PFAM.db', '', bioconductor_options), - ('perm', '1.0-0.0', ext_options), - ('baySeq', '2.4.1', bioconductor_options), - ('qvalue', '2.2.2', bioconductor_options), - ('impute', '1.44.0', bioconductor_options), - ('samr', '2.0', ext_options), - ('DEGseq', '1.24.0', bioconductor_options), - ('hgu133plus2.db', '', bioconductor_options), - ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.2', bioconductor_options), - ('biomaRt', '2.26.1', bioconductor_options), - ('GenomicFeatures', '1.22.13', bioconductor_options), - ('bumphunter', '1.10.0', bioconductor_options), - ('multtest', '2.26.0', bioconductor_options), - ('siggenes', '1.44.0', bioconductor_options), - ('DynDoc', '1.48.0', bioconductor_options), - ('genoset', '1.24.0', bioconductor_options), - ('NOISeq', '2.14.1', bioconductor_options), - ('Rgraphviz', '2.14.0', bioconductor_options), - ('RNASeqPower', '1.10.0', bioconductor_options), - ('annotate', '1.48.0', bioconductor_options), - ('GSEABase', '1.32.0', bioconductor_options), - ('genefilter', '1.52.1', bioconductor_options), - ('Category', '2.36.0', bioconductor_options), - ('GOstats', '2.36.0', bioconductor_options), - ('BSgenome', '1.38.0', bioconductor_options), - ('VariantAnnotation', '1.16.4', bioconductor_options), - ('biovizBase', '1.18.0', bioconductor_options), - ('OrganismDbi', '1.12.1', bioconductor_options), - ('ggbio', '1.18.5', bioconductor_options), - ('geneplotter', '1.48.0', bioconductor_options), - ('DESeq2', '1.10.1', bioconductor_options), - ('ReportingTools', '2.10.0', bioconductor_options), - ('affycoretools', '1.42.0', bioconductor_options), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '', bioconductor_options), - ('Homo.sapiens', '', bioconductor_options), - ('BSgenome.Hsapiens.UCSC.hg19', '', bioconductor_options), - ('AgiMicroRna', '2.20.0', bioconductor_options), - ('GenomeGraphs', '1.30.0', bioconductor_options), - ('geneLenDataBase', '', bioconductor_options), - ('goseq', '1.22.0', bioconductor_options), - ('KEGGREST', '1.10.1', bioconductor_options), - ('KEGGgraph', '1.28.0', bioconductor_options), - ('KEGGprofile', '1.12.0', bioconductor_options), - ('GEOquery', '2.36.0', bioconductor_options), - ('minfi', '1.16.1', bioconductor_options), - ('FDb.InfiniumMethylation.hg19', '', bioconductor_options), - ('methylumi', '2.16.0', bioconductor_options), - ('lumi', '2.22.1', bioconductor_options), - ('widgetTools', '1.48.0', bioconductor_options), - ('tkWidgets', '1.48.0', bioconductor_options), - ('Mfuzz', '2.30.0', bioconductor_options), - ('maSigPro', '1.42.0', bioconductor_options), - ('SPIA', '2.22.0', bioconductor_options), - ('Gviz', '1.14.4', bioconductor_options), - ('cummeRbund', '2.12.1', bioconductor_options), - ('GenomicFiles', '1.6.2', bioconductor_options), - ('derfinderHelper', '1.4.1', bioconductor_options), - ('derfinder', '1.4.4', bioconductor_options), - ('polyester', '1.6.0', bioconductor_options), - ('Rsubread', '1.20.3', bioconductor_options), - ('pcaMethods', '1.60.0', bioconductor_options), - ('marray', '1.48.0', bioconductor_options), - ('CGHbase', '1.30.0', bioconductor_options), - ('sigaR', '1.14.0', bioconductor_options), - ('HCsnip', '1.10.0', bioconductor_options), - ('metagenomeSeq', '1.12.0', bioconductor_options), - ('gdsfmt', '1.6.2', bioconductor_options), - ('SNPRelate', '1.4.2', bioconductor_options), -] - -modextrapaths = {'R_LIBS': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], -} - -moduleclass = 'bio' -- GitLab From 3b61720f9d6aba21e540624b2805dff29f21ad84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 10:44:27 +0100 Subject: [PATCH 0950/2133] drop 'release' URLs, don't use %(rver)s yet --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 7 +++---- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 8 +++----- 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 747435a5bf..d5dcde11e2 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -13,7 +13,9 @@ toolchain = {'name': 'foss', 'version': '2016a'} exts_defaultclass = 'RPackage' exts_filter = ("R -q --no-save", "library(%(ext_name)s)") -dependencies = [('R', '3.2.3')] +rver = '3.2.3' +versionsuffix = '-R-%s' % rver +dependencies = [('R', rver)] name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { @@ -26,9 +28,6 @@ ext_options = { } bioconductor_options = { 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index f4c9219e9d..dce3357e77 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -2,7 +2,6 @@ easyblock = 'Bundle' name = 'R-bundle-Bioconductor' version = '3.2' -versionsuffix = '-R-%(rver)s' homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -13,7 +12,9 @@ toolchain = {'name': 'intel', 'version': '2016a'} exts_defaultclass = 'RPackage' exts_filter = ("R -q --no-save", "library(%(ext_name)s)") -dependencies = [('R', '3.2.3')] +rver = '3.2.3' +versionsuffix = '-R-%s' % rver +dependencies = [('R', rver)] name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { @@ -26,9 +27,6 @@ ext_options = { } bioconductor_options = { 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', -- GitLab From 782e024dbab561cbe68d02bfd5d917f995130911 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 11 Mar 2016 12:28:22 +0200 Subject: [PATCH 0951/2133] add easyconfig GDB-7.11-intel-2016a.eb --- .../easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb new file mode 100644 index 0000000000..fa5295e98e --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.11' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('expat', '2.1.0'), + ('Python', '2.7.11'), +] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' -- GitLab From 90276c29d80a68782f1eb9b092ac8265f4c2baf1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 13:04:48 +0200 Subject: [PATCH 0952/2133] add easyconfig PHYLIP-3.696-intel-2016a.eb --- .../p/PHYLIP/PHYLIP-3.696-intel-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb new file mode 100644 index 0000000000..337f4f3b90 --- /dev/null +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'PHYLIP' +version = '3.696' + +homepage = 'http://evolution.genetics.washington.edu/phylip' +description = "PHYLIP is a free package of programs for inferring phylogenies." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://evolution.gs.washington.edu/phylip/download/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' + +files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.so', 'src/libdrawtree.so'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' -- GitLab From 0b7c8c0733734518db9d852ba8a112126cbe20bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 13:06:50 +0200 Subject: [PATCH 0953/2133] add easyconfig BWA-0.7.13-intel-2016a.eb --- .../b/BWA/BWA-0.7.13-intel-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb new file mode 100644 index 0000000000..f4774cbbbe --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.13 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.13' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +moduleclass = 'bio' -- GitLab From d264046fac6218f20a0610d5c0b069e3a1324253 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 13:17:08 +0200 Subject: [PATCH 0954/2133] add easyconfig SNPhylo-20140701-intel-2016a.eb, add easyconfig SNPhylo-20140701-foss-2016a.eb --- .../s/SNPhylo/SNPhylo-20140701-foss-2016a.eb | 22 +++++++++++++++++++ .../s/SNPhylo/SNPhylo-20140701-intel-2016a.eb | 22 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb new file mode 100644 index 0000000000..e61334d314 --- /dev/null +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'SNPhylo' +version = '20140701' + +homepage = 'http://chibba.pgml.uga.edu/snphylo/' +description = """SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# download from http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz and rename +# see http://chibba.pgml.uga.edu/snphylo/ for version +sources = ['%(namelower)s-%(version)s.tar.gz'] + +checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] + +dependencies = [ + ('R', '3.2.3'), + ('Python', '2.7.11'), + ('MUSCLE', '3.8.31'), + ('PHYLIP', '3.696'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb new file mode 100644 index 0000000000..cea99bc814 --- /dev/null +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'SNPhylo' +version = '20140701' + +homepage = 'http://chibba.pgml.uga.edu/snphylo/' +description = """SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# download from http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz and rename +# see http://chibba.pgml.uga.edu/snphylo/ for version +sources = ['%(namelower)s-%(version)s.tar.gz'] + +checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] + +dependencies = [ + ('R', '3.2.3'), + ('Python', '2.7.11'), + ('MUSCLE', '3.8.31'), + ('PHYLIP', '3.696'), +] + +moduleclass = 'bio' -- GitLab From 5649cc342580e1a881db0e6a949b4a118bf45f9b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 14:47:59 +0200 Subject: [PATCH 0955/2133] add easyconfig npstat-0.99-intel-2016a.eb --- .../n/npstat/npstat-0.99-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/npstat/npstat-0.99-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/npstat/npstat-0.99-intel-2016a.eb b/easybuild/easyconfigs/n/npstat/npstat-0.99-intel-2016a.eb new file mode 100644 index 0000000000..b8f9940b59 --- /dev/null +++ b/easybuild/easyconfigs/n/npstat/npstat-0.99-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'npstat' +version = '0.99' + +homepage = 'https://code.google.com/archive/p/npstat/' +description = """npstat implements some population genetics tests and estimators that can be applied + to pooled sequences from Next Generation Sequencing experiments.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://storage.googleapis.com/google-code-archive-source/v2/code.google.com/npstat/'] +sources = ['source-archive.zip'] + +patches = ['npstat-%(version)s_fix-hardcoding-Makefile.patch'] + +# commit 14, Oct 31st 2013 +checksums = ['a1595b7c46312d0f51b8b68987289337'] + +dependencies = [ + ('GSL', '1.16'), +] + +start_dir = 'trunk' + +files_to_copy = [(['npstat'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/npstat'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 69480c1a1e0803e198c1d9a449bcb849fde15c03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 14:53:38 +0200 Subject: [PATCH 0956/2133] modify easyconfig SNPhylo-20140701-intel-2016a.eb, modify easyconfig SNPhylo-20140701-foss-2016a.eb --- easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb | 1 + easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb index e61334d314..6fb5d3516e 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb @@ -14,6 +14,7 @@ checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] dependencies = [ ('R', '3.2.3'), + ('R-bundle-Bioconductor', '3.2', 'R-%(rver)s'), ('Python', '2.7.11'), ('MUSCLE', '3.8.31'), ('PHYLIP', '3.696'), diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb index cea99bc814..45955d802a 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb @@ -14,6 +14,7 @@ checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] dependencies = [ ('R', '3.2.3'), + ('R-bundle-Bioconductor', '3.2', 'R-%(rver)s'), ('Python', '2.7.11'), ('MUSCLE', '3.8.31'), ('PHYLIP', '3.696'), -- GitLab From 1cc3e64db7e1faa91730799ae3c9c25281139c4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 14:55:28 +0200 Subject: [PATCH 0957/2133] modify easyconfig SNPhylo-20140701-intel-2016a.eb, modify easyconfig SNPhylo-20140701-foss-2016a.eb --- easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb | 2 +- easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb index 6fb5d3516e..701dafb78c 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb @@ -14,7 +14,7 @@ checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] dependencies = [ ('R', '3.2.3'), - ('R-bundle-Bioconductor', '3.2', 'R-%(rver)s'), + ('R-bundle-Bioconductor', '3.2', '-R-%(rver)s'), ('Python', '2.7.11'), ('MUSCLE', '3.8.31'), ('PHYLIP', '3.696'), diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb index 45955d802a..71e1b6e3e1 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb @@ -14,7 +14,7 @@ checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] dependencies = [ ('R', '3.2.3'), - ('R-bundle-Bioconductor', '3.2', 'R-%(rver)s'), + ('R-bundle-Bioconductor', '3.2', '-R-%(rver)s'), ('Python', '2.7.11'), ('MUSCLE', '3.8.31'), ('PHYLIP', '3.696'), -- GitLab From 9538cef30f7081f37b819bb5edf8b5542f397432 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 14:02:37 +0100 Subject: [PATCH 0958/2133] fix remark --- easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb index 090561e4d6..90aea78df7 100644 --- a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb @@ -9,7 +9,7 @@ description = "PHYLIP is a free package of programs for inferring phylogenies." toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://evolution.gs.washington.edu/phylip/download/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb index 337f4f3b90..312062d04f 100644 --- a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb @@ -9,7 +9,7 @@ description = "PHYLIP is a free package of programs for inferring phylogenies." toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://evolution.gs.washington.edu/phylip/download/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' -- GitLab From 10e9af18743b647aedec72e30e300e9d8cf249f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 15:15:16 +0200 Subject: [PATCH 0959/2133] modify easyconfig SNPhylo-20140701-intel-2016a.eb, modify easyconfig SNPhylo-20140701-foss-2016a.eb --- easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb | 2 +- easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb index 701dafb78c..f27160e9e4 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} # download from http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz and rename # see http://chibba.pgml.uga.edu/snphylo/ for version -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb index 71e1b6e3e1..d54fcc2b47 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # download from http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz and rename # see http://chibba.pgml.uga.edu/snphylo/ for version -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] -- GitLab From 994c84656ccbe2f1b81547066f44e9cf6d531008 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 14:49:25 +0100 Subject: [PATCH 0960/2133] add missing dependencines in Python 3.5.x easyconfigs --- easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index ae86e7bce7..6b562baa0c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -19,6 +19,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index 38309ea23d..ec80435d9b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -19,6 +19,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index e610aff618..aa7a7d9034 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -19,6 +19,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -- GitLab From dc3792dcd107de914d6f2c690f76e425570727bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 17:22:01 +0200 Subject: [PATCH 0961/2133] add easyconfig attr-2.4.47-GCC-4.6.3.eb --- .../a/attr/attr-2.4.47-GCC-4.6.3.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb diff --git a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb new file mode 100644 index 0000000000..7d040cf36d --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.4.47' + +homepage = 'http://savannah.nongnu.org/projects/attr' +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCC', 'version': '4.6.3'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = ['attr-%(version)s.src.tar.gz'] + +installopts = 'install-lib' + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'lib/libattr.so.1', 'lib/libattr.so.1.1.0'], + 'dirs': ['share'], +} + +moduleclass = 'tools' -- GitLab From de64fa3397823e88d287c726e03037d5950b5733 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 16:36:40 +0100 Subject: [PATCH 0962/2133] add 'attr' as dep in MVAPICH2 easyconfig w/ checkpointing support enabled --- .../MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 6cd874bb9a..04c6dccfe0 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -11,24 +11,26 @@ toolchain = {'name': 'GCC', 'version': '4.6.3'} sources = [SOURCELOWER_TGZ] # note: this URL will only work for the most recent version (previous versions no longer available?) source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] +dependencies = [ + ('hwloc', '1.5.1'), + ('attr', '2.4.47'), +] + +builddependencies = [('Bison', '2.5')] + +osdependencies = [('libcr-dev', 'blcr-devel'),] -rdma_type = "gen2" # 'gen2' or 'udapl' +# 'gen2' or 'udapl' +rdma_type = 'gen2' # enable building of MPE routines withmpe = True # enable hwloc support withhwloc = True -dependencies = [('hwloc', '1.5.1')] # enable checkpointing support withchkpt = True -osdependencies = [ - ('libcr-dev', 'blcr-devel'), - ('libattr1-dev', 'libattr-devel'), -] - -builddependencies = [('Bison', '2.5')] # parallel build tends to fail parallel = 1 -- GitLab From 0ca0ceb1e538326be9741280b130b54e399a4a77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 18:09:52 +0200 Subject: [PATCH 0963/2133] modify easyconfig attr-2.4.47-GCC-4.6.3.eb --- easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb index 7d040cf36d..5c73e6a27b 100644 --- a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb @@ -11,11 +11,11 @@ toolchain = {'name': 'GCC', 'version': '4.6.3'} source_urls = [GNU_SAVANNAH_SOURCE] sources = ['attr-%(version)s.src.tar.gz'] -installopts = 'install-lib' +installopts = 'install-dev install-lib' sanity_check_paths = { 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'lib/libattr.so.1', 'lib/libattr.so.1.1.0'], - 'dirs': ['share'], + 'dirs': ['include/attr', 'share'], } moduleclass = 'tools' -- GitLab From a3451e115fa85fef0f3ccaeeb6bec8be8a6070ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 18:22:53 +0200 Subject: [PATCH 0964/2133] modify easyconfig attr-2.4.47-GCC-4.6.3.eb --- easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb index 5c73e6a27b..3f29b7d6d3 100644 --- a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb @@ -14,7 +14,7 @@ sources = ['attr-%(version)s.src.tar.gz'] installopts = 'install-dev install-lib' sanity_check_paths = { - 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'lib/libattr.so.1', 'lib/libattr.so.1.1.0'], + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'lib/libattr.a', 'lib/libattr.%s' % SHLIB_EXT], 'dirs': ['include/attr', 'share'], } -- GitLab From d51a1b8e4a249e60c7872f858a1207e59138e134 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 18:58:56 +0200 Subject: [PATCH 0965/2133] modify easyconfig attr-2.4.47-GCC-4.6.3.eb --- easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb index 3f29b7d6d3..8a4e822bba 100644 --- a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb @@ -14,8 +14,9 @@ sources = ['attr-%(version)s.src.tar.gz'] installopts = 'install-dev install-lib' sanity_check_paths = { - 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'lib/libattr.a', 'lib/libattr.%s' % SHLIB_EXT], - 'dirs': ['include/attr', 'share'], + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'include/attr/attributes.h', 'include/attr/error_context.h', + 'include/attr/libattr.h', 'include/attr/xattr.h', 'lib/libattr.a', 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], } moduleclass = 'tools' -- GitLab From 4754be502808e9896a96f2dc2acd816aa62e40ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 18:46:05 +0100 Subject: [PATCH 0966/2133] consistently add checksums --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 3 +++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb | 2 ++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb | 1 - .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb | 1 - .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb | 1 - easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb | 1 - .../m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb | 1 - easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb | 2 ++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb | 2 ++ .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb | 2 ++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb | 2 ++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb | 1 - 12 files changed, 13 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index a2fae1e4c8..0d8dbcbf47 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -11,6 +11,9 @@ toolchain = {'name': 'GCC', 'version': '4.6.3'} sources = [SOURCELOWER_TGZ] # note: this URL will only work for the most recent version (previous versions no longer available?) source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] + +checksums = ['b05c3cde3d181b2499500b4bd8962e3f'] + dependencies = [ ('hwloc', '1.5.1'), ('attr', '2.4.47'), diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb index 76de06e6fd..8f93aad7e1 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb @@ -11,6 +11,8 @@ sources = [SOURCELOWER_TGZ] # note: this URL will only work for the most recent version (previous versions no longer available?) source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] +checksums = ['b05c3cde3d181b2499500b4bd8962e3f'] + builddependencies = [('Bison', '2.5')] # enable building of MPE routines diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb index dbf130a107..f289c8d654 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['ef4ae05e3b5ad485326505db7381246c'] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb index f8ed601fa4..09e0392913 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['5dc58ed08fd3142c260b70fe297e127c'] dependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb index ec3097f101..8c81cfba65 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'ClangGCC', 'version': '1.2.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['5dc58ed08fd3142c260b70fe297e127c'] dependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb index fc82223d21..87eee23607 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['5dc58ed08fd3142c260b70fe297e127c'] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb index 2ff528acce..5bcb7de6da 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb @@ -10,7 +10,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['5dc58ed08fd3142c260b70fe297e127c'] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb index 86fdc73adc..372dd0b722 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb @@ -9,6 +9,8 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +checksums = ['9d517d6fe483ad339ea01fa234f0c4c9'] + builddependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb index 1c45f04807..657cf1ea16 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb @@ -9,6 +9,8 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +checksums = ['dfc86a014666776c8a76bb8e78356c8b'] + builddependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb index 892dac4687..efbb18826b 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb @@ -9,6 +9,8 @@ toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +checksums = ['0a236f526e368e12a1b3de90716a12d7'] + builddependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb index 9e7d8d7641..46ea0c6676 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb @@ -9,6 +9,8 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +checksums = ['0a236f526e368e12a1b3de90716a12d7'] + builddependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb index bf2762a1a1..b07b0a30f4 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/'] sources = [SOURCELOWER_TAR_GZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['77bba29442f81e196155e87869cdceda'] builddependencies = [('Bison', '2.7')] -- GitLab From 5def8be0d16d4175188ecd8eb939b2ba7bb14829 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 20:01:23 +0200 Subject: [PATCH 0967/2133] add easyconfig SAMtools-1.3-foss-2016a.eb, add easyconfig SAMtools-1.3-intel-2016a.eb --- .../s/SAMtools/SAMtools-1.3-foss-2016a.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3-intel-2016a.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb new file mode 100644 index 0000000000..96d3b95f0f --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb new file mode 100644 index 0000000000..d869d21007 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' -- GitLab From 2067db8a1de479e20c7faee94ee6e93ec9704021 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 20:02:26 +0200 Subject: [PATCH 0968/2133] add easyconfig VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb, add easyconfig VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb --- .../VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb | 37 +++++++++++++++++++ ...VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..c7db740277 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.14' +versionsuffix = '-Perl-%(perlver)s' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.22.1'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..9f1d001bfa --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.14' +versionsuffix = '-Perl-%(perlver)s' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.22.1'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 84ad66c690b657863777d5b1f16621ffc995a0d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 19:05:58 +0100 Subject: [PATCH 0969/2133] fix source URLs for Bioconductor 3.2 --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 6 +++--- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index d5dcde11e2..d1392d23cc 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -28,9 +28,9 @@ ext_options = { } bioconductor_options = { 'source_urls': [ - 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/data/experiment/src/contrib/', ], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index dce3357e77..60d39797ec 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -27,9 +27,9 @@ ext_options = { } bioconductor_options = { 'source_urls': [ - 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/data/experiment/src/contrib/', ], 'source_tmpl': name_tmpl, } -- GitLab From 4606a7f6ce37e1ca5222629d13d1842c4ede1411 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 23:00:30 +0100 Subject: [PATCH 0970/2133] drop patch for XML-Bare that's specific to icc --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb index 652f0d5227..2ecf3ea45f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -419,7 +419,6 @@ exts_list = [ ('XML::Bare', '0.53', { 'source_tmpl': 'XML-Bare-0.53.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], - 'patches': ['XML-Bare-0.53_icc.patch'], }), ('Dist::CheckConflicts', '0.11', { 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', -- GitLab From 1de3ad9229b8db13719eb839de0939eca5ac260d Mon Sep 17 00:00:00 2001 From: perettig Date: Sat, 12 Mar 2016 12:29:15 +0100 Subject: [PATCH 0971/2133] dropping -XC suffix for Cray toolchains --- .../b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb | 22 ++++ .../b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb | 15 +++ .../b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb | 22 ++++ .../c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb | 22 ++++ .../c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb | 22 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb | 38 ++++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb | 38 ++++++ .../CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb | 48 ++++++++ .../c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb | 45 +++++++ ...ayCCE-2015.06-XC.eb => CrayCCE-2015.06.eb} | 2 +- ...ayCCE-2015.11-XC.eb => CrayCCE-2015.11.eb} | 2 +- ...ayGNU-2015.06-XC.eb => CrayGNU-2015.06.eb} | 2 +- ...ayGNU-2015.11-XC.eb => CrayGNU-2015.11.eb} | 2 +- ...tel-2015.06-XC.eb => CrayIntel-2015.06.eb} | 2 +- ...tel-2015.11-XC.eb => CrayIntel-2015.11.eb} | 2 +- .../f/flex/flex-2.5.39-CrayGNU-2015.06.eb | 14 +++ .../f/flex/flex-2.5.39-CrayGNU-2015.11.eb | 14 +++ .../GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb | 45 +++++++ .../GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb | 45 +++++++ .../GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb | 45 +++++++ .../h/HPL/HPL-2.1-CrayCCE-2015.06.eb | 22 ++++ .../h/HPL/HPL-2.1-CrayCCE-2015.11.eb | 22 ++++ .../h/HPL/HPL-2.1-CrayGNU-2015.06.eb | 18 +++ .../h/HPL/HPL-2.1-CrayGNU-2015.11.eb | 18 +++ .../h/HPL/HPL-2.1-CrayIntel-2015.06.eb | 18 +++ .../h/HPL/HPL-2.1-CrayIntel-2015.11.eb | 18 +++ .../JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb | 21 ++++ .../JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb | 21 ++++ .../JasPer-1.900.1-CrayIntel-2015.11.eb | 21 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb | 24 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb | 24 ++++ .../libreadline-6.3-CrayGNU-2015.06.eb | 30 +++++ .../libreadline-6.3-CrayGNU-2015.11.eb | 30 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb | 32 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb | 32 +++++ .../l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb | 33 +++++ .../m/M4/M4-1.4.17-CrayGNU-2015.06.eb | 23 ++++ .../m/M4/M4-1.4.17-CrayGNU-2015.11.eb | 23 ++++ .../n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb | 25 ++++ .../n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb | 25 ++++ .../n/ncurses/ncurses-5.9-CrayGNU-2015.06.eb | 34 ++++++ .../n/ncurses/ncurses-5.9-CrayGNU-2015.11.eb | 34 ++++++ .../ncurses/ncurses-5.9-CrayIntel-2015.11.eb | 34 ++++++ ...umpy-1.9.2-CrayGNU-2015.06-Python-2.7.9.eb | 26 ++++ ...umpy-1.9.2-CrayGNU-2015.11-Python-2.7.9.eb | 26 ++++ .../Python-2.7.9-CrayGNU-2015.06-bare.eb | 39 ++++++ .../p/Python/Python-2.7.9-CrayGNU-2015.06.eb | 115 ++++++++++++++++++ .../Python-2.7.9-CrayGNU-2015.11-bare.eb | 39 ++++++ .../p/Python/Python-2.7.9-CrayGNU-2015.11.eb | 115 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-2015.06.eb | 23 ++++ .../s/Szip/Szip-2.1-CrayGNU-2015.11.eb | 23 ++++ ...ipy-0.15.1-CrayGNU-2015.06-Python-2.7.9.eb | 19 +++ ...ipy-0.15.1-CrayGNU-2015.11-Python-2.7.9.eb | 19 +++ .../s/spglib/spglib-1.7.3-CrayGNU-2015.06.eb | 21 ++++ .../s/spglib/spglib-1.7.3-CrayGNU-2015.11.eb | 21 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb | 38 ++++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb | 38 ++++++ .../t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb | 38 ++++++ .../w/WRF/WRF-3.6.1-CrayGNU-2015.06-dmpar.eb | 41 +++++++ .../w/WRF/WRF-3.6.1-CrayGNU-2015.11-dmpar.eb | 41 +++++++ .../WRF/WRF-3.6.1-CrayIntel-2015.11-dmpar.eb | 41 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb | 22 ++++ .../z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb | 22 ++++ 65 files changed, 1827 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb rename easybuild/easyconfigs/c/CrayCCE/{CrayCCE-2015.06-XC.eb => CrayCCE-2015.06.eb} (96%) rename easybuild/easyconfigs/c/CrayCCE/{CrayCCE-2015.11-XC.eb => CrayCCE-2015.11.eb} (96%) rename easybuild/easyconfigs/c/CrayGNU/{CrayGNU-2015.06-XC.eb => CrayGNU-2015.06.eb} (96%) rename easybuild/easyconfigs/c/CrayGNU/{CrayGNU-2015.11-XC.eb => CrayGNU-2015.11.eb} (96%) rename easybuild/easyconfigs/c/CrayIntel/{CrayIntel-2015.06-XC.eb => CrayIntel-2015.06.eb} (96%) rename easybuild/easyconfigs/c/CrayIntel/{CrayIntel-2015.11-XC.eb => CrayIntel-2015.11.eb} (96%) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..1e373e5c59 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..fbde1c1bed --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..afe1e361bf --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..4907113147 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..3de7ff42c3 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..1f3739c57e --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb new file mode 100644 index 0000000000..7c87dffeab --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..428626aef1 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..1b2b44d855 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb new file mode 100644 index 0000000000..d34361f252 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb @@ -0,0 +1,48 @@ +# contributed by Luca Marsella (CSCS) +name = 'CP2K' +version = "3.0" +cudaversion = '7.0' +versionsuffix = '-cuda-%s' % cudaversion + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.2'), +] + +builddependencies = [ + ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test +runtest = False +# regression test reports failures +#ignore_regtest_fails = True + +# build type +type = 'psmp' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..e7bf9550c7 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb @@ -0,0 +1,45 @@ +# contributed by Luca Marsella (CSCS) +name = 'CP2K' +version = "3.0" + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.2'), +] + +builddependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test +runtest = False +# regression test reports failures +#ignore_regtest_fails = True + +# build type +type = 'psmp' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb rename to easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb index bf91772267..da34dc3b82 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayCCE' -version = '2015.06-XC' +version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb rename to easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb index dbf091ccf3..f6426373dd 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayCCE' -version = '2015.11-XC' +version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb index 0612076d5a..af4314daa9 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayGNU' -version = '2015.06-XC' +version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1506' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb index 370978db76..fdcd8836c8 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayGNU' -version = '2015.11-XC' +version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb rename to easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb index c80854490a..5d9b4c1609 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayIntel' -version = '2015.06-XC' +version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb rename to easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb index cc105734db..8632b007b7 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayIntel' -version = '2015.11-XC' +version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..24e3dfb5dc --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..8c57faa309 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb new file mode 100644 index 0000000000..7fae7e2b3f --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/include && " + +dependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb new file mode 100644 index 0000000000..83b2732fb5 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " + +dependencies = [ + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb new file mode 100644 index 0000000000..350a3d6cfa --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " + +dependencies = [ + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb new file mode 100644 index 0000000000..934cc8d3eb --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '2015.06'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb new file mode 100644 index 0000000000..7a8e5a0800 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '2015.11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..4f4dbfc813 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..455f495e6e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb new file mode 100644 index 0000000000..00ee4facc9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.06'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb new file mode 100644 index 0000000000..651ae824ba --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..274dc46093 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..1a379efce9 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.eb new file mode 100644 index 0000000000..3cd71b46bf --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..173c7dbd1e --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..ef47d32bbf --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..883868add2 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..d828f262a5 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..d9d2ff8c6b --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..254367cee7 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..ae74d150b0 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb @@ -0,0 +1,33 @@ +# contributed by Luca Marsella (CSCS) +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..31c851b3d9 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..3010711346 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..a33090c4b6 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), +] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..c9ebfcb9f5 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..16fc4ff0ea --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..cb88b8202d --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11.eb new file mode 100644 index 0000000000..c1260d9ce2 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-Python-2.7.9.eb new file mode 100644 index 0000000000..aa3c00b163 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-Python-2.7.9.eb new file mode 100644 index 0000000000..5c8368180f --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb new file mode 100644 index 0000000000..92748077e8 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb @@ -0,0 +1,39 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..21613bcfb7 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb new file mode 100644 index 0000000000..f7679002a1 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb @@ -0,0 +1,39 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..9958308892 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..de900f73b2 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True, } + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..58f5db7a33 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True, } + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-Python-2.7.9.eb new file mode 100644 index 0000000000..bec11c9016 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-Python-2.7.9.eb new file mode 100644 index 0000000000..35ad3eac24 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..7601dde601 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..0395e331ec --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..bf01430fff --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..57a30b1d87 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb new file mode 100644 index 0000000000..558feb7579 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-dmpar.eb new file mode 100644 index 0000000000..c88ec72408 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-dmpar.eb new file mode 100644 index 0000000000..ab4cacf6da --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-dmpar.eb new file mode 100644 index 0000000000..ac5084ad2d --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..9daa7bba81 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True, } + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..ec75812a65 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True, } + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From bbb4bf36f5f8bcd852aade02c94232fdaa899bbf Mon Sep 17 00:00:00 2001 From: perettig Date: Sat, 12 Mar 2016 12:32:09 +0100 Subject: [PATCH 0972/2133] delete old -XC files --- .../b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb | 22 ---- .../b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb | 22 ---- .../b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb | 15 --- .../b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb | 15 --- .../c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb | 22 ---- .../c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb | 22 ---- .../CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb | 22 ---- .../c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb | 38 ------ .../c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb | 38 ------ .../CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb | 48 -------- .../c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb | 45 ------- .../f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb | 14 --- .../f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb | 14 --- .../GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb | 45 ------- .../GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb | 45 ------- .../GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb | 45 ------- .../h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb | 22 ---- .../h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb | 22 ---- .../h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb | 18 --- .../h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb | 18 --- .../h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb | 18 --- .../h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb | 18 --- 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...y-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb | 26 ---- .../Python-2.7.9-CrayGNU-2015.06-XC-bare.eb | 39 ------ .../Python/Python-2.7.9-CrayGNU-2015.06-XC.eb | 115 ------------------ .../Python-2.7.9-CrayGNU-2015.11-XC-bare.eb | 39 ------ .../Python/Python-2.7.9-CrayGNU-2015.11-XC.eb | 115 ------------------ .../s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb | 23 ---- .../s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb | 23 ---- ...-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb | 19 --- ...-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb | 19 --- .../spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb | 21 ---- .../spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb | 21 ---- .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb | 38 ------ .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb | 38 ------ .../tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb | 38 ------ .../WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb | 41 ------- .../WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb | 41 ------- .../WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb | 41 ------- 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easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb delete mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 77bb4a043c..0000000000 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.0.2' - -homepage = 'http://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [('M4', '1.4.17')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb deleted file mode 100644 index cfb18be138..0000000000 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.0.2' - -homepage = 'http://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [('M4', '1.4.17')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 5b74aeb4ae..0000000000 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,15 +0,0 @@ -name = 'bzip2' -version = '1.0.6' - -homepage = 'http://www.bzip.org/' -description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically - compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical - compressors), whilst being around twice as fast at compression and six times faster at decompression.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.bzip.org/%(version)s'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 5666a2e9f5..0000000000 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,15 +0,0 @@ -name = 'bzip2' -version = '1.0.6' - -homepage = 'http://www.bzip.org/' -description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically - compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical - compressors), whilst being around twice as fast at compression and six times faster at decompression.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.bzip.org/%(version)s'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb deleted file mode 100644 index d4b9c66352..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.2.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 1a73916b52..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.2.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb deleted file mode 100644 index 8fe0d6e4d8..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.2.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb deleted file mode 100644 index c1c02c3bcf..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'CP2K' -version = '2.6.0' - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.1'), -] - -builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test reports failures -ignore_regtest_fails = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 18250df781..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'CP2K' -version = '2.6.0' - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.1'), -] - -builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test reports failures -ignore_regtest_fails = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb deleted file mode 100644 index aeb506b2a1..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -# contributed by Luca Marsella (CSCS) -name = 'CP2K' -version = "3.0" -cudaversion = '7.0' -versionsuffix = '-cuda-%s' % cudaversion - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.2'), -] - -builddependencies = [ - ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE), - ('fftw/3.3.4.3', EXTERNAL_MODULE), - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test -runtest = False -# regression test reports failures -#ignore_regtest_fails = True - -# build type -type = 'psmp' - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 55e00d968f..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,45 +0,0 @@ -# contributed by Luca Marsella (CSCS) -name = 'CP2K' -version = "3.0" - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.2'), -] - -builddependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test -runtest = False -# regression test reports failures -#ignore_regtest_fails = True - -# build type -type = 'psmp' - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb deleted file mode 100644 index d9b2e6f439..0000000000 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,14 +0,0 @@ -name = 'flex' -version = '2.5.39' - -homepage = 'http://flex.sourceforge.net/' -description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 7fbee438c5..0000000000 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,14 +0,0 @@ -name = 'flex' -version = '2.5.39' - -homepage = 'http://flex.sourceforge.net/' -description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb deleted file mode 100644 index eb693a5ca3..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.7' -versionsuffix = '-mpi' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'usempi': True} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " -preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/include && " - -dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), -] - -builddependencies = [('CMake', '3.2.2')] - -runtest = False - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb deleted file mode 100644 index 7d022ac778..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.7' -versionsuffix = '-mpi' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'usempi': True} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " -preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " - -dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), -] - -builddependencies = [('CMake', '3.2.2')] - -runtest = False - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb deleted file mode 100644 index 492e226263..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.7' -versionsuffix = '-mpi' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'usempi': True} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " -preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " - -dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), -] - -builddependencies = [('CMake', '3.2.2')] - -runtest = False - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb deleted file mode 100644 index 845802b504..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayCCE', 'version': '2015.06-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -patches = [ - # fix Make dependencies, so parallel build also works - 'HPL_parallel-make.patch', - 'HPL-2.1_LINKER-ld.patch', -] - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb deleted file mode 100644 index f4a0256f79..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayCCE', 'version': '2015.11-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -patches = [ - # fix Make dependencies, so parallel build also works - 'HPL_parallel-make.patch', - 'HPL-2.1_LINKER-ld.patch', -] - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb deleted file mode 100644 index fe0de8812c..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb deleted file mode 100644 index ecd5998b8d..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb deleted file mode 100644 index 32e943a8d6..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.06-XC'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb deleted file mode 100644 index 370ce49b4c..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 057b6423c3..0000000000 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'JasPer' -version = '1.900.1' - -homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' -description = """The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_ZIP] -source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] - -sanity_check_paths = { - 'files': ["bin/jasper", "lib/libjasper.a"], - 'dirs': ["include"], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb deleted file mode 100644 index b3d235faba..0000000000 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'JasPer' -version = '1.900.1' - -homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' -description = """The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_ZIP] -source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] - -sanity_check_paths = { - 'files': ["bin/jasper", "lib/libjasper.a"], - 'dirs': ["include"], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb deleted file mode 100644 index 45bc1007dd..0000000000 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'JasPer' -version = '1.900.1' - -homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' -description = """The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_ZIP] -source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] - -sanity_check_paths = { - 'files': ["bin/jasper", "lib/libjasper.a"], - 'dirs': ["include"], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 8c50a3c766..0000000000 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'Libint' -version = '1.1.4' - -homepage = 'https://sourceforge.net/p/libint/' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'opt': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') - -configopts = "--enable-deriv --enable-r12" - -sanity_check_paths = { - 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + - ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + - ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb deleted file mode 100644 index ba7eabefb4..0000000000 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'Libint' -version = '1.1.4' - -homepage = 'https://sourceforge.net/p/libint/' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'opt': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') - -configopts = "--enable-deriv --enable-r12" - -sanity_check_paths = { - 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + - ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + - ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 86d9535460..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '6.3' - -homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' -description = """The GNU Readline library provides a set of functions for use by applications that - allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. - The Readline library includes additional functions to maintain a list of previously-entered command lines, - to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '5.9')] - -# for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" - -sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 9f6f591568..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '6.3' - -homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' -description = """The GNU Readline library provides a set of functions for use by applications that - allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. - The Readline library includes additional functions to maintain a list of previously-entered command lines, - to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '5.9')] - -# for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" - -sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 3ef89d660d..0000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '2.2.1' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'opt': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] - -configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' - -# From the libxc mailing list -# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -# a fully working testsuite soon (unless someone wants to volunteer to do -# it, of course ) In the meantime, unless the majority of the tests -# fail, your build should be fine. -#runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc.a'], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb deleted file mode 100644 index bfd88b3c4b..0000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '2.2.1' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'opt': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] - -configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' - -# From the libxc mailing list -# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -# a fully working testsuite soon (unless someone wants to volunteer to do -# it, of course ) In the meantime, unless the majority of the tests -# fail, your build should be fine. -#runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc.a'], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 99ad1db263..0000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,33 +0,0 @@ -# contributed by Luca Marsella (CSCS) -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '2.2.2' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'opt': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] - -configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' - -# From the libxc mailing list -# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -# a fully working testsuite soon (unless someone wants to volunteer to do -# it, of course ) In the meantime, unless the majority of the tests -# fail, your build should be fine. -#runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc.a', 'lib/libxc.so'], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 68ee7aa23b..0000000000 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'M4' -version = '1.4.17' - -homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -configopts = "--enable-cxx" - -sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb deleted file mode 100644 index fd7cafa798..0000000000 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'M4' -version = '1.4.17' - -homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -configopts = "--enable-cxx" - -sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb deleted file mode 100644 index f016964748..0000000000 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'NFFT' -version = '3.3.0' - -homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' -description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine - library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more - dimensions, of arbitrary input size, and of complex data.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), -] - -sanity_check_paths = { - 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 10957199be..0000000000 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'NFFT' -version = '3.3.0' - -homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' -description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine - library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more - dimensions, of arbitrary input size, and of complex data.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), -] - -sanity_check_paths = { - 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb deleted file mode 100644 index f11ad3873e..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 0c15e725f4..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb deleted file mode 100644 index 6caf9a9b85..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb deleted file mode 100644 index 09f3884a76..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'numpy' -version = '1.9.2' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['numpy-1.8.0-mkl.patch'] - -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb deleted file mode 100644 index 91375139ee..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'numpy' -version = '1.9.2' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['numpy-1.8.0-mkl.patch'] - -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb deleted file mode 100644 index ae58dbb498..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'Python' -version = '2.7.9' -versionsuffix = '-bare' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True, 'opt': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -# bare installation: no extensions included -exts_list = [] - -buildopts = 'LINKCC="$CC -dynamic"' - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb deleted file mode 100644 index d2018b8970..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,115 +0,0 @@ -name = 'Python' -version = '2.7.9' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.9.1' -scipyversion = '0.14.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -buildopts = 'LINKCC="$CC -dynamic"' - -# order is important! -# package versions updated Jan 19th 2015 -exts_list = [ - ('setuptools', '11.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.4.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.13', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), -] - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb deleted file mode 100644 index f91af70f07..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'Python' -version = '2.7.9' -versionsuffix = '-bare' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True, 'opt': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -# bare installation: no extensions included -exts_list = [] - -buildopts = 'LINKCC="$CC -dynamic"' - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb deleted file mode 100644 index da85447313..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,115 +0,0 @@ -name = 'Python' -version = '2.7.9' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.9.1' -scipyversion = '0.14.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -buildopts = 'LINKCC="$CC -dynamic"' - -# order is important! -# package versions updated Jan 19th 2015 -exts_list = [ - ('setuptools', '11.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.4.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.13', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), -] - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb deleted file mode 100644 index a075d53839..0000000000 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1' - -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' -description = "Szip compression software, providing lossless compression of scientific data" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True, } - -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 6340c63211..0000000000 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1' - -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' -description = "Szip compression software, providing lossless compression of scientific data" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True, } - -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb deleted file mode 100644 index b47cc99c57..0000000000 --- a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'scipy' -version = '0.15.1' -versionsuffix = '-Python-2.7.9' - -homepage = 'http://www.scipy.org' -description = """SciPy is a collection of mathematical algorithms and convenience - functions built on the Numpy extension for Python.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('numpy', '1.9.2', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb deleted file mode 100644 index b69de1aa3b..0000000000 --- a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'scipy' -version = '0.15.1' -versionsuffix = '-Python-2.7.9' - -homepage = 'http://www.scipy.org' -description = """SciPy is a collection of mathematical algorithms and convenience - functions built on the Numpy extension for Python.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('numpy', '1.9.2', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 68086c7c98..0000000000 --- a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'spglib' -version = '1.7.3' - -homepage = 'http://spglib.sourceforge.net/' -description = """Spglib is a C library for finding and handling crystal symmetries.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -start_dir = '%(name)s-%(version)s' - -sanity_check_paths = { - 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], - 'dirs': ['include/spglib'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb deleted file mode 100644 index bdb5c45a5a..0000000000 --- a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'spglib' -version = '1.7.3' - -homepage = 'http://spglib.sourceforge.net/' -description = """Spglib is a C library for finding and handling crystal symmetries.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -start_dir = '%(name)s-%(version)s' - -sanity_check_paths = { - 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], - 'dirs': ['include/spglib'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb deleted file mode 100644 index c5db50a961..0000000000 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -# Authors:: Valentin Plugaru -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html -## -easyblock = 'ConfigureMake' - -name = 'tcsh' -version = '6.18.01' - -homepage = 'http://www.tcsh.org' -description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). - It is a command language interpreter usable both as an interactive login shell and a shell script command - processor. It includes a command-line editor, programmable word completion, spelling correction, a history - mechanism, job control and a C-like syntax.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.astron.com/pub/%(namelower)s', - 'ftp://ftp.astron.com/pub/%(namelower)s/old', -] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/tcsh"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 3b456bd5d5..0000000000 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -# Authors:: Valentin Plugaru -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html -## -easyblock = 'ConfigureMake' - -name = 'tcsh' -version = '6.18.01' - -homepage = 'http://www.tcsh.org' -description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). - It is a command language interpreter usable both as an interactive login shell and a shell script command - processor. It includes a command-line editor, programmable word completion, spelling correction, a history - mechanism, job control and a C-like syntax.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.astron.com/pub/%(namelower)s', - 'ftp://ftp.astron.com/pub/%(namelower)s/old', -] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/tcsh"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb deleted file mode 100644 index df83e70f3b..0000000000 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -# Authors:: Valentin Plugaru -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html -## -easyblock = 'ConfigureMake' - -name = 'tcsh' -version = '6.18.01' - -homepage = 'http://www.tcsh.org' -description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). - It is a command language interpreter usable both as an interactive login shell and a shell script command - processor. It includes a command-line editor, programmable word completion, spelling correction, a history - mechanism, job control and a C-like syntax.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.astron.com/pub/%(namelower)s', - 'ftp://ftp.astron.com/pub/%(namelower)s/old', -] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/tcsh"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb deleted file mode 100644 index 0b7fd5cfb3..0000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb +++ /dev/null @@ -1,41 +0,0 @@ -name = 'WRF' -version = '3.6.1' - -homepage = 'http://www.wrf-model.org' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -sources = ['%(name)sV%(version)s.TAR.gz'] -source_urls = [ - 'http://www2.mmm.ucar.edu/wrf/src/', - 'http://www.mmm.ucar.edu/wrf/src/', -] - -# csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] - -dependencies = [ - ('JasPer', '1.900.1'), - ('cray-netcdf/4.3.2', EXTERNAL_MODULE), - ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), -] - -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-3.6.1_known_problems.patch', - 'WRF_tests_limit-runtimes.patch', -] - -# limit parallel build to 20 -maxparallel = 20 - -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -runtest = False - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb deleted file mode 100644 index d353e6742c..0000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb +++ /dev/null @@ -1,41 +0,0 @@ -name = 'WRF' -version = '3.6.1' - -homepage = 'http://www.wrf-model.org' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -sources = ['%(name)sV%(version)s.TAR.gz'] -source_urls = [ - 'http://www2.mmm.ucar.edu/wrf/src/', - 'http://www.mmm.ucar.edu/wrf/src/', -] - -# csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] - -dependencies = [ - ('JasPer', '1.900.1'), - ('cray-netcdf/4.3.2', EXTERNAL_MODULE), - ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), -] - -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-3.6.1_known_problems.patch', - 'WRF_tests_limit-runtimes.patch', -] - -# limit parallel build to 20 -maxparallel = 20 - -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -runtest = False - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb deleted file mode 100644 index dc552a3235..0000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb +++ /dev/null @@ -1,41 +0,0 @@ -name = 'WRF' -version = '3.6.1' - -homepage = 'http://www.wrf-model.org' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -sources = ['%(name)sV%(version)s.TAR.gz'] -source_urls = [ - 'http://www2.mmm.ucar.edu/wrf/src/', - 'http://www.mmm.ucar.edu/wrf/src/', -] - -# csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] - -dependencies = [ - ('JasPer', '1.900.1'), - ('cray-netcdf/4.3.2', EXTERNAL_MODULE), - ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), -] - -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-3.6.1_known_problems.patch', - 'WRF_tests_limit-runtimes.patch', -] - -# limit parallel build to 20 -maxparallel = 20 - -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -runtest = False - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb deleted file mode 100644 index fbc74998eb..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.8' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True, } - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 0c6915d7cd..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.8' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True, } - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' -- GitLab From 1a04d6640a63dcb22c3ca78d7ce4c477867f8572 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 13 Mar 2016 20:50:25 +0000 Subject: [PATCH 0973/2133] Add packed binary version of sratoolkit 2.5.7 --- .../s/sratoolkit/sratoolkit-2.5.7.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb diff --git a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb new file mode 100644 index 0000000000..e8e5e37a6b --- /dev/null +++ b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb @@ -0,0 +1,34 @@ +easyblock = 'PackedBinary' + +name = 'sratoolkit' +version = '2.5.7' + +homepage = 'http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] +sources = ['sratoolkit.%(version)s-centos_linux64.tar.gz'] + +executables = [ +'abi-dump*', 'abi-load*', 'align-info*', 'bam-load*', 'blastn_vdb*', 'cache-mgr*', +'cg-load*', 'fastq-dump*', 'fastq-load*', 'helicos-load*', 'illumina-dump*', +'illumina-load*', 'kar*', 'kdbmeta*', 'latf-load*', 'ncbi', 'pacbio-load*', +'prefetch*', 'rcexplain*', 'remote-fuser*', 'sam-dump*', 'sff-dump*', +'sff-load*', 'sra-kar*', 'sra-pileup*', 'sra-sort*', 'sra-stat*', 'srapath*', +'srf-load*', 'tblastn_vdb*', 'test-sra*', 'vdb-config*', 'vdb-copy*', +'vdb-decrypt*', 'vdb-dump*', 'vdb-encrypt*', 'vdb-lock*', 'vdb-passwd*', +'vdb-unlock*', 'vdb-validate*', +] + +files_to_copy = [('*', 'bin')] + +sanity_check_paths = { + 'files': ['bin/abi-dump', 'bin/illumina-load', 'bin/srf-load', ], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From c09c304722a69796d45d2678918508534f225b37 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 13 Mar 2016 20:53:24 +0000 Subject: [PATCH 0974/2133] Add proper header with attribution --- easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb index e8e5e37a6b..fc210435ee 100644 --- a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb +++ b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb @@ -1,3 +1,10 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute +# Based on work by npklein + easyblock = 'PackedBinary' name = 'sratoolkit' -- GitLab From b036c179c5d355f5ac43abfceaad55fd120fee2d Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 14 Mar 2016 11:16:38 +0100 Subject: [PATCH 0975/2133] removed -xc suffix --- ...-CrayGNU-2015.11-XC.eb => freetype-2.6.2-CrayGNU-2015.11.eb} | 2 +- ...6.1.0-CrayGNU-2015.11-XC.eb => GMP-6.1.0-CrayGNU-2015.11.eb} | 2 +- ...1-CrayGNU-2015.11-XC.eb => libpng-1.6.21-CrayGNU-2015.11.eb} | 2 +- ....11.eb => matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb} | 2 +- ...1-CrayGNU-2015.11-XC.eb => Python-2.7.11-CrayGNU-2015.11.eb} | 2 +- ....2-CrayGNU-2015.11-XC.eb => SQLite-3.9.2-CrayGNU-2015.11.eb} | 2 +- ...8.6.4-CrayGNU-2015.11-XC.eb => Tcl-8.6.4-CrayGNU-2015.11.eb} | 2 +- ...-8.6.4-CrayGNU-2015.11-XC.eb => Tk-8.6.4-CrayGNU-2015.11.eb} | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/f/freetype/{freetype-2.6.2-CrayGNU-2015.11-XC.eb => freetype-2.6.2-CrayGNU-2015.11.eb} (92%) rename easybuild/easyconfigs/g/GMP/{GMP-6.1.0-CrayGNU-2015.11-XC.eb => GMP-6.1.0-CrayGNU-2015.11.eb} (91%) rename easybuild/easyconfigs/l/libpng/{libpng-1.6.21-CrayGNU-2015.11-XC.eb => libpng-1.6.21-CrayGNU-2015.11.eb} (92%) rename easybuild/easyconfigs/m/matplotlib/{matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb => matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb} (95%) rename easybuild/easyconfigs/p/Python/{Python-2.7.11-CrayGNU-2015.11-XC.eb => Python-2.7.11-CrayGNU-2015.11.eb} (98%) rename easybuild/easyconfigs/s/SQLite/{SQLite-3.9.2-CrayGNU-2015.11-XC.eb => SQLite-3.9.2-CrayGNU-2015.11.eb} (94%) rename easybuild/easyconfigs/t/Tcl/{Tcl-8.6.4-CrayGNU-2015.11-XC.eb => Tcl-8.6.4-CrayGNU-2015.11.eb} (91%) rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-CrayGNU-2015.11-XC.eb => Tk-8.6.4-CrayGNU-2015.11.eb} (91%) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb similarity index 92% rename from easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb index 113ad0ada9..7f9b603bc6 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb @@ -6,7 +6,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.""" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb similarity index 91% rename from easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb index 34e4ce0776..6658db36ac 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb @@ -8,7 +8,7 @@ homepage = 'http://gmplib.org/' description = """GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. """ -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'lowopt': True} sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb similarity index 92% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb index bb061f924f..1b97f39104 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb @@ -6,7 +6,7 @@ version = '1.6.21' homepage = 'http://www.libpng.org/pub/png/libpng.html' description = "libpng is the official PNG reference library" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb similarity index 95% rename from easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb rename to easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb index 9a9609ca9e..7b58f1b605 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb @@ -9,7 +9,7 @@ description = """matplotlib is a python 2D plotting library which produces publi hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb similarity index 98% rename from easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb index 8c373b7caf..03be62fd52 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb @@ -6,7 +6,7 @@ version = "2.7.11" homepage = 'http://python.org/' description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} numpyversion = '1.10.4' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb similarity index 94% rename from easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb index f8f253cac7..429cfc37d8 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb @@ -18,7 +18,7 @@ version = '3.9.2' homepage = 'http://www.sqlite.org/' description = 'SQLite: SQL Database Engine in a C Library' -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} # eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz source_urls = ['http://www.sqlite.org/2015/'] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.eb similarity index 91% rename from easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.eb index 45169d651c..0a0ed38e56 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.eb @@ -7,7 +7,7 @@ homepage = 'http://www.tcl.tk/' description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11.eb similarity index 91% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11.eb index 8aeedf1e3d..44900c63c7 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11.eb @@ -7,7 +7,7 @@ homepage = 'http://www.tcl.tk/' description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.""" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -- GitLab From 9750d399b67a70e27e331d3ed0227bf30d373ea5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 13:55:10 +0100 Subject: [PATCH 0976/2133] include pandas as extension in Python 3.5.1 easyconfigs --- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index ec80435d9b..782d02fe62 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -107,6 +107,9 @@ exts_list = [ ('netaddr', '0.7.18', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index aa7a7d9034..5dcd8c848b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -111,6 +111,9 @@ exts_list = [ ('netaddr', '0.7.18', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' -- GitLab From dc22f84516afbdee12bbc87d59077c30d83704a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 15:10:34 +0200 Subject: [PATCH 0977/2133] modify easyconfig scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb, modify easyconfig matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb --- ...tplotlib-1.5.1-intel-2016a-Python-3.5.1.eb | 45 +++++++++++++++++++ ...t-learn-0.17.1-intel-2016a-Python-3.5.1.eb | 30 +++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..2c2c674d2c --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c "import %(ext_name)s"', '') + +dependencies = [ + ('Python', '3.5.1'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..f49a608d87 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.17.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From a22ef3361ebc08e4296092d559b97071e024068d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 17:57:47 +0200 Subject: [PATCH 0978/2133] add easyconfig ADF-2016.101.eb --- easybuild/easyconfigs/a/ADF/ADF-2016.101.eb | 31 +++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/ADF/ADF-2016.101.eb diff --git a/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb b/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb new file mode 100644 index 0000000000..5fe5e14c14 --- /dev/null +++ b/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'ADF' +version = '2016.101' + +homepage = 'http://www.scm.com/ADF/' +description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and + predict chemical structure and reactivity with density functional theory (DFT).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['adf%(version)s.pc64_linux.intelmpi.tgz'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +modextravars = { + 'ADFHOME': '%(installdir)s', + 'ADFBIN': '%(installdir)s/bin', + 'ADFRESOURCES': '%(installdir)s/atomicdata', +} + +modloadmsg = "These environment variables need to be defined before using ADF:\n" +modloadmsg += " * $SCMLICENSE: path to ADF license file\n" +modloadmsg += " * $SCM_TMPDIR: path to user scratch directory" + +moduleclass = 'chem' -- GitLab From 600a222f07887960db797217fe7d058dfeb7a046 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 18:13:18 +0200 Subject: [PATCH 0979/2133] add easyconfig statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb --- ...tsmodels-0.6.1-intel-2016a-Python-3.5.1.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..a2ab69cdf5 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,40 @@ +easyblock = 'Bundle' + +name = 'statsmodels' +version = '0.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/statsmodels' +description = """Statsmodels is a Python package that provides a complement to scipy for statistical computations + including descriptive statistics and estimation and inference for statistical models.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.1'), +] + +exts_list = [ + ('patsy', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], + 'source_tmpl': 'patsy-%(version)s.zip', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'math' -- GitLab From 7c545ed144d07424dff4f16fffbb9dc94b1f950d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 14 Mar 2016 17:14:09 +0000 Subject: [PATCH 0980/2133] Fix indent and sanity check --- .../s/sratoolkit/sratoolkit-2.5.7.eb | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb index fc210435ee..da9654c11e 100644 --- a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb +++ b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb @@ -21,21 +21,21 @@ source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s-centos_linux64.tar.gz'] executables = [ -'abi-dump*', 'abi-load*', 'align-info*', 'bam-load*', 'blastn_vdb*', 'cache-mgr*', -'cg-load*', 'fastq-dump*', 'fastq-load*', 'helicos-load*', 'illumina-dump*', -'illumina-load*', 'kar*', 'kdbmeta*', 'latf-load*', 'ncbi', 'pacbio-load*', -'prefetch*', 'rcexplain*', 'remote-fuser*', 'sam-dump*', 'sff-dump*', -'sff-load*', 'sra-kar*', 'sra-pileup*', 'sra-sort*', 'sra-stat*', 'srapath*', -'srf-load*', 'tblastn_vdb*', 'test-sra*', 'vdb-config*', 'vdb-copy*', -'vdb-decrypt*', 'vdb-dump*', 'vdb-encrypt*', 'vdb-lock*', 'vdb-passwd*', -'vdb-unlock*', 'vdb-validate*', + 'abi-dump*', 'abi-load*', 'align-info*', 'bam-load*', 'blastn_vdb*', 'cache-mgr*', + 'cg-load*', 'fastq-dump*', 'fastq-load*', 'helicos-load*', 'illumina-dump*', + 'illumina-load*', 'kar*', 'kdbmeta*', 'latf-load*', 'ncbi', 'pacbio-load*', + 'prefetch*', 'rcexplain*', 'remote-fuser*', 'sam-dump*', 'sff-dump*', + 'sff-load*', 'sra-kar*', 'sra-pileup*', 'sra-sort*', 'sra-stat*', 'srapath*', + 'srf-load*', 'tblastn_vdb*', 'test-sra*', 'vdb-config*', 'vdb-copy*', + 'vdb-decrypt*', 'vdb-dump*', 'vdb-encrypt*', 'vdb-lock*', 'vdb-passwd*', + 'vdb-unlock*', 'vdb-validate*', ] files_to_copy = [('*', 'bin')] sanity_check_paths = { - 'files': ['bin/abi-dump', 'bin/illumina-load', 'bin/srf-load', ], - 'dirs': [] + 'files': [], + 'dirs': ['bin'] } moduleclass = 'bio' -- GitLab From 24f917cdef4c9a335c64052ea227ee67623450fc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 14 Mar 2016 17:37:12 +0000 Subject: [PATCH 0981/2133] Remove executables and add detail to sanity check --- .../s/sratoolkit/sratoolkit-2.5.7.eb | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb index da9654c11e..b3d358e4a3 100644 --- a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb +++ b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb @@ -20,22 +20,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s-centos_linux64.tar.gz'] -executables = [ - 'abi-dump*', 'abi-load*', 'align-info*', 'bam-load*', 'blastn_vdb*', 'cache-mgr*', - 'cg-load*', 'fastq-dump*', 'fastq-load*', 'helicos-load*', 'illumina-dump*', - 'illumina-load*', 'kar*', 'kdbmeta*', 'latf-load*', 'ncbi', 'pacbio-load*', - 'prefetch*', 'rcexplain*', 'remote-fuser*', 'sam-dump*', 'sff-dump*', - 'sff-load*', 'sra-kar*', 'sra-pileup*', 'sra-sort*', 'sra-stat*', 'srapath*', - 'srf-load*', 'tblastn_vdb*', 'test-sra*', 'vdb-config*', 'vdb-copy*', - 'vdb-decrypt*', 'vdb-dump*', 'vdb-encrypt*', 'vdb-lock*', 'vdb-passwd*', - 'vdb-unlock*', 'vdb-validate*', -] - -files_to_copy = [('*', 'bin')] - sanity_check_paths = { - 'files': [], - 'dirs': ['bin'] + 'files': ['bin/abi-load', 'bin/fastq-dump', 'bin/sff-load', 'bin/vdb-dump'], + 'dirs': [] } moduleclass = 'bio' -- GitLab From 594901c38692154ba44bae343882354bc7c0af7d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 19:34:41 +0100 Subject: [PATCH 0982/2133] stick to binutils 2.25 for now --- .../b/binutils/binutils-2.26-GCCcore-4.9.3.eb | 41 ------------------- ...26.eb => icc-2016.2.181-GCC-4.9.3-2.25.eb} | 2 +- ... => iccifort-2016.2.181-GCC-4.9.3-2.25.eb} | 2 +- ....eb => ifort-2016.2.181-GCC-4.9.3-2.25.eb} | 2 +- ....26.eb => iimpi-2016.02-GCC-4.9.3-2.25.eb} | 2 +- ...1.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb} | 2 +- ...181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb} | 2 +- .../i/intel/intel-2016.02-GCC-4.9.eb | 2 +- 8 files changed, 7 insertions(+), 48 deletions(-) delete mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb rename easybuild/easyconfigs/i/icc/{icc-2016.2.181-GCC-4.9.3-2.26.eb => icc-2016.2.181-GCC-4.9.3-2.25.eb} (98%) rename easybuild/easyconfigs/i/iccifort/{iccifort-2016.2.181-GCC-4.9.3-2.26.eb => iccifort-2016.2.181-GCC-4.9.3-2.25.eb} (93%) rename easybuild/easyconfigs/i/ifort/{ifort-2016.2.181-GCC-4.9.3-2.26.eb => ifort-2016.2.181-GCC-4.9.3-2.25.eb} (98%) rename easybuild/easyconfigs/i/iimpi/{iimpi-2016.02-GCC-4.9.3-2.26.eb => iimpi-2016.02-GCC-4.9.3-2.25.eb} (94%) rename easybuild/easyconfigs/i/imkl/{imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb => imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb} (95%) rename easybuild/easyconfigs/i/impi/{impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb => impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb} (99%) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb deleted file mode 100644 index 0d3fdd2d17..0000000000 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'binutils' -version = '2.26' - -homepage = 'http://directory.fsf.org/project/binutils/' -description = "binutils: GNU binary utilities" - -toolchain = {'name': 'GCCcore', 'version': '4.9.3'} - -sources = [SOURCE_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [ - ('flex', '2.6.0'), - ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep - ('zlib', '1.2.8'), - # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) -] - -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb similarity index 98% rename from easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index ec73b70b03..569030c764 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -13,7 +13,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update checksums = ['d6f8529a44231e427219c8e025dec3b2'] gccver = '4.9.3' -binutilsver = '2.26' +binutilsver = '2.25' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb similarity index 93% rename from easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 93577bed54..871fae395a 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ easyblock = "Toolchain" name = 'iccifort' version = '2016.2.181' -versionsuffix = '-GCC-4.9.3-2.26' +versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb similarity index 98% rename from easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index c55e928942..01be1aa191 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -13,7 +13,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] gccver = '4.9.3' -binutilsver = '2.26' +binutilsver = '2.25' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb similarity index 94% rename from easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb index 0be81ea753..3d1b981714 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ easyblock = "Toolchain" name = 'iimpi' version = '2016.02' -versionsuffix = '-GCC-4.9.3-2.26' +versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb similarity index 95% rename from easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index 78baf11191..34b7b8bb07 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-4.9.3-2.26'} +toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['536dbd82896d6facc16de8f961d17d65'] diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb similarity index 99% rename from easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 147e9c1ec1..d3526d68e5 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -8,7 +8,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" -toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-4.9.3-2.26'} +toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-4.9.3-2.25'} sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb index 955db91710..41552f25a9 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.2.181' gccver = '%s.3' % gcc_maj_min -binutilsver = '2.26' +binutilsver = '2.25' gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ ('GCCcore', gccver), -- GitLab From a1164904bfbae01fbb12a988aaef505d6dc5bf0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 20:39:31 +0100 Subject: [PATCH 0983/2133] fix binutils version in flex easyconfig --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb index 5a3de111fc..4015f41291 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -14,7 +14,7 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] dependencies = [('Bison', '3.0.4')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.25', '', True)] parallel = 1 -- GitLab From 83cfd2deaf27fe0045109af043a5552e36fe47de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 10:33:31 +0100 Subject: [PATCH 0984/2133] use HOME constant in new icc/ifort/imkl/impi easyconfigs --- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb | 4 +--- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb | 4 +--- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb | 4 +--- .../impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 3 +-- 4 files changed, 4 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index 569030c764..9338983477 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -28,8 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index 01be1aa191..5db05e1948 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -28,8 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index 34b7b8bb07..53630f7111 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -16,9 +16,7 @@ checksums = ['536dbd82896d6facc16de8f961d17d65'] dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index d3526d68e5..d059a83720 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -16,8 +16,7 @@ checksums = ['1c14656859d48bf8b90c71dace2a977b'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From d8bf857a307113e1541033bfc4af67cbef5a358f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 10:35:31 +0100 Subject: [PATCH 0985/2133] use HOME constant in new icc/ifort/imkl/impi easyconfigs --- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 4 +--- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 4 +--- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 4 +--- .../impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 3 +-- 4 files changed, 4 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index 080cfccc9a..fad8d6d04d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,8 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 3ee926155e..16a589b7f3 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,8 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index 74cc4cff3a..dd75357fc5 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -16,9 +16,7 @@ checksums = ['536dbd82896d6facc16de8f961d17d65'] dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index ef29e9af70..faa72cc81c 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -16,8 +16,7 @@ checksums = ['1c14656859d48bf8b90c71dace2a977b'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From 1f16832a0cfc461c45b7c35a796f53db2ab4b4c6 Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 11:44:31 +0100 Subject: [PATCH 0986/2133] QuickFF and Yaff for DEFNET --- ...QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb | 34 ++++++++++++++++++ ....develop.2.13-intel-2015b-Python-2.7.10.eb | 35 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..e48df83b5c --- /dev/null +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'QuickFF' +version = '2.0.1' + +homepage = 'http://molmod.github.io/QuickFF/' +description = """QuickFF is a Python package developed at the Center for +Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio +calculations.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/molmod/QuickFF/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.5.0', versionsuffix), + ('molmod', '1.1', versionsuffix), + ('yaff', 'thesissven2.13', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..36a2dc281d --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'yaff' +version = '1.0.develop.2.13' + +homepage = 'http://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.10' + +hdf5ver = '1.8.15-patch1' +versionsuffix = '-Python-%s-HDF5-%s-serial' %(pyver, hdf5ver) + +dependencies = [ + ('Python', pyver), + ('h5py', '2.5.0', versionsuffix), + ('molmod', '1.1', '-Python-%s' %(pyver)), +] + +options = {'modulename': name} +#runtest = 'python setup.py build_ext -i; nosetests -v' + + +pyshortver = ".".join(pyver.split(".")[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver, name)] +} + +moduleclass = 'chem' -- GitLab From 4143001890fac7735da939e011118aed9d4c120b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 13:07:31 +0100 Subject: [PATCH 0987/2133] add missing '/' --- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index 9338983477..4d0d75afae 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index 5db05e1948..ffe995c4ac 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index 53630f7111..91dcce3df9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -16,7 +16,7 @@ checksums = ['536dbd82896d6facc16de8f961d17d65'] dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index d059a83720..845f7631f8 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -16,7 +16,7 @@ checksums = ['1c14656859d48bf8b90c71dace2a977b'] dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From d8b707a6e21dba177b222b93322c3798dd0677ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 13:09:20 +0100 Subject: [PATCH 0988/2133] add missing '/' --- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index fad8d6d04d..5c1c6d97c5 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 16a589b7f3..5844c8abd9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index dd75357fc5..d1edf0b015 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -16,7 +16,7 @@ checksums = ['536dbd82896d6facc16de8f961d17d65'] dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index faa72cc81c..eaf9a3b7a7 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -16,7 +16,7 @@ checksums = ['1c14656859d48bf8b90c71dace2a977b'] dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From 4e9120dea53da6a178d82c6c2c61f56300116ace Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 13:50:41 +0100 Subject: [PATCH 0989/2133] Fix yaff version in quickff eb, fix yaff eb filename and fix yaff nosetests --- ...QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb | 2 +- ....develop.2.13-intel-2015b-Python-2.7.10.eb | 35 ------------------- 2 files changed, 1 insertion(+), 36 deletions(-) delete mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb index e48df83b5c..5d737222c9 100644 --- a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb @@ -23,7 +23,7 @@ dependencies = [ (python, pythonversion), ('matplotlib', '1.5.0', versionsuffix), ('molmod', '1.1', versionsuffix), - ('yaff', 'thesissven2.13', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) + ('yaff', '1.0.develop.2.13', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb deleted file mode 100644 index 36a2dc281d..0000000000 --- a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = "PythonPackage" - -name = 'yaff' -version = '1.0.develop.2.13' - -homepage = 'http://molmod.github.io/yaff/' -description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] - -pyver = '2.7.10' - -hdf5ver = '1.8.15-patch1' -versionsuffix = '-Python-%s-HDF5-%s-serial' %(pyver, hdf5ver) - -dependencies = [ - ('Python', pyver), - ('h5py', '2.5.0', versionsuffix), - ('molmod', '1.1', '-Python-%s' %(pyver)), -] - -options = {'modulename': name} -#runtest = 'python setup.py build_ext -i; nosetests -v' - - -pyshortver = ".".join(pyver.split(".")[:-1]) -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver, name)] -} - -moduleclass = 'chem' -- GitLab From 64f041f458140135cc968ab38b501f064d5b48ab Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 14:06:57 +0100 Subject: [PATCH 0990/2133] Update eb file to new yaff version with fixed nose tests --- ...Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb new file mode 100644 index 0000000000..235257521b --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'yaff' +version = '1.0.develop.2.14' + +homepage = 'http://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.10' + +hdf5ver = '1.8.15-patch1' +versionsuffix = '-Python-%s-HDF5-%s-serial' %(pyver, hdf5ver) + +dependencies = [ + ('Python', pyver), + ('h5py', '2.5.0', versionsuffix), + ('molmod', '1.1', '-Python-%s' %(pyver)), +] + +options = {'modulename': name} +runtest = 'python setup.py build_ext -i; nosetests -v' + + +pyshortver = ".".join(pyver.split(".")[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver, name)] +} + +moduleclass = 'chem' -- GitLab From 91129f8059eb0c9f1fa4fa0dc74b8ea1d0fb46c8 Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 14:10:49 +0100 Subject: [PATCH 0991/2133] Update QuickFF eb file to new yaff version --- .../q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb index 5d737222c9..8eea2d3e11 100644 --- a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb @@ -23,7 +23,7 @@ dependencies = [ (python, pythonversion), ('matplotlib', '1.5.0', versionsuffix), ('molmod', '1.1', versionsuffix), - ('yaff', '1.0.develop.2.13', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) + ('yaff', '1.0.develop.2.14', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) ] sanity_check_paths = { -- GitLab From ac747bc3fc479757aa6d8eee896e4afab6afbb07 Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 16:28:10 +0100 Subject: [PATCH 0992/2133] Add eb file to build the molmod dependency of yaff and QuickFF --- .../molmod-1.1-intel-2015b-Python-2.7.10.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..c36da2b123 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0 on 2015-10-01_15-35-44 +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.1' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.5.0', versionsuffix), +] + +options = {'modulename': 'molmod'} +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion] +} + +moduleclass = 'math' -- GitLab From 9cb1e88ea4838c9df0b08239be240363570cdbce Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 15 Mar 2016 16:47:53 +0100 Subject: [PATCH 0993/2133] added segemehl-0.2.0-goolf-1.4.10.eb --- .../s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..39c950b357 --- /dev/null +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = "segemehl" +version = "0.2.0" + +homepage = 'http://www.bioinf.uni-leipzig.de/Software/segemehl/' +description = """ segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping + and split read mapping. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/'] +sources = ['%s_%s.tar.gz' % (name, version.replace('.','_'))] + +parallel = 1 + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +files_to_copy = [(["lack.x", "segemehl.x", "testrealign.x"], "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["lack.x" , "segemehl.x", "testrealign.x"]], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From c6064624c6bb7e484e21937dab0998fe75398bd4 Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 19:05:38 +0100 Subject: [PATCH 0994/2133] Fix matplotlib bug in yaff eb --- ....2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb index 235257521b..29a3cca013 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -23,7 +23,7 @@ dependencies = [ ] options = {'modulename': name} -runtest = 'python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' pyshortver = ".".join(pyver.split(".")[:-1]) -- GitLab From 914b6e8207bd07567fb6c7b86c037e9ed21862fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 22:45:23 +0100 Subject: [PATCH 0995/2133] style fixes --- .../molmod-1.1-intel-2015b-Python-2.7.10.eb | 18 ++++++----------- ...QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb | 15 +++++--------- ...Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 20 ++++++++----------- 3 files changed, 19 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb index c36da2b123..4fd3ed9a53 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb @@ -1,8 +1,8 @@ -# Built with EasyBuild version 2.2.0 on 2015-10-01_15-35-44 -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'molmod' version = '1.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" @@ -12,23 +12,17 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/molmod/molmod/releases/download/v%(version)s'] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.10' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - dependencies = [ - (python, pythonversion), + ('Python', '2.7.10'), ('matplotlib', '1.5.0', versionsuffix), ] -options = {'modulename': 'molmod'} -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion] + 'dirs': ['lib/python%(pyshortver)s/site-packages/molmod'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb index 8eea2d3e11..1920995e1b 100644 --- a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb @@ -1,7 +1,8 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'QuickFF' version = '2.0.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/QuickFF/' description = """QuickFF is a Python package developed at the Center for @@ -13,22 +14,16 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/molmod/QuickFF/releases/download/v%(version)s'] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.10' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - dependencies = [ - (python, pythonversion), + ('Python', '2.7.10'), ('matplotlib', '1.5.0', versionsuffix), ('molmod', '1.1', versionsuffix), - ('yaff', '1.0.develop.2.14', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) + ('yaff', '1.0.develop.2.14', '%s-HDF5-1.8.15-patch1-serial' % versionsuffix), ] sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb index 29a3cca013..8d4f8961ee 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -1,7 +1,9 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'yaff' version = '1.0.develop.2.14' +hdf5ver = '1.8.15-patch1' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s-serial' % hdf5ver homepage = 'http://molmod.github.io/yaff/' description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" @@ -11,25 +13,19 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -pyver = '2.7.10' - -hdf5ver = '1.8.15-patch1' -versionsuffix = '-Python-%s-HDF5-%s-serial' %(pyver, hdf5ver) - dependencies = [ - ('Python', pyver), + ('Python', '2.7.10'), ('h5py', '2.5.0', versionsuffix), - ('molmod', '1.1', '-Python-%s' %(pyver)), + ('molmod', '1.1', '-Python-%(pyver)s'), ] options = {'modulename': name} -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' - +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" -pyshortver = ".".join(pyver.split(".")[:-1]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver, name)] + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], } moduleclass = 'chem' -- GitLab From e67988bafa0f2ee3059dc1d3611aabf40343ff48 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 10:00:06 +0200 Subject: [PATCH 0996/2133] Contributing Python package CosmoloPy --- ...oloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..61bd20053b --- /dev/null +++ b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'CosmoloPy' +version = '0.1.104' + +homepage = 'https://github.com/roban/CosmoloPy' +description = """A cosmology package for Python. CosmoloPy is +built on and designed for use with NumPy and SciPy.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('numpy', '1.7.1', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' -- GitLab From 73c4c8939f69bd0fbb50a0a028c6205dd963ec1f Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 10:34:47 +0200 Subject: [PATCH 0997/2133] Contributing Python package astropy --- ...astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..bab7a31bcf --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'astropy' +version = '1.0.6' + +homepage = 'http://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('setuptools', '18.4', versionsuffix), + ('numpy', '1.7.1', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' -- GitLab From 58f33889facc9683c075bd35e88b4001ca178c81 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 10:36:10 +0200 Subject: [PATCH 0998/2133] Contriburing Python package Whoosh --- .../Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..db2dcb5741 --- /dev/null +++ b/easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'Whoosh' +version = '2.7.0' + +homepage = 'https://pypi.python.org/pypi/Whoosh/' +description = """Fast, pure-Python full text indexing, +search, and spell checking library.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pyver = '2.7.3' +pyshortver = ".".join(pyver.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), + ('numpy','1.6.2', versionsuffix), + ('scipy', '0.11.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'lib' -- GitLab From ff336d5b553615453f6611f73f2be8e247eba528 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 12:29:49 +0200 Subject: [PATCH 0999/2133] Adding setuptools config --- ...oloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb | 31 ------------------- ...tuptools-18.4-goolf-1.4.10-Python-2.7.3.eb | 29 +++++++++++++++++ 2 files changed, 29 insertions(+), 31 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb deleted file mode 100644 index 61bd20053b..0000000000 --- a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = "PythonPackage" - -name = 'CosmoloPy' -version = '0.1.104' - -homepage = 'https://github.com/roban/CosmoloPy' -description = """A cosmology package for Python. CosmoloPy is -built on and designed for use with NumPy and SciPy.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -python = 'Python' -pyver = '2.7.3' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('numpy', '1.7.1', versionsuffix), -] - -pyshortver = '.'.join(pyver.split('.')[:2]) - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..e4b06a51e1 --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = "setuptools" +version = "18.4" + +homepage = "http://pypi.python.org/pypi/setuptools/" +description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.3" + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +py_short_ver = ".".join(pythonversion.split(".")[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], + 'dirs': [] + } + +moduleclass = 'devel' -- GitLab From 06e9ae546aa45bcdec0db8857ed5e251dfbd9e2a Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 12:34:27 +0200 Subject: [PATCH 1000/2133] Updated PR, deleted unwanted files --- ...astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb | 33 ------------------- ...oloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb | 31 ----------------- 2 files changed, 64 deletions(-) delete mode 100644 easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb delete mode 100644 easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb deleted file mode 100644 index bab7a31bcf..0000000000 --- a/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = "PythonPackage" - -name = 'astropy' -version = '1.0.6' - -homepage = 'http://www.astropy.org/' -description = """The Astropy Project is a community effort to develop -a single core package for Astronomy in Python and foster interoperability -between Python astronomy packages.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -python = 'Python' -pyver = '2.7.3' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('setuptools', '18.4', versionsuffix), - ('numpy', '1.7.1', versionsuffix), -] - -pyshortver = '.'.join(pyver.split('.')[:2]) - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb deleted file mode 100644 index 61bd20053b..0000000000 --- a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = "PythonPackage" - -name = 'CosmoloPy' -version = '0.1.104' - -homepage = 'https://github.com/roban/CosmoloPy' -description = """A cosmology package for Python. CosmoloPy is -built on and designed for use with NumPy and SciPy.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -python = 'Python' -pyver = '2.7.3' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('numpy', '1.7.1', versionsuffix), -] - -pyshortver = '.'.join(pyver.split('.')[:2]) - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'tools' -- GitLab From 43d5d37b7ce6fea2f8c9ef312f9543b99a245175 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Wed, 16 Mar 2016 12:40:08 +0100 Subject: [PATCH 1001/2133] Fix typo --- easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb index 391d1f7f0c..d81b50276d 100644 --- a/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb +++ b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb @@ -26,7 +26,7 @@ comp_mpi_tc = (comp_mpi_tc_name, version) # For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ ('GCC', gccver), - ('MVAPICH2', '2.2b', '', ('GCC', gccver)), + ('MPICH', '3.2', '', ('GCC', gccver)), (blaslib, blasver, blassuff, ('GCC', gccver)), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), -- GitLab From 82a53a3c9515ca386991a88206c2d6f51549e672 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Wed, 16 Mar 2016 12:40:22 +0100 Subject: [PATCH 1002/2133] Cleanup --- easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb | 5 +---- easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb | 5 +---- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb index d495830401..45cf27aa8b 100644 --- a/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb +++ b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb @@ -13,13 +13,10 @@ compname = 'GCC' compver = '4.9.3-2.25' comp = (compname, compver) -mpilib = 'MPICH' -mpiver = '3.2' - # compiler toolchain dependencies dependencies = [ comp, - (mpilib, mpiver, '', comp), + ('MPICH', '3.2', '', comp), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb index efd6351300..80a9588d01 100644 --- a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb +++ b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb @@ -13,13 +13,10 @@ compname = 'GCC' compver = '4.9.3-2.25' comp = (compname, compver) -mpilib = 'MVAPICH2' -mpiver = '2.2b' - # compiler toolchain dependencies dependencies = [ comp, - (mpilib, mpiver, '', comp), + ('MVAPICH2', '2.2b', '', comp), ] moduleclass = 'toolchain' -- GitLab From dff5ae0ec1e64be935bb7cb8270f1fa2b67eeeb3 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Wed, 16 Mar 2016 12:43:53 +0100 Subject: [PATCH 1003/2133] Add easyconfig for HPL with the two new toolchain gmpolf/2016a and gmvpolf/2016a --- .../easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb | 18 ++++++++++++++++++ .../easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb new file mode 100644 index 0000000000..ae8a971cbf --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gmpolf', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb new file mode 100644 index 0000000000..d581afc6f7 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gmvolf', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From a8ab9324ac69573f4d59b9a6242c17dbe2a39137 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 14:15:18 +0200 Subject: [PATCH 1004/2133] Fixing indent --- .../setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb index e4b06a51e1..0b0cd4ff22 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb @@ -22,8 +22,8 @@ py_short_ver = ".".join(pythonversion.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], - 'dirs': [] - } + 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], + 'dirs': [] +} moduleclass = 'devel' -- GitLab From 879367d44a6c35a140b66f19552ca12bf4bcf09b Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 16 Mar 2016 14:00:40 +0100 Subject: [PATCH 1005/2133] RAxML 8.2.4-hybrid-avx2 for foss 2016a --- .../RAxML-8.2.4-foss-2016a-hybrid-avx2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb new file mode 100644 index 0000000000..431ef0ff1d --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.4' +versionsuffix ='-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-HYBRID-AVX2"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 4f13a60ee4d93dc68fb5a87bd68698ec5c406b6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 15:03:14 +0100 Subject: [PATCH 1006/2133] add postinstall command to fix permission issues in molmod easyconfig file --- .../m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb index 4fd3ed9a53..ee1c589750 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb @@ -20,6 +20,9 @@ dependencies = [ runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" runtest += "python setup.py build_ext -i; nosetests -v" +# fix permissions issue on files in share/molmod subdir +postinstallcmds = ['chmod -R o+r %(installdir)s/share/molmod'] + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/molmod'], -- GitLab From 38320cfa41dcfd4886d5f64b5c19244705106374 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 16:14:22 +0100 Subject: [PATCH 1007/2133] Revert "Updated PR, deleted unwanted files" This reverts commit 06e9ae546aa45bcdec0db8857ed5e251dfbd9e2a. --- ...astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb | 33 +++++++++++++++++++ ...oloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb | 31 +++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..bab7a31bcf --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'astropy' +version = '1.0.6' + +homepage = 'http://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('setuptools', '18.4', versionsuffix), + ('numpy', '1.7.1', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..61bd20053b --- /dev/null +++ b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'CosmoloPy' +version = '0.1.104' + +homepage = 'https://github.com/roban/CosmoloPy' +description = """A cosmology package for Python. CosmoloPy is +built on and designed for use with NumPy and SciPy.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('numpy', '1.7.1', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' -- GitLab From 1a564ebd3f7b674fc01c16277f53d0ba79399ff2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 17:45:23 +0200 Subject: [PATCH 1008/2133] add easyconfig PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb --- .../PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyAMG/PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..25956cf16e --- /dev/null +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'PyAMG' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pyamg.org' +description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +options = {'modulename': 'pyamg'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pyamg'], +} + +moduleclass = 'math' -- GitLab From df381842df1ab423a230a44afd0921ec33e2f3d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 18:39:27 +0100 Subject: [PATCH 1009/2133] reinstate Velvet easyconfigs that were removed in #2495 --- .../Velvet-1.2.10-intel-2015b-mt-kmer_100.eb | 29 ++++++++++++++++++ .../Velvet-1.2.10-intel-2015b-mt-kmer_31.eb | 30 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb create mode 100644 easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb new file mode 100644 index 0000000000..70b05647b0 --- /dev/null +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute +# Authors:: Cedric Laczny , Fotis Georgatos , +# Thekla Loizou , Andreas Panteli +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Velvet' +version = '1.2.10' +versionsuffix = '-mt-kmer_100' + +homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +description = """Sequence assembler for very short reads""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} + +sources = ['%(namelower)s_%(version)s.tgz'] +source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] + +buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb new file mode 100644 index 0000000000..fff6a988ab --- /dev/null +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute +# Authors:: Cedric Laczny , Fotis Georgatos , +# Thekla Loizou , Andreas Panteli +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Velvet' +version = '1.2.10' +versionsuffix = '-mt-kmer_31' + +homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +description = """Sequence assembler for very short reads""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} + +sources = ['%(namelower)s_%(version)s.tgz'] +source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] + +# by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous +buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] + +moduleclass = 'bio' -- GitLab From 90fa22472b6cfc099996ca3b9335d92339d1041e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 16 Mar 2016 18:45:42 +0100 Subject: [PATCH 1010/2133] rainbow-2.0.4-goolf-1.4.10.eb --- .../r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..c431cc2a4f --- /dev/null +++ b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'rainbow' +version = '2.0.4' + +homepage = 'https://sourceforge.net/projects/bio-rainbow/' +description = """Efficient tool for clustering and assembling short reads, especially for RAD.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://downloads.sourceforge.net/project/bio-rainbow/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +buildopts = ' CC=$CC' + +files_to_copy = [(['rainbow', 'ezmsim', 'rbasm', 'select_sec_rbcontig.pl', + 'select_best_rbcontig_plus_read1.pl', 'select_sec_rbcontig.pl', 'select_all_rbcontig.pl'], 'bin')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/rainbow', 'bin/ezmsim', 'bin/rbasm'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 7e1d2ba87aabccafdc34a72438f79de067394201 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 16 Mar 2016 18:47:49 +0100 Subject: [PATCH 1011/2133] PEAR-0.9.6-goolf-1.4.10.eb --- .../p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb new file mode 100644 index 0000000000..5ee2eb89d1 --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.6' + +homepage = 'http://sco.h-its.org/exelixis/web/software/pear/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sco.h-its.org/exelixis/web/software/pear/files/'] +sources = ['%(namelower)s-%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/pear'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 0e5d1dc188f3920467c8ddd6ff17c9fd7ac64b5c Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 16 Mar 2016 18:50:52 +0100 Subject: [PATCH 1012/2133] Mawk-1.3.4-goolf-1.4.10-20150503.eb --- .../Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb diff --git a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb new file mode 100644 index 0000000000..7235621e5d --- /dev/null +++ b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'Mawk' +version = '1.3.4' +versionsuffix = '-20150503' + +homepage = 'http://invisible-island.net/mawk/' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['ftp://invisible-island.net/mawk/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 8ac95fa17358dc9aa92a48df101ea2a2074e3dae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 20:30:58 +0100 Subject: [PATCH 1013/2133] reinstate building MetaVelvet and copying contrib in Velvet easyconfigs --- .../v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb | 2 ++ .../v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb index 70b05647b0..52c0ab85db 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb @@ -26,4 +26,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb index fff6a988ab..c23584dddd 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb @@ -27,4 +27,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] + moduleclass = 'bio' -- GitLab From 97559c46c82ca98f9214ed35f1ba78d4349a81ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 20:55:24 +0100 Subject: [PATCH 1014/2133] bump version to 2.7.0 and update release notes --- RELEASE_NOTES | 73 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 73 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a3e8287af7..b2548fe550 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,80 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 5,093 easyconfig files, for 799 different software packages, +The latest version of easybuild-easyconfig provides 5,580 easyconfig files, for 862 different software packages, 34 different (compiler) toolchains, 12 software bundles and 1 meta-package. +v2.7.0 (March 18th 2016) +------------------------ + +feature + bugfix release +- added example easyconfig files for 63 new software packages: + ATSAS (#616, #2587), astropy (#2724, #2727), attr (#2706), BamUtil (#2654), BBMap (#2322), BH (#2508), + CheMPS2 (#2445), CosmoloPy (#2723, #2727), csvkit (#2639), Firefox (#2648), FreeXL (#2422), GL2PS (#2667), + Glade (#2631), htop (#2538), IGV (#2019), IGVTools (#2019), ImageMagick (#2438), jModelTest (#2529), + KEALib (#2420), libcerf (#2656), libgcrypt (#2201), libglade (#2631), libgpg-error (#2201), libspatialite (#2431), + LittleCMS (#2438), MAST (#2542), MLC (#2577), MPJ-Express (#2529), mutil (#2201), neon (#758), NextClip (#2544), + npstat (#2686, #2703), Octopus (#2643), QuickFF (#2721), p4vasp (#2328), PCMSolver (#2445), PFFT (#2643), + PHYLIP (#2694), pkgconfig (#2475, #2476), Platypus (#2618), pplacer (#1056), PRINSEQ (#2437, #2444, #2585), + PyFFmpeg (#2501, #2519), PyGObject (#2443), PyGTK (#2443), PyOpenGL (#2628), pyringe (#2533), qrupdate (#2675), + rgeos (#2635), rpmrebuild (#2402), shift (#2201), SNAPE-pooled (#2688), SNPhylo (#2701), sratoolkit (#2715), + STAR-Fusion (#2463), statsmodels (#2719), StringTie (#2527), synchronicity (#2508), testpath (#2461), + USEARCH (#2537), VarScan (#2464), vsc-install (#2165), Whoosh (#2725), xprop (#2645) +- added new easyconfigs for existing toolchains: + intel/2016.02-GCC-4.9 (#2620), gmpolf/2016a & gmvolf/2016a (#2589) +- stable Cray-specific easyconfigs + - delete deprecated Cray toolchains and easyconfig files (#2400) + - don't hardcode PrgEnv version, remove craype and fftw components in Cray toolchains (#2554) + - remove -XC versionsuffix for stable definitions for Cray* toolchains (#2714) + - support for various software packages with CrayGNU and CrayIntel toolchains: CP2K, GROMACS, WRF +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including BWA 0.7.13, CMake 3.4.3, GATE 7.2, GROMACS 5.1.2, Mesa 11.1.2, netCDF 4.4.0, Perl 5.22.1, Python 3.5.1, + R 3.2.3, R-bundle-Bioconductor 3.2, scipy 0.17.0, SuiteSparse 4.5.1 +- various other enhancements, including: + - copy contrib dir in Velvet easyconfigs so scripts are also available (#2456) + - redefine matplotlib 1.5.1 easyconfig as a bundle, also include cycler extension (dep for matplotlib) (#2470) + - add bitstring extension to Python 2.7.11 easyconfigs (#2471) + - enable building of MetaVelvet in Velvet 1.2.10 easyconfigs (#2473) + - add custom sanity check for libjpeg-turbo (#2480) + - add Velvet easyconfigs that include BioPerl dependency, so VelvetOptimizer can use it (#2495, #2729, #2733) + - add source URL in RAxML 7.2.6 easyconfigs (#2536) + - update MPICH easyconfigs to use new MPICH easyblock (#2589) + - free libX11 & co from unneeded Python dependency/versionsuffix (#2549, #2563, #2605, #2664) + - add '--enable-utf --enable-unicode-properties' configure options in PCRE easyconfigs (#2561) + - required for latest R versions + - add HCsnip, metagenomeSeq in Bioconductor 3.1 bundles (#2553, #2578) + - add additional extensions in R 3.2.x easyconfigs that are required for extra Bioconductor extensions (#2547, #2556) + - update psmpi easyconfig files to use the new psmpi easyblock (#2619) + - add easyconfig for Python 2.7.11 on top of X11-enabled Tk (#2614, #2621) + - add virtualenv as extension in Python 2.7.11 easyconfigs (#2660) +- various bug fixes, including: + - fix software name for GTK+ (was 'gtk+'), PyCairo (was 'pycairo') and Gdk-Pixbuf (was 'gdk-pixbuf') (#2468) + - don't hardcode CC/CXX in OpenMPI easyconfigs (#2472) + - remove Google Code source URL for mpi4py (#2474) + - rename ffmpeg to FFmpeg (#2425, #2481) + - use available easyblock for flex (#2486) + - fix determining list of easyconfigs in unit test suite, don't assume locations are correct (#2530) + - fix specifying DB dependency in DB_File easyconfigs (#2539) + - remove hard-coded -xSSE4.2 for numpy/scipy with Intel compilers (#2546) + - fix license headers: Hercules foundation is now FWO (#2550) + - add --with-zlib configure argument in libxml easyconfigs (#2555) + - don't hardcode optarch=True in xextproto/xtrans easyconfigs (#2601) + - change toolchain version to '' in easyconfigs that use dummy toolchain and include dependencies (#2612) + - GLib doesn't require libxml2 with Python bindings (#2632) + - add patch file to imkl 10.2.6.038 32-bit easyconfig to fix installer not being able to deal with '--' in build path (#2634) + - add missing 'pkgconfig' dependency for h5py (#2476, #2650) + - correct software name in FastQC easyconfigs (was 'fastqc'), use 'dummy' toolchain for all FastQC version (#2657, #2666) + - add missing libxml2 dependencies in GLib easyconfigs (#2658) + - fix Xerces-C++ download location (#2668) + - enable XML::Bare extension in all Perl easyconfigs (#2672) + - update dead link for SuiteSparse (#2679) + - remove custom exts_filter in easyconfigs used PythonPackage easyblock (#2683, #2685) + - add M4 as build dep for binutils & flex (#2681) + - add missing dependencies in Python 3.5.x easyconfigs: SQLite, Tk, GMP (#2704) + - fix (OS) deps, add checksums, remove parameter definition with default values in MVAPICH2 easyconfigs (#2707) +- style cleanup in various easyconfigs (#2378, #2387, #2395, #2396, #2488-#2493, #2496-#2500, #2502-#2504, #2602) + - working towards automated style review of pull requests + v2.6.0 (January 26th 2016) -------------------------- diff --git a/setup.py b/setup.py index e1abe096bf..bbfef2ebfa 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.7.0.dev0' +VERSION = '2.7.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 887023130eadcc6a55f01d695d6cec31ef56a599 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 17 Mar 2016 14:17:05 -0500 Subject: [PATCH 1015/2133] Adding an Easyconfig file for gtool-v0.7.5 --- .../g/gtool/gtool-0.7.5_linux_x86_64.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb new file mode 100644 index 0000000000..276283587b --- /dev/null +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: + +easyblock = "Binary" + +name = 'gtool' +version = '0.7.5' +versionsuffix = '_linux_x86_64' + +homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' +description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] +sources = ['gtool_v%(version)s_x86_64.tgz'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["gtool", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' -- GitLab From 02c80db3e5edf4c515e7c2e84cba772f41ed4867 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 17 Mar 2016 16:55:18 -0500 Subject: [PATCH 1016/2133] Adding Easyconfig file for shapeit_v2.r837_GLIBCv2.12 --- ...shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb diff --git a/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb new file mode 100644 index 0000000000..a71ba8d96d --- /dev/null +++ b/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi + +easyblock = "Binary" + +name = 'shapeit' +version = '2.r837.GLIBCv2.12' +versionsuffix = '_linux_x86_64' + +homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html' +description = """ SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] +sources = ['shapeit.v%(version)s.Linux.static.tgz'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "tar xzvf shapeit.v%(version)s.Linux.static.tgz && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["bin/shapeit", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' -- GitLab From 4ac34ac670957972ae454538b960cf7b2b57bd5e Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 17 Mar 2016 17:08:51 -0500 Subject: [PATCH 1017/2133] Adding author to the Easyconfig file for gtool --- easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb index 276283587b..aa280fb576 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -1,5 +1,5 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: +# Author: Ravi Tripathi easyblock = "Binary" -- GitLab From b42b09ef2b1fdebe5b1d98891eed75169834e0f9 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 18 Mar 2016 02:12:56 -0500 Subject: [PATCH 1018/2133] Changing the name of Easyconfig file for gtool v0.7.5 --- .../g/gtool/gtool-0.7.5-linux_x86_64.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb new file mode 100644 index 0000000000..aa280fb576 --- /dev/null +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi + +easyblock = "Binary" + +name = 'gtool' +version = '0.7.5' +versionsuffix = '_linux_x86_64' + +homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' +description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] +sources = ['gtool_v%(version)s_x86_64.tgz'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["gtool", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' -- GitLab From 38474722b49c807cdbe36716e92088c8f989803d Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 18 Mar 2016 02:15:47 -0500 Subject: [PATCH 1019/2133] Changing the name of Easyconfig file for gtool v0.7.5 --- .../g/gtool/gtool-0.7.5_linux_x86_64.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb deleted file mode 100644 index aa280fb576..0000000000 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ /dev/null @@ -1,27 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Ravi Tripathi - -easyblock = "Binary" - -name = 'gtool' -version = '0.7.5' -versionsuffix = '_linux_x86_64' - -homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' -description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] -sources = ['gtool_v%(version)s_x86_64.tgz'] - -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " -install_cmd += "cp -a %(builddir)s/* %(installdir)s" - -sanity_check_paths = { - 'files': ["gtool", "LICENCE"], - 'dirs': ["example"] -} - -moduleclass = 'bio' -- GitLab From 9f51538585027769015932d76f80f27967b610f7 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 18 Mar 2016 02:19:51 -0500 Subject: [PATCH 1020/2133] Change the name of easyconfig file for shapeit-v2.r837_GLIBCv2.12 --- ...linux_x86_64.eb => shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/shapeit/{shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb => shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb} (100%) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb rename to easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb -- GitLab From 73c1f0a92e6ba69c9a6e6b0aaee1edc1ec9a395a Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Fri, 18 Mar 2016 10:39:18 -0400 Subject: [PATCH 1021/2133] Add easyconfig BWA-0.7.13-goolf-1.4.10 --- .../b/BWA/BWA-0.7.13-goolf-1.4.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb new file mode 100644 index 0000000000..403c2a7c2e --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos , Daniel Navarro +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'BWA' +version = '0.7.13' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] + +moduleclass = 'bio' -- GitLab From 808d1eb56e319ed017b07fb3b2e748acb67f7686 Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Fri, 18 Mar 2016 11:03:07 -0400 Subject: [PATCH 1022/2133] Including zlib as dependency for BWA-0.7.13-goolf-1.4.10.eb --- easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb index 403c2a7c2e..439ab3ce81 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -19,6 +19,7 @@ description = """Burrows-Wheeler Aligner (BWA) is an efficient program that alig toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} +dependencies = [('zlib', '1.2.8')] sources = [SOURCELOWER_TAR_BZ2] source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] -- GitLab From 4e25132c4035aabb3f79d24934f93419d26090b7 Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Fri, 18 Mar 2016 11:07:02 -0400 Subject: [PATCH 1023/2133] Style fix --- easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb index 439ab3ce81..9cbb01f191 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -19,9 +19,10 @@ description = """Burrows-Wheeler Aligner (BWA) is an efficient program that alig toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -dependencies = [('zlib', '1.2.8')] sources = [SOURCELOWER_TAR_BZ2] source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] +dependencies = [('zlib', '1.2.8')] + moduleclass = 'bio' -- GitLab From 9f856123b6f4837cfafad3e129861c9e1fb14293 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sat, 19 Mar 2016 10:54:21 +0100 Subject: [PATCH 1024/2133] fixed foss easyconfig --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb index 2ecf3ea45f..67cfd94871 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -153,7 +153,7 @@ exts_list = [ }), ('Archive::Extract', '0.76', { 'source_tmpl': 'Archive-Extract-0.76.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "BINGOS"'], + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS'], }), ('DBIx::Simple', '1.35', { 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', @@ -405,7 +405,7 @@ exts_list = [ }), ('Date::Language', '2.30', { 'source_tmpl': 'TimeDate-2.30.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "GBARR"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], }), ('version', '0.9915', { 'source_tmpl': 'version-0.9915.tar.gz', @@ -546,7 +546,7 @@ exts_list = [ }), ('boolean', '0.45', { 'source_tmpl': 'boolean-0.45.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "INGY"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], }), ('Number::Format', '1.75', { 'source_tmpl': 'Number-Format-1.75.tar.gz', -- GitLab From 3fad4beecd206cdad60adebf2b8719dc3051d37c Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sat, 19 Mar 2016 10:56:24 +0100 Subject: [PATCH 1025/2133] fixed intel easyconfig --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index ae84220ef2..fd9ccde670 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -153,7 +153,7 @@ exts_list = [ }), ('Archive::Extract', '0.76', { 'source_tmpl': 'Archive-Extract-0.76.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "BINGOS"'], + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS'], }), ('DBIx::Simple', '1.35', { 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', @@ -405,7 +405,7 @@ exts_list = [ }), ('Date::Language', '2.30', { 'source_tmpl': 'TimeDate-2.30.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "GBARR"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], }), ('version', '0.9915', { 'source_tmpl': 'version-0.9915.tar.gz', @@ -547,7 +547,7 @@ exts_list = [ }), ('boolean', '0.45', { 'source_tmpl': 'boolean-0.45.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "INGY"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], }), ('Number::Format', '1.75', { 'source_tmpl': 'Number-Format-1.75.tar.gz', -- GitLab From 8e71210d0960333d22b625b7fac297dd84f5a7a0 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sat, 19 Mar 2016 12:12:16 +0100 Subject: [PATCH 1026/2133] updated url --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb index 67cfd94871..404b98df7e 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -153,7 +153,7 @@ exts_list = [ }), ('Archive::Extract', '0.76', { 'source_tmpl': 'Archive-Extract-0.76.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), ('DBIx::Simple', '1.35', { 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index fd9ccde670..aed8a467d0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -153,7 +153,7 @@ exts_list = [ }), ('Archive::Extract', '0.76', { 'source_tmpl': 'Archive-Extract-0.76.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), ('DBIx::Simple', '1.35', { 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', -- GitLab From df78df46c817032519ddcb787df100b0c846983d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 20 Mar 2016 08:50:34 +0100 Subject: [PATCH 1027/2133] fix release date for EasyBuild v2.7.0 --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b2548fe550..b5c225454e 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,7 +6,7 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 5,580 easyconfig files, for 862 different software packages, 34 different (compiler) toolchains, 12 software bundles and 1 meta-package. -v2.7.0 (March 18th 2016) +v2.7.0 (March 20th 2016) ------------------------ feature + bugfix release -- GitLab From 972a0974247a5f3641728f8fcdce30c47e4b4835 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 20 Mar 2016 10:45:38 +0100 Subject: [PATCH 1028/2133] bump version to 2.8.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index bbfef2ebfa..72cf85df21 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.7.0' +VERSION = '2.8.0dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From f2ecb8a398d2a16aecb24c378131202077b6f485 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 20 Mar 2016 11:45:55 +0200 Subject: [PATCH 1029/2133] add easyconfig EasyBuild-2.7.0.eb --- .../e/EasyBuild/EasyBuild-2.7.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb new file mode 100644 index 0000000000..1ca29896e8 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.7.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.4.18.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 4dcdd9aa5726c945a7301332f00b431d1db3da86 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 08:30:39 +0100 Subject: [PATCH 1030/2133] add easyconfig inputproto-2.3.1-foss-2016a.eb, add easyconfig kbproto-1.0.7-foss-2016a.eb, add easyconfig libpthread-stubs-0.3-foss-2016a.eb, add easyconfig libX11-1.6.3-foss-2016a.eb, add easyconfig libXau-1.0.8-foss-2016a.eb, add easyconfig libxcb-1.11.1-foss-2016a.eb, add easyconfig libXdmcp-1.1.2-foss-2016a.eb, add easyconfig xextproto-7.3.0-foss-2016a.eb, add easyconfig xproto-7.0.28-foss-2016a.eb, add easyconfig xtrans-1.3.5-foss-2016a.eb --- .../inputproto/inputproto-2.3.1-foss-2016a.eb | 19 ++++++++++ .../k/kbproto/kbproto-1.0.7-foss-2016a.eb | 19 ++++++++++ .../l/libX11/libX11-1.6.3-foss-2016a.eb | 37 +++++++++++++++++++ .../l/libXau/libXau-1.0.8-foss-2016a.eb | 25 +++++++++++++ .../l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 25 +++++++++++++ .../libpthread-stubs-0.3-foss-2016a.eb | 20 ++++++++++ .../l/libxcb/libxcb-1.11.1-foss-2016a.eb | 33 +++++++++++++++++ .../x/xextproto/xextproto-7.3.0-foss-2016a.eb | 24 ++++++++++++ .../x/xproto/xproto-7.0.28-foss-2016a.eb | 23 ++++++++++++ .../x/xtrans/xtrans-1.3.5-foss-2016a.eb | 22 +++++++++++ 10 files changed, 247 insertions(+) create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb new file mode 100644 index 0000000000..be4171cde7 --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb new file mode 100644 index 0000000000..bca5ddd7ca --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb new file mode 100644 index 0000000000..7bbdcf2dc4 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..8694ab5ad2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c12e65e6e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb new file mode 100644 index 0000000000..fcb767cfdb --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb new file mode 100644 index 0000000000..d818b47843 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb new file mode 100644 index 0000000000..9bc6335cdf --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb new file mode 100644 index 0000000000..3e787177f0 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb new file mode 100644 index 0000000000..1d32cb1ae6 --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From a07b7c3608e80cb5bbbcd8ad159231b462582047 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 08:39:44 +0100 Subject: [PATCH 1031/2133] add easyconfig libXext-1.3.3-foss-2016a.eb --- .../l/libXext/libXext-1.3.3-foss-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000..fc57003279 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From ada59b306cff8427daa61380d50f9e4419e1f6dc Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 08:56:07 +0100 Subject: [PATCH 1032/2133] add easyconfig libXft-2.3.2-foss-2016a.eb, add easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig freetype-2.6.2-foss-2016a.eb, add easyconfig libXrender-0.9.9-foss-2016a.eb, add easyconfig renderproto-0.11-foss-2016a.eb --- .../fontconfig-2.11.94-foss-2016a.eb | 22 +++++++++++++ .../f/freetype/freetype-2.6.2-foss-2016a.eb | 22 +++++++++++++ .../l/libXft/libXft-2.3.2-foss-2016a.eb | 31 +++++++++++++++++++ .../libXrender/libXrender-0.9.9-foss-2016a.eb | 28 +++++++++++++++++ .../renderproto-0.11-foss-2016a.eb | 20 ++++++++++++ 5 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb new file mode 100644 index 0000000000..d955835431 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.94' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.6.2'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb new file mode 100644 index 0000000000..41c2f0204e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb new file mode 100644 index 0000000000..1a968a5ada --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXrender', '0.9.9'), + ('freetype', '2.6.2'), + ('fontconfig', '2.11.94'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb new file mode 100644 index 0000000000..eee347a314 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb new file mode 100644 index 0000000000..48199d0511 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 61e73501ae42f1a56e50031555bd20d3cf4aeb0d Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 09:00:48 +0100 Subject: [PATCH 1033/2133] add easyconfig PCRE-8.38-foss-2016a.eb --- .../p/PCRE/PCRE-8.38-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb new file mode 100644 index 0000000000..1fe2fcb26c --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.38' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' -- GitLab From d84ea63b7582b3cf1d54b1bc07bdc32a2da5222c Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Mon, 21 Mar 2016 17:30:01 +0100 Subject: [PATCH 1034/2133] New TAMkin easyconfig --- .../TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..9f28a619eb --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'TAMkin' +version = '1.0.8' + +homepage = 'http://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.5.0', versionsuffix), + ('molmod', '1.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion], +} + +moduleclass = 'chem' -- GitLab From 85471cb0716f38691dff6baf1aa00a73ba0845b8 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 17:49:48 +0100 Subject: [PATCH 1035/2133] add easyconfig gperf-3.0.4-foss-2016a.eb --- .../g/gperf/gperf-3.0.4-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb new file mode 100644 index 0000000000..0547875020 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 1017f5824cdac5303667b828d4b0c54a1b5d73eb Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 18:10:54 +0100 Subject: [PATCH 1036/2133] modify easyconfig bzip2-1.0.6-foss-2016a.eb, add easyconfig gettext-0.19.6-foss-2016a.eb, add easyconfig GraphicsMagick-1.3.23-foss-2016a.eb, modify easyconfig libjpeg-turbo-1.4.2-foss-2016a.eb, add easyconfig LibTIFF-4.0.6-foss-2016a.eb, modify easyconfig libtool-2.4.6-foss-2016a.eb, modify easyconfig libxml2-2.9.3-foss-2016a.eb, add easyconfig XZ-5.2.2-foss-2016a.eb --- .../GraphicsMagick-1.3.23-foss-2016a.eb | 34 +++++++++++++++++++ .../g/gettext/gettext-0.19.6-foss-2016a.eb | 18 ++++++++++ .../l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb | 33 ++++++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb | 30 ++++++++++++++++ 4 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb new file mode 100644 index 0000000000..e3433e3f0b --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.23' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('libtool', '2.4.6'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('bzip2', '1.0.6'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libxml2', '2.9.3'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb new file mode 100644 index 0000000000..1fdb744032 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.6' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb new file mode 100644 index 0000000000..d7aa3b2df4 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.6' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb new file mode 100644 index 0000000000..2a89ca6af6 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('gettext', '0.19.6'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From e5236a98d2ea36fb4c3a4aa8ed4eb98f0f43f076 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 18:29:11 +0100 Subject: [PATCH 1037/2133] add easyconfig qrupdate-1.1.2-foss-2016a.eb --- .../q/qrupdate/qrupdate-1.1.2-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..27976f981b --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['%(name)s-%(version)s_makeconf.patch'] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 994d6f447d81fb081150ce1a1aec518a4bd2d45b Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 18:40:00 +0100 Subject: [PATCH 1038/2133] add easyconfig HDF5-1.8.16-foss-2016a-serial.eb --- .../h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb new file mode 100644 index 0000000000..2936e9795e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.16' +versionsuffix = '-serial' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From 7a94c71bd384f3f1dc82777fc7abd5c24f5fcfab Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 20:51:41 +0100 Subject: [PATCH 1039/2133] add easyconfig GLib-2.47.5-foss-2016a.eb, add easyconfig libffi-3.2.1-foss-2016a.eb, add easyconfig libICE-1.0.9-foss-2016a.eb, add easyconfig libSM-1.2.2-foss-2016a.eb, add easyconfig libXt-1.1.5-foss-2016a.eb, add easyconfig Qt-4.8.7-foss-2016a.eb --- .../g/GLib/GLib-2.47.5-foss-2016a.eb | 33 ++++++++++++++++ .../l/libICE/libICE-1.0.9-foss-2016a.eb | 27 +++++++++++++ .../l/libSM/libSM-1.2.2-foss-2016a.eb | 28 +++++++++++++ .../l/libXt/libXt-1.1.5-foss-2016a.eb | 39 +++++++++++++++++++ .../l/libffi/libffi-3.2.1-foss-2016a.eb | 23 +++++++++++ .../easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb | 24 ++++++++++++ 6 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb new file mode 100644 index 0000000000..06841954c4 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb new file mode 100644 index 0000000000..fa49f6c97c --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libICE' +version = '1.0.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xtrans', '1.3.5'), +] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb new file mode 100644 index 0000000000..fe3df1bbcf --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libSM' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Session Management library, which allows for applications to both manage sessions, + and make use of session managers to save and restore their state for later use.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libICE', '1.0.9'), +] +builddependencies = [ + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb new file mode 100644 index 0000000000..e37e36b1f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'libXt' +version = '1.1.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are + based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('kbproto', '1.0.7'), +] + +dependencies = [ + ('libSM', '1.2.2'), + ('libICE', '1.0.9'), + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', + 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', + 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', + 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', + 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb new file mode 100644 index 0000000000..c7c638b6fa --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb new file mode 100644 index 0000000000..fd0d5932c9 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb @@ -0,0 +1,24 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +dependencies = [ + ('GLib', '2.47.5'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXrender', '0.9.9'), +] + +moduleclass = 'devel' -- GitLab From 27b9000a75e68f57f624ad38be815faa1baeb57f Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Mon, 21 Mar 2016 21:45:37 +0100 Subject: [PATCH 1040/2133] Simplify python dependency info in TAMkin easyconfig --- .../t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb index 9f28a619eb..808f61dc12 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb @@ -13,14 +13,10 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/molmod/tamkin/releases/download/v%(version)s'] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.10' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-Python-%(pyver)s" dependencies = [ - (python, pythonversion), + ('Python', '2.7.10'), ('matplotlib', '1.5.0', versionsuffix), ('molmod', '1.1', versionsuffix), ] -- GitLab From 27c1ecfe7002a2e31f8b1719dfd7ee9f8cfa0a41 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Mon, 21 Mar 2016 21:47:46 +0100 Subject: [PATCH 1041/2133] Move line in TAMkin easyconfig --- .../t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb index 808f61dc12..b5bff455c0 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb @@ -2,6 +2,7 @@ easyblock = "PythonPackage" name = 'TAMkin' version = '1.0.8' +versionsuffix = "-Python-%(pyver)s" homepage = 'http://molmod.github.io/tamkin/' description = """TAMkin is a post-processing toolkit for normal mode analysis, @@ -13,8 +14,6 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/molmod/tamkin/releases/download/v%(version)s'] sources = [SOURCE_TAR_GZ] -versionsuffix = "-Python-%(pyver)s" - dependencies = [ ('Python', '2.7.10'), ('matplotlib', '1.5.0', versionsuffix), -- GitLab From 916e9d74d7e679b04d4ac0e44f1f3df12ca03d13 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:23:46 +0100 Subject: [PATCH 1042/2133] add easyconfig eudev-3.1.5-foss-2016a.eb, add easyconfig fixesproto-5.0-foss-2016a.eb, add easyconfig fontsproto-2.1.3-foss-2016a.eb, add easyconfig glproto-1.4.17-foss-2016a.eb, add easyconfig libdrm-2.4.67-foss-2016a.eb, add easyconfig libfontenc-1.1.3-foss-2016a.eb, add easyconfig libpciaccess-0.13.4-foss-2016a.eb, add easyconfig libXdamage-1.1.4-foss-2016a.eb, add easyconfig libXfixes-5.0.1-foss-2016a.eb, add easyconfig libXfont-1.5.1-foss-2016a.eb, add easyconfig makedepend-1.0.5-foss-2016a.eb, add easyconfig Mesa-11.1.2-foss-2016a.eb, add easyconfig pkg-config-0.29-foss-2016a.eb, add easyconfig xorg-macros-1.19.0-foss-2016a.eb --- .../e/eudev/eudev-3.1.5-foss-2016a.eb | 32 +++++++++ .../f/fixesproto/fixesproto-5.0-foss-2016a.eb | 19 ++++++ .../fontsproto/fontsproto-2.1.3-foss-2016a.eb | 20 ++++++ .../g/glproto/glproto-1.4.17-foss-2016a.eb | 20 ++++++ .../libXdamage/libXdamage-1.1.4-foss-2016a.eb | 25 +++++++ .../l/libXfixes/libXfixes-5.0.1-foss-2016a.eb | 24 +++++++ .../l/libXfont/libXfont-1.5.1-foss-2016a.eb | 31 +++++++++ .../l/libdrm/libdrm-2.4.67-foss-2016a.eb | 28 ++++++++ .../libfontenc/libfontenc-1.1.3-foss-2016a.eb | 23 +++++++ .../libpciaccess-0.13.4-foss-2016a.eb | 26 +++++++ .../m/Mesa/Mesa-11.1.2-foss-2016a.eb | 68 +++++++++++++++++++ .../makedepend/makedepend-1.0.5-foss-2016a.eb | 20 ++++++ .../pkg-config/pkg-config-0.29-foss-2016a.eb | 27 ++++++++ .../xorg-macros-1.19.0-foss-2016a.eb | 22 ++++++ 14 files changed, 385 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb new file mode 100644 index 0000000000..3265e4fdb4 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.1.5' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-3.1.2_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb new file mode 100644 index 0000000000..4fe8f2b4dc --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb new file mode 100644 index 0000000000..0d7fd4a4a2 --- /dev/null +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'fontsproto' +version = '2.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X11 font extension wire protocol" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb new file mode 100644 index 0000000000..d26077ac1e --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'glproto' +version = '1.4.17' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb new file mode 100644 index 0000000000..19c75463d3 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdamage' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Damage extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xdamage.h', 'lib/libXdamage.%s' % SHLIB_EXT, 'lib/libXdamage.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb new file mode 100644 index 0000000000..aa11951f76 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb new file mode 100644 index 0000000000..b62ce08a63 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', '2.6.2'), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb new file mode 100644 index 0000000000..93d87d9533 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.67' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000..b21fd6654e --- /dev/null +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfontenc' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/xlibs/' +description = """X11 font encoding library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/fonts/fontenc.h', 'lib/libfontenc.%s' % SHLIB_EXT, 'lib/libfontenc.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb new file mode 100644 index 0000000000..75924f159f --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.4' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('Autotools', '20150215'), + ('xorg-macros', '1.19.0'), +] + +preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c9dd66c1c1 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.1.2' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.67'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1'), + ('LLVM', '3.7.1'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb new file mode 100644 index 0000000000..8bd95eee91 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb new file mode 100644 index 0000000000..2796515752 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 441307a0cbfd668e39a248b8a868d3edfa9e331c Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:28:31 +0100 Subject: [PATCH 1043/2133] add easyconfig GLPK-4.58-foss-2016a.eb --- .../g/GLPK/GLPK-4.58-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb new file mode 100644 index 0000000000..d5751eec2a --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.58' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.1.0')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 20a9dff4b702a113c5e9375b03ff2aeb68147707 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:38:33 +0100 Subject: [PATCH 1044/2133] add easyconfig freeglut-3.0.0-foss-2016a.eb, add easyconfig GL2PS-1.3.9-foss-2016a.eb, add easyconfig libGLU-9.0.0-foss-2016a.eb, add easyconfig libXi-1.7.6-foss-2016a.eb, add easyconfig libXmu-1.1.2-foss-2016a.eb, add easyconfig libXpm-3.5.11-foss-2016a.eb, add easyconfig libXrandr-1.5.0-foss-2016a.eb, add easyconfig randrproto-1.5.0-foss-2016a.eb --- .../f/freeglut/freeglut-3.0.0-foss-2016a.eb | 37 +++++++++++++++++++ .../g/GL2PS/GL2PS-1.3.9-foss-2016a.eb | 34 +++++++++++++++++ .../l/libGLU/libGLU-9.0.0-foss-2016a.eb | 24 ++++++++++++ .../l/libXi/libXi-1.7.6-foss-2016a.eb | 30 +++++++++++++++ .../l/libXmu/libXmu-1.1.2-foss-2016a.eb | 25 +++++++++++++ .../l/libXpm/libXpm-3.5.11-foss-2016a.eb | 22 +++++++++++ .../l/libXrandr/libXrandr-1.5.0-foss-2016a.eb | 31 ++++++++++++++++ .../randrproto/randrproto-1.5.0-foss-2016a.eb | 19 ++++++++++ 8 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb new file mode 100644 index 0000000000..aa4fa34ea2 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', '11.1.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb new file mode 100644 index 0000000000..f83060a449 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('freeglut', '3.0.0'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb new file mode 100644 index 0000000000..087bd589cb --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '11.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb new file mode 100644 index 0000000000..bd92d68db6 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' +name = 'libXi' +version = '1.7.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('inputproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c219eeb168 --- /dev/null +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXmu' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. + libXmuu is a lighter-weight version that does not depend on libXt or libXext""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libXt', '1.1.5'), + ('libXpm', '3.5.11'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%%(name)s.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb new file mode 100644 index 0000000000..1cc567cb36 --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libXpm' +version = '3.5.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [('gettext', '0.19.6')] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..b6614e79e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXrandr' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Resize, Rotate and Reflection extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('randrproto', '1.5.0'), + ('renderproto', '0.11'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrandr.%s' % SHLIB_EXT, 'lib/libXrandr.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..eab697bf89 --- /dev/null +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'randrproto' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrandr protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 40ee838e51bc76352a13168ef86058d8d4dfa8dc Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:53:41 +0100 Subject: [PATCH 1045/2133] add easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig gnuplot-5.0.3-foss-2016a.eb, add easyconfig GObject-Introspection-1.47.1-foss-2016a.eb, add easyconfig HarfBuzz-1.1.3-foss-2016a.eb, add easyconfig libcerf-1.4-foss-2016a.eb, add easyconfig libgd-2.1.1-foss-2016a.eb, add easyconfig Pango-1.39.0-foss-2016a.eb, add easyconfig pixman-0.34.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 49 +++++++++++++++++++ ...GObject-Introspection-1.47.1-foss-2016a.eb | 47 ++++++++++++++++++ .../g/gnuplot/gnuplot-5.0.3-foss-2016a.eb | 42 ++++++++++++++++ .../h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb | 34 +++++++++++++ .../l/libcerf/libcerf-1.4-foss-2016a.eb | 28 +++++++++++ .../l/libgd/libgd-2.1.1-foss-2016a.eb | 26 ++++++++++ .../p/Pango/Pango-1.39.0-foss-2016a.eb | 31 ++++++++++++ .../p/pixman/pixman-0.34.0-foss-2016a.eb | 20 ++++++++ 8 files changed, 277 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb new file mode 100644 index 0000000000..3684c31e54 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +glibver = '2.47.5' + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), +] +builddependencies = [ + ('renderproto', '0.11'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb new file mode 100644 index 0000000000..3c83530c29 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.47.1' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +pyver = '2.7.11' + +dependencies = [ + ('Python', pyver), + ('GLib', '2.47.5'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6'), + ('libffi', '3.2.1'), +] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb new file mode 100644 index 0000000000..7e42e00e67 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.3' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.14.6'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('libgd', '2.1.1'), + ('Pango', '1.39.0'), + ('libcerf', '1.4'), + ('Qt', '4.8.7'), +] + +configopts = '--with-qt=qt4 ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000..91db4cfacd --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6'), + ('freetype', '2.6.2'), + ('GObject-Introspection', '1.47.1') +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb new file mode 100644 index 0000000000..4f3471b4f6 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libcerf' +version = '1.4' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """libcerf is a self-contained numeric library that provides an efficient and accurate + implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TGZ] +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000..b645a00595 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.1.1' + +homepage = 'http://libgd.bitbucket.org/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/libgd/gd-libgd/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fontconfig', '2.11.94'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb new file mode 100644 index 0000000000..80529d5bda --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.39.0' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6'), + ('HarfBuzz', '1.1.3'), + ('GObject-Introspection', '1.47.1'), + ('fontconfig', '2.11.94') +] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb new file mode 100644 index 0000000000..896aab1550 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 1aa7665c7c05b88a165667d0c2b727827d2b2f70 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Tue, 22 Mar 2016 09:42:54 +0100 Subject: [PATCH 1046/2133] Fix string substitution issues in TAMkin easyconfig --- .../t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb index b5bff455c0..baf9ff6145 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb @@ -26,7 +26,7 @@ runtest += 'export OMP_NUM_THREADS=1; nosetests -v test' sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion], + 'dirs': ['lib/python-%(pyshortver)s/site-packages/%(namelower)s'], } moduleclass = 'chem' -- GitLab From 3cf1a6a9ba4ea24407a165db18bb20e91aa8e5da Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Tue, 22 Mar 2016 09:50:39 +0100 Subject: [PATCH 1047/2133] Fix typo in TAMkin easyconfig --- .../t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb index baf9ff6145..c4a906b243 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb @@ -26,7 +26,7 @@ runtest += 'export OMP_NUM_THREADS=1; nosetests -v test' sanity_check_paths = { 'files': [], - 'dirs': ['lib/python-%(pyshortver)s/site-packages/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } moduleclass = 'chem' -- GitLab From 10ce3ec28443fcbb03da191301541162aa2ad8b7 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 22 Mar 2016 10:10:33 +0100 Subject: [PATCH 1048/2133] OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb --- .../OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..37166d7311 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,59 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +name = "OpenMM" +version = "6.1" + +easyblock = "CMakeMake" + +homepage = 'https://simtk.org/home/openmm' +description = """OpenMM is a toolkit for molecular simulation.""" + +toolchain = {'version': '1.4.10', 'name': 'goolf'} + +source_urls = ['https://github.com/pandegroup/openmm/archive/'] +sources = ['%(version)s.tar.gz'] + +parallel = 1 + +builddependencies = [ + ('CMake', '2.8.12'), +] + +separate_build_dir = True + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SWIG', '2.0.4', '-Python-2.7.5'), +] + +runtest = ' test' + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ["lib/libOpenMM.so", "lib/python%s/site-packages/simtk/openmm/openmm.py" % (pyshortver)], + 'dirs': [] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%s/site-packages' % (pyshortver), +} + +modextravars = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' -- GitLab From 09f2c97bc278a4a2ea87de7137f1a2234a539801 Mon Sep 17 00:00:00 2001 From: hajgato Date: Tue, 22 Mar 2016 10:26:15 +0100 Subject: [PATCH 1049/2133] add easyconfig FLTK-1.3.3-foss-2016a.eb, add easyconfig libXcursor-1.1.14-foss-2016a.eb, add easyconfig libXinerama-1.1.3-foss-2016a.eb, add easyconfig xineramaproto-1.2.1-foss-2016a.eb, add easyconfig xprop-1.2.2-foss-2016a.eb --- .../f/FLTK/FLTK-1.3.3-foss-2016a.eb | 37 +++++++++++++++++++ .../libXcursor-1.1.14-foss-2016a.eb | 29 +++++++++++++++ .../libXinerama-1.1.3-foss-2016a.eb | 31 ++++++++++++++++ .../xineramaproto-1.2.1-foss-2016a.eb | 19 ++++++++++ .../x/xprop/xprop-1.2.2-foss-2016a.eb | 26 +++++++++++++ 5 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000..650bf33743 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb @@ -0,0 +1,37 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.3' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + + +dependencies = [ + ('libX11', '1.6.3'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('xprop', '1.2.2'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid'], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb new file mode 100644 index 0000000000..1fc949ad4e --- /dev/null +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXcursor' +version = '1.1.14' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Cursor management library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXfixes', '5.0.1'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['include/X11/Xcursor/Xcursor.h', 'lib/libXcursor.%s' % SHLIB_EXT, 'lib/libXcursor.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000..e0a2e3d206 --- /dev/null +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXinerama' +version = '1.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Xinerama multiple monitor library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('xineramaproto', '1.2.1'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXinerama.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb new file mode 100644 index 0000000000..a40280e419 --- /dev/null +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xineramaproto' +version = '1.2.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers for xinerama" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/panoramiXproto.h'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb new file mode 100644 index 0000000000..bd60b7c873 --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.2' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftp.x.org/archive/individual/app/'] + +builddependencies = [ + ('xorg-macros', '1.19.0'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 6ccd02bdb1d7397de31d2b3f8060e559b373798e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Tue, 22 Mar 2016 11:29:53 +0100 Subject: [PATCH 1050/2133] Update GraphicsMagick-1.3.23-foss-2016a.eb -fpic needed by Octacve --- .../g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb index e3433e3f0b..6fa3747197 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb @@ -7,6 +7,7 @@ homepage = 'http://www.graphicsmagick.org/' description = """GraphicsMagick is the swiss army knife of image processing.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} source_urls = [ SOURCEFORGE_SOURCE, -- GitLab From 803e8384f663f340a66fa4ea79d36fc448b63b3b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 22 Mar 2016 11:32:09 +0100 Subject: [PATCH 1051/2133] Octave needs pic --- .../g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb index 755ecbe16c..ea37c3e81c 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb @@ -7,6 +7,7 @@ homepage = 'http://www.graphicsmagick.org/' description = """GraphicsMagick is the swiss army knife of image processing.""" toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} source_urls = [ SOURCEFORGE_SOURCE, -- GitLab From e8b93739a75d8c20e97ab89028bb9b58fb7cf0cf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 22 Mar 2016 11:53:27 +0100 Subject: [PATCH 1052/2133] BayeScEnv-1.1-goolf-1.4.10.eb --- .../b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..7a976185d2 --- /dev/null +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BayeScEnv' +version = '1.1' + +homepage = 'https://github.com/devillemereuil/bayescenv' +description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/devillemereuil/bayescenv/archive/'] +sources = ['v%(version)s.tar.gz'] + +start_dir = 'source' + +files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/bayescenv'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 620bbf6dd938b5325c24e02d890e19c1383dae0f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 22 Mar 2016 11:55:29 +0100 Subject: [PATCH 1053/2133] added dependency SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb --- .../SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/s/SWIG/SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..55068068d1 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '2.0.4' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with +a variety of high-level programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [('http://sourceforge.net/projects/swig/files/swig/swig-%s/' % version, 'download')] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.12'), +] + +moduleclass = 'devel' -- GitLab From 1527993f12857255edb7ffbd9efcf6da5fd95aee Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 22 Mar 2016 21:47:20 +0000 Subject: [PATCH 1054/2133] Update rtracklayer to 1.30.3 --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 2 +- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index d1392d23cc..78a36e128c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -80,7 +80,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.2', bioconductor_options), + ('rtracklayer', '1.30.3', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index 60d39797ec..42093e636a 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -79,7 +79,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.2', bioconductor_options), + ('rtracklayer', '1.30.3', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), -- GitLab From d2f49d06ce3607de57e4bb93705bde9247dfdd3e Mon Sep 17 00:00:00 2001 From: fenoyc Date: Thu, 24 Mar 2016 14:25:31 +0100 Subject: [PATCH 1055/2133] add easyconfig OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb --- .../OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..456a180ae7 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.2' + +homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': benchmark_dirs, +} + +moduleclass = 'perf' -- GitLab From 95827494b4f314243b046063bd45bbc3eafc50f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Mar 2016 16:32:58 +0200 Subject: [PATCH 1056/2133] modify easyconfig GCCcore-4.9.3.eb --- easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index 268b052687..78428e12c5 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -25,7 +25,10 @@ sources = [ 'mpc-1.0.2.tar.gz', ] -builddependencies = [('binutils', '2.25')] +builddependencies = [ + ('Autotools', '20150215'), + ('binutils', '2.25'), +] patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] -- GitLab From af28806336f567e64466ba8f29d19006bfd9612a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Mar 2016 17:58:21 +0200 Subject: [PATCH 1057/2133] add easyconfig Saxon-HE-9.7.0.4-Java-1.7.0_79.eb --- .../Saxon-HE-9.7.0.4-Java-1.7.0_79.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb new file mode 100644 index 0000000000..eed56a9078 --- /dev/null +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'Saxon-HE' +version = '9.7.0.4' + +homepage = 'http://saxon.sourceforge.net' +description = """Open Source SAXON XSLT processor developed by Saxonica Limited.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['SaxonHE%sJ.zip' % version.replace(".","-")] + +source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s' , 'download'] + +versionsuffix = '-Java-%(javaver)s' + +dependencies = [('Java', '1.7.0_79')] + +jarfiles = ['saxon%(version_major)she.jar', 'saxon%(version_major)s-test.jar', 'saxon%(version_major)s-xqj.jar'] + +sanity_check_paths = { + 'files': jarfiles, + 'dirs': [], +} + +modextrapaths = {'CLASSPATH': jarfiles} + +moduleclass = 'devel' -- GitLab From cca33c128a3ac475714f4c99fea45fb369affbb2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Mar 2016 18:18:48 +0200 Subject: [PATCH 1058/2133] modify easyconfig M4-1.4.17-GCCcore-4.9.3.eb --- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb index c1c8a52948..02f06d5cfe 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 73a8f1353ac0011e1c698eee8587510a306c8898 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 24 Mar 2016 17:24:33 +0100 Subject: [PATCH 1059/2133] Bump FSL to intel/2016a --- .../f/FSL/FSL-5.0.9-intel-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb new file mode 100644 index 0000000000..145ff09b91 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb @@ -0,0 +1,23 @@ +name = 'FSL' +version = '5.0.9' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] + +patches = [ + 'FSL-%(version)s_makefile_fixes.patch', + 'FSL_icc_nan-inf_fix.patch', +] + +dependencies = [ + ('freeglut', '3.0.0'), + ('expat', '2.1.0'), + ('libX11', '1.6.3'), +] + +moduleclass = 'bio' -- GitLab From 4f63d5fd457e914b17b505a79ab9b948dac38ef5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 08:42:15 +0200 Subject: [PATCH 1060/2133] modify easyconfig Tk-8.6.4-foss-2016a-no-X11.eb --- easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb index 6f98f7076c..449ce63a29 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8') ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' -- GitLab From 7d31e07e4d50572096fe299846f23480ab5f8264 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 08:50:57 +0200 Subject: [PATCH 1061/2133] modify easyconfig M4-1.4.17-foss-2016a.eb --- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb index 0d030e3264..ce563e7def 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 123ca05e26b955947108f4f3a2bb414138e46df9 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 10:40:25 +0200 Subject: [PATCH 1062/2133] add easyconfig ant-1.9.6-Java-1.7.0_79.eb --- .../a/ant/ant-1.9.6-Java-1.7.0_79.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb new file mode 100644 index 0000000000..3ee7c5b406 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb @@ -0,0 +1,23 @@ +name = 'ant' +version = '1.9.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.7.0_79')] + +builddependencies = [('JUnit', '4.11', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9bcdda139d149aac176a17a5aa9f38b137e55d83 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 25 Mar 2016 13:48:00 +0000 Subject: [PATCH 1063/2133] Update Bowtie2 to 2.2.8 for recent foss --- .../b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb | 40 +++++++++++++++++++ .../b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb | 40 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb new file mode 100644 index 0000000000..29bf068b6a --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.8' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb new file mode 100644 index 0000000000..e48888855e --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.8' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' -- GitLab From 9f4fb4098262af3f3388b25be24f4eeb890274b2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:17:01 +0200 Subject: [PATCH 1064/2133] add easyconfig Blitz++-0.10-foss-2016a.eb --- .../b/Blitz++/Blitz++-0.10-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb new file mode 100644 index 0000000000..03886c8db9 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Blitz++' +version = '0.10' + +homepage = 'http://blitz.sourceforge.net/' +description = """Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ + with a speed comparable to Fortran implementations, while preserving an object-oriented interface""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['blitz-%(version)s.tar.gz'] +source_urls = ['https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', + 'download'] + +sanity_check_paths = { + 'files': ['lib/libblitz.a'], + 'dirs': ['include/blitz/array', + 'include/blitz/gnu', + 'include/blitz/meta', + 'include/random', + 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 020f92e1035043d6dbfcc9e9e7bfe2a80e9f9aa0 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:19:45 +0200 Subject: [PATCH 1065/2133] add easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig freetype-2.6.2-foss-2016a.eb, add easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig pixman-0.34.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 29 +++++++++++++++++++ .../fontconfig-2.11.94-foss-2016a.eb | 22 ++++++++++++++ .../f/freetype/freetype-2.6.2-foss-2016a.eb | 21 ++++++++++++++ .../p/pixman/pixman-0.34.0-foss-2016a.eb | 20 +++++++++++++ 4 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb new file mode 100644 index 0000000000..4afe79dcce --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb new file mode 100644 index 0000000000..d955835431 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.94' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.6.2'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb new file mode 100644 index 0000000000..3111a314be --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb new file mode 100644 index 0000000000..896aab1550 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 1d95e0d44afa8bd2a6d3dd12f779f03f377eab75 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:22:11 +0200 Subject: [PATCH 1066/2133] add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb --- .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' -- GitLab From a429536dc79733a15a2ecdbf335fcbed1f2990df Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:24:03 +0200 Subject: [PATCH 1067/2133] add easyconfig MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- ...-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb new file mode 100644 index 0000000000..a11de24d4f --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus' +version = '7.0.67' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['stable_release-%s.zip' % version.replace('.','-')] + +dependencies = [ + ('Java', '1.7.0_79', '', True), + ('Python', '2.7.11'), + ('HDF5', '1.8.16'), + ('libxml2', '2.9.3', '-Python-%(pyver)s') +] + +configopts = '--with-jdk=$JAVA_HOME' + +preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' + +buildopts = '-j 1' + +moduleclass = 'data' -- GitLab From 0f7f918444396849cefb3ddd10ec622ceb292c8a Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 28 Mar 2016 13:42:38 -0500 Subject: [PATCH 1068/2133] Adding Email to the easyconfig --- easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb index aa280fb576..6d1dad133e 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb @@ -1,5 +1,6 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Ravi Tripathi +# Email: ravi89@uab.edu easyblock = "Binary" -- GitLab From 7665efa01e6c846d6fcc6299b62552125d23d5de Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 28 Mar 2016 13:45:45 -0500 Subject: [PATCH 1069/2133] Adding email to shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb Easyconfig file --- .../s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb index a71ba8d96d..7441bd58af 100644 --- a/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb +++ b/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb @@ -1,5 +1,6 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Ravi Tripathi +# Email: ravi89@uab.edu easyblock = "Binary" -- GitLab From 4bc1fe85404268c258d800beb130fe6597928b40 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 28 Mar 2016 14:07:21 -0500 Subject: [PATCH 1070/2133] Adding an Easyconfig file for MRICron built on 06/22/2015 --- .../m/mricron/mricron-062215-linux_x86_64.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb diff --git a/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb b/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb new file mode 100644 index 0000000000..a7fb738545 --- /dev/null +++ b/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Binary" + +name = 'mricron' +version = '062215' +versionsuffix = '_linux_x86_64' + +homepage = 'http://www.mccauslandcenter.sc.edu/mricro/mricron/' +description = """ MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] +sources = ['lx.zip'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "unzip lx.zip && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], + 'dirs': ["example", "lut", "templates"] +} + +moduleclass = 'bio' -- GitLab From cff82a7a7cce953ae7c746a6227a1e01777bf81f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 28 Mar 2016 23:40:39 +0100 Subject: [PATCH 1071/2133] Use latest numpy and fix tests --- .../r/RSeQC/RSeQC-2.6.3-foss-2015b.eb | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb index c0f1f917f6..c33eb72992 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb @@ -1,3 +1,7 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + easyblock = 'PythonPackage' name = 'RSeQC' @@ -16,20 +20,22 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCE_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] -patches = [] - -Python = 'Python' +python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('R', '3.2.3'), - ('numpy', '1.9.2'), + ('numpy', '1.10.1', versionsuffix), ] +runtest = "python setup.py test" + sanity_check_paths = { 'files': [], - 'dirs': ["."] + 'dirs': ["bin", "lib"] } +options = {'modulename': 'qcmodule'} + moduleclass = 'bio' -- GitLab From 9403a1c1ed2e243ded00fd181b7c3e74f6f8061c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 28 Mar 2016 23:48:28 +0100 Subject: [PATCH 1072/2133] Remove obsolete numpy dep for RSeQC --- .../numpy-1.9.2-foss-2015b-Python-2.7.10.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb deleted file mode 100644 index f55df325cf..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'numpy' -version = '1.9.2' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'foss', 'version': '2015b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['numpy-1.8.0-mkl.patch'] - -python = 'Python' -pyver = '2.7.10' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('SuiteSparse', '4.4.5', '-METIS-5.1.0'), -] - -moduleclass = 'math' -- GitLab From bda5cb872c43f93c6f7207cdf42e96364661b7a0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Mar 2016 07:45:09 +0100 Subject: [PATCH 1073/2133] Add BEDTools 2.25.0 to foss-2015b and foss-2016a --- .../b/BEDTools/BEDTools-2.25.0-foss-2015b.eb | 33 +++++++++++++++++++ .../b/BEDTools/BEDTools-2.25.0-foss-2016a.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb new file mode 100644 index 0000000000..50f76cdae7 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.25.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb new file mode 100644 index 0000000000..89147e0b20 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.25.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 9e31cc2f81179ae76942ac50899220609c8d5438 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Mar 2016 07:59:12 +0100 Subject: [PATCH 1074/2133] Fix version, description, sanity check and build options --- .../s/Subread/Subread-1.5.0p1-foss-2015b.eb | 28 +++++++++---------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb index 245a7b2f5a..4fd69f051e 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb @@ -1,30 +1,28 @@ -# Note: -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# It was auto-generated based on a template easyconfig, so it should be used with care. +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute easyblock = 'MakeCp' name = 'Subread' -version = '1.5.0p1' +version = '1.5.0-p1' homepage = 'http://subread.sourceforge.net/' -description = """TEMPLATE DESCRIPTION""" +description = """High performance read alignment, quantification and mutation discovery""" -# toolchain name should be 'TEMPLATE' if this is a template, so EasyBuild knows and is willing to use it as a template toolchain = {'name': 'foss', 'version': '2015b'} -toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... -# For sources line to work correctly with --try-software-version, you MUST employ %s OR use a construct like SOURCE_TAR_GZ -sources = ['%(namelower)s-%version)s-source.tar.gz'] -source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -patches = [] +prebuildopts = 'cd src;' +buildopts = '-f Makefile.Linux' + +files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] -dependencies = [] -# The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['LICENSE', 'README.txt'], + 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] } moduleclass = 'bio' -- GitLab From 4b1b8e1b10c5d5378efc01381b9deb998f20c8f5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Mar 2016 08:02:18 +0100 Subject: [PATCH 1075/2133] Add foss-2016a port of Subread --- .../s/Subread/Subread-1.5.0p1-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb new file mode 100644 index 0000000000..1312eb0648 --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'MakeCp' + +name = 'Subread' +version = '1.5.0-p1' + +homepage = 'http://subread.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] + +prebuildopts = 'cd src;' +buildopts = '-f Makefile.Linux' + +files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] + + +sanity_check_paths = { + 'files': ['LICENSE', 'README.txt'], + 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] +} + +moduleclass = 'bio' -- GitLab From a64db51afb19dbd910faa66e8d84b4d7c4239e0b Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 29 Mar 2016 10:19:18 +0200 Subject: [PATCH 1076/2133] Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb --- .../Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..47cae92462 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'Pysam' +version = '0.9.0' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': False, 'pic': False} + +parallel = 1 + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('ncurses', '5.9'), + ('zlib', '1.2.8'), + ('cURL', '7.29.0'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('Cython', '0.23.4', { + 'source_urls': ['http://cython.org/release/'], + }), + ('pysam', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pysam-%s-py%s-linux-x86_64.egg' % (pyshortver, version, pyshortver)] +} + +moduleclass = 'bio' -- GitLab From 31ee1fa4cc65d4d311b091272768ca615aa67949 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 29 Mar 2016 10:21:36 +0200 Subject: [PATCH 1077/2133] Revert "Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb" This reverts commit a64db51afb19dbd910faa66e8d84b4d7c4239e0b. --- .../Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb | 55 ------------------- 1 file changed, 55 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb deleted file mode 100644 index 47cae92462..0000000000 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb +++ /dev/null @@ -1,55 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'Bundle' - -name = 'Pysam' -version = '0.9.0' - -homepage = 'https://github.com/pysam-developers/pysam' -description = """Pysam is a python module for reading and manipulating Samfiles. - It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': False, 'pic': False} - -parallel = 1 - -python = 'Python' -pyver = '2.7.5' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('ncurses', '5.9'), - ('zlib', '1.2.8'), - ('cURL', '7.29.0'), -] - -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - -exts_list = [ - ('Cython', '0.23.4', { - 'source_urls': ['http://cython.org/release/'], - }), - ('pysam', version, { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], - }), -] - -modextrapaths = { - 'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver], -} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/pysam-%s-py%s-linux-x86_64.egg' % (pyshortver, version, pyshortver)] -} - -moduleclass = 'bio' -- GitLab From 8466e1b77b8a8c23b3a659045371f9db70b304f4 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Tue, 29 Mar 2016 22:02:06 +0200 Subject: [PATCH 1078/2133] New `.eb` files for LinBox 1.4.0, FFLAS-FFPACK 2.2.0, and Givaro 4.0.1 --- .../FFLAS-FFPACK-2.2.0-foss-2016a.eb | 70 +++++++++++++++++++ .../g/Givaro/Givaro-4.0.1-foss-2016a.eb | 45 ++++++++++++ .../l/LinBox/LinBox-1.4.0-foss-2016a.eb | 70 +++++++++++++++++++ 3 files changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb new file mode 100644 index 0000000000..382acef001 --- /dev/null +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -0,0 +1,70 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'FFLAS-FFPACK' +version = '2.2.0' + +homepage = 'https://linbox-team.github.io/fflas-ffpack/' +description = "Finite Field Linear Algebra Subroutines / Package" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v2.2.0.zip'] +source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] + +builddependencies = [ + ('Autoconf', '2.69', '', True), + ('Automake', '1.15', '', True), + ('libtool', '2.4.6', '', True), +] +dependencies = [ + ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), + ('Givaro', '4.0.1'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' + +parallel = 4 + +unwanted_env_vars = {} +start_dir = '%(builddir)s/%(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.8.0dev0", + "easybuild-easyblocks_version": "2.8.0dev0", + "timestamp": 1459270041, + "build_time": 30.84, + "install_size": 1762928, + "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'FFLAS-FFPACK-2.2.0-foss-2015a.eb'], + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), + "core_count": 4, + "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", + "cpu_speed": 2400.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", + "glibc_version": "2.21", + "hostname": "xenia", + "os_name": "ubuntu", + "os_type": "Linux", + "os_version": "15.10", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", + "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", + "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", +}] diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb new file mode 100644 index 0000000000..56ed27ad72 --- /dev/null +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'Givaro' +version = '4.0.1' + +homepage = 'http://givaro.forge.imag.fr/' +description = "C++ library for arithmetic and algebraic computations" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v4.0.1.zip'] +source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] + +builddependencies = [ + ('Autoconf', '2.69', '', True), + ('Automake', '1.15', '', True), + ('libtool', '2.4.6', '', True), +] +dependencies = [ + ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = "--with-gmp=$EBROOTGMP --enable-inline" + +parallel = 4 + +unwanted_env_vars = {} +start_dir = '%(builddir)s/%(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s-config.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb new file mode 100644 index 0000000000..042673b61a --- /dev/null +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -0,0 +1,70 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'LinBox' +version = '1.4.0' + +homepage = 'http://linalg.org/' +description = "C++ library for exact, high-performance linear algebra" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v1.4.0.zip'] +source_urls = ['https://github.com/%(namelower)s-team/%(namelower)s/archive'] + +builddependencies = [ + ('Autoconf', '2.69', '', True), + ('Automake', '1.15', '', True), + ('libtool', '2.4.6', '', True), +] +dependencies = [ + ('FFLAS-FFPACK', '2.2.0'), + ('Givaro', '4.0.1'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = "--with-givaro=$EBROOTGIVARO --with-fflas-ffpack=$EBROOTFFLASMINFFPACK --enable-openmp" + +parallel = 4 + +unwanted_env_vars = {} +start_dir = '%(builddir)s/%(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s-config.h', 'lib/liblinbox.a'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.8.0dev0", + "easybuild-easyblocks_version": "2.8.0dev0", + "timestamp": 1459270157, + "build_time": 64.4, + "install_size": 8769443, + "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'LinBox-1.4.0-foss-2015a.eb'], + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), + "core_count": 4, + "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", + "cpu_speed": 2400.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", + "glibc_version": "2.21", + "hostname": "xenia", + "os_name": "ubuntu", + "os_type": "Linux", + "os_version": "15.10", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", + "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", + "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", +}] -- GitLab From 842135094fa8af11889df5460b3aa58906661c11 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Tue, 29 Mar 2016 22:33:16 +0200 Subject: [PATCH 1079/2133] Remove "buildstatistics" section that sneaked in --- .../FFLAS-FFPACK-2.2.0-foss-2016a.eb | 24 ------------------- .../l/LinBox/LinBox-1.4.0-foss-2016a.eb | 24 ------------------- 2 files changed, 48 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 382acef001..153536ed7b 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -44,27 +44,3 @@ sanity_check_paths = { } moduleclass = 'math' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.8.0dev0", - "easybuild-easyblocks_version": "2.8.0dev0", - "timestamp": 1459270041, - "build_time": 30.84, - "install_size": 1762928, - "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'FFLAS-FFPACK-2.2.0-foss-2015a.eb'], - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), - "core_count": 4, - "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", - "cpu_speed": 2400.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", - "glibc_version": "2.21", - "hostname": "xenia", - "os_name": "ubuntu", - "os_type": "Linux", - "os_version": "15.10", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", - "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", - "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", -}] diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index 042673b61a..df00b437d1 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -44,27 +44,3 @@ sanity_check_paths = { } moduleclass = 'math' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.8.0dev0", - "easybuild-easyblocks_version": "2.8.0dev0", - "timestamp": 1459270157, - "build_time": 64.4, - "install_size": 8769443, - "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'LinBox-1.4.0-foss-2015a.eb'], - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), - "core_count": 4, - "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", - "cpu_speed": 2400.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", - "glibc_version": "2.21", - "hostname": "xenia", - "os_name": "ubuntu", - "os_type": "Linux", - "os_version": "15.10", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", - "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", - "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", -}] -- GitLab From 1f0c0f48cdee7708fbcbbd1584e5539528823e2f Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Tue, 29 Mar 2016 15:42:59 -0700 Subject: [PATCH 1080/2133] add Nvidia OptiX 3.8.0 easyconfig --- .../o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..db096d2117 --- /dev/null +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors:: Stephane Thiell +## +easyblock = 'Binary' +name = 'OptiX' +version = '3.8.0' + +homepage = 'https://developer.nvidia.com/optix' +description = """OptiX is NVIDIA SDK for easy ray tracing performance. + It provides a simple framework for accessing the GPU’s massive ray tracing + power using state-of-the-art GPU algorithms.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +#source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.run'] + +checksums = [ + 'ecf63cf32b87defa36d3cd283d085314', # NVIDIA-OptiX-SDK-3.8.0-linux64.run +] + +install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.so", "lib64/liboptixu.so"], + 'dirs': [] +} + +modextravars = { 'OPTIX_HOME': '%(installdir)s' } + +moduleclass = 'vis' -- GitLab From a192c8e8addf0c4d566a728cca056b438cc1e3fb Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 10:41:23 +0200 Subject: [PATCH 1081/2133] Edits suggested by @boegel and general cleanup. Some cruft was added by EB as a result of saving back the file, and it gets dutifully removed now. (Well, hopefully!) --- .../FFLAS-FFPACK-2.2.0-foss-2016a.eb | 24 ++++++++----------- .../g/Givaro/Givaro-4.0.1-foss-2016a.eb | 21 +++++++--------- .../l/LinBox/LinBox-1.4.0-foss-2016a.eb | 21 +++++++--------- 3 files changed, 26 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 153536ed7b..282843bbc7 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -17,30 +17,26 @@ description = "Finite Field Linear Algebra Subroutines / Package" toolchain = {'version': '2016a', 'name': 'foss'} -sources = ['v2.2.0.zip'] -source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/fflas-ffpack/archive'] builddependencies = [ - ('Autoconf', '2.69', '', True), - ('Automake', '1.15', '', True), - ('libtool', '2.4.6', '', True), + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('libtool', '2.4.6'), ] dependencies = [ - ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), + ('GMP', '6.1.0'), ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " -configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' - -parallel = 4 - -unwanted_env_vars = {} -start_dir = '%(builddir)s/%(namelower)s-%(version)s/' +configopts = ('--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' + ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp') sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s.h'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/fflas-ffpack-config', 'include/fflas-ffpack/fflas-ffpack.h'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb index 56ed27ad72..fe391b51b5 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -17,29 +17,24 @@ description = "C++ library for arithmetic and algebraic computations" toolchain = {'version': '2016a', 'name': 'foss'} -sources = ['v4.0.1.zip'] -source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/givaro/archive'] builddependencies = [ - ('Autoconf', '2.69', '', True), - ('Automake', '1.15', '', True), - ('libtool', '2.4.6', '', True), + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('libtool', '2.4.6'), ] dependencies = [ - ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), + ('GMP', '6.1.0'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " configopts = "--with-gmp=$EBROOTGMP --enable-inline" -parallel = 4 - -unwanted_env_vars = {} -start_dir = '%(builddir)s/%(namelower)s-%(version)s/' - sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s-config.h'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/givaro-config', 'include/givaro-config.h'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index df00b437d1..4d00ba2bf0 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -17,30 +17,25 @@ description = "C++ library for exact, high-performance linear algebra" toolchain = {'version': '2016a', 'name': 'foss'} -sources = ['v1.4.0.zip'] -source_urls = ['https://github.com/%(namelower)s-team/%(namelower)s/archive'] +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/linbox/archive'] builddependencies = [ - ('Autoconf', '2.69', '', True), - ('Automake', '1.15', '', True), - ('libtool', '2.4.6', '', True), + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('libtool', '2.4.6'), ] dependencies = [ ('FFLAS-FFPACK', '2.2.0'), - ('Givaro', '4.0.1'), + ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " configopts = "--with-givaro=$EBROOTGIVARO --with-fflas-ffpack=$EBROOTFFLASMINFFPACK --enable-openmp" -parallel = 4 - -unwanted_env_vars = {} -start_dir = '%(builddir)s/%(namelower)s-%(version)s/' - sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s-config.h', 'lib/liblinbox.a'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/linbox-config', 'include/linbox/linbox-config.h', 'lib/liblinbox.a'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' -- GitLab From e0e12f2bcce4f121fbc00a1d3787a62d35c8766e Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 11:00:47 +0200 Subject: [PATCH 1082/2133] Use `Autotools` bundle instead of depending on each tool separately. --- .../f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb | 4 +--- easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb | 4 +--- easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb | 4 +--- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 282843bbc7..94cd13bd81 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -21,9 +21,7 @@ sources = ['v%(version)s.zip'] source_urls = ['https://github.com/linbox-team/fflas-ffpack/archive'] builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15'), - ('libtool', '2.4.6'), + ('Autotools', '20150215'), ] dependencies = [ ('GMP', '6.1.0'), diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb index fe391b51b5..4f0fbad866 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -21,9 +21,7 @@ sources = ['v%(version)s.zip'] source_urls = ['https://github.com/linbox-team/givaro/archive'] builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15'), - ('libtool', '2.4.6'), + ('Autotools', '20150215'), ] dependencies = [ ('GMP', '6.1.0'), diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index 4d00ba2bf0..640a495db8 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -21,9 +21,7 @@ sources = ['v%(version)s.zip'] source_urls = ['https://github.com/linbox-team/linbox/archive'] builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15'), - ('libtool', '2.4.6'), + ('Autotools', '20150215'), ] dependencies = [ ('FFLAS-FFPACK', '2.2.0'), -- GitLab From 236a8879552482ac855d3c1fbbf69c0089fb53d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 12:47:31 +0200 Subject: [PATCH 1083/2133] {lang}[intel/2016a] numba 0.24.0 w/ Python 2.7.11 & 3.5.1 --- .../llvmlite-0.9.0_fix-ffi-Makefile.patch | 29 +++++++++++++ .../numba-0.24.0-intel-2016a-Python-2.7.11.eb | 41 +++++++++++++++++++ .../numba-0.24.0-intel-2016a-Python-3.5.1.eb | 41 +++++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch create mode 100644 easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch new file mode 100644 index 0000000000..7a74cc0623 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch @@ -0,0 +1,29 @@ +don't use -static-libstdc++, causing problems like "glibc detected *** python: free(): invalid pointer" +cfr. https://github.com/numba/llvmlite/issues/93; +don't hardcode -lLLVMOProfileJIT, not required anymore +cfr. https://github.com/numba/llvmlite/issues/121 +author: Kenneth Hoste (HPC-UGent) +--- llvmlite-0.9.0/ffi/Makefile.linux.orig 2016-01-26 15:11:43.000000000 +0100 ++++ llvmlite-0.9.0/ffi/Makefile.linux 2016-03-30 12:41:34.102307156 +0200 +@@ -4,9 +4,7 @@ + # -flto and --exclude-libs allow us to remove those parts of LLVM we don't use + CXXFLAGS = $(LLVM_CXXFLAGS) -flto + LDFLAGS = $(LLVM_LDFLAGS) -flto -Wl,--exclude-libs=ALL +-# Need to add LLVMOProfileJIT by hand +-# see https://llvm.org/bugs/show_bug.cgi?id=25091 +-LIBS = $(LLVM_LIBS) -lLLVMOProfileJIT ++LIBS = $(LLVM_LIBS) + SRC = assembly.cpp bitcode.cpp core.cpp initfini.cpp module.cpp value.cpp \ + executionengine.cpp transforms.cpp passmanagers.cpp targets.cpp dylib.cpp \ + linker.cpp +@@ -15,9 +13,7 @@ + all: $(OUTPUT) + + $(OUTPUT): $(SRC) +- # static-libstdc++ avoids runtime dependencies on a +- # particular libstdc++ version. +- $(CXX) -static-libstdc++ -shared $(CXXFLAGS) $(SRC) -o $(OUTPUT) $(LDFLAGS) $(LIBS) ++ $(CXX) -shared $(CXXFLAGS) $(SRC) -o $(OUTPUT) $(LDFLAGS) $(LIBS) + + clean: + rm -rf test diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0ddf57da7d --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,41 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.24.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('LLVM', '3.7.1'), +] + +exts_list = [ + ('llvmlite', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..e0e36eeb79 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,41 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.24.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.1'), + ('LLVM', '3.7.1'), +] + +exts_list = [ + ('llvmlite', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' -- GitLab From a45e7509603391b8a42eb3f1d333cfd902bfefc9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 12:53:43 +0200 Subject: [PATCH 1084/2133] use right patch file for llvmlite --- .../n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb | 2 +- .../n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb index 0ddf57da7d..1ed8278597 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ dependencies = [ exts_list = [ ('llvmlite', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], - 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + 'patches': ['llvmlite-0.9.0_fix-ffi-Makefile.patch'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb index e0e36eeb79..c11e1bdb17 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb @@ -21,7 +21,7 @@ dependencies = [ exts_list = [ ('llvmlite', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], - 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + 'patches': ['llvmlite-0.9.0_fix-ffi-Makefile.patch'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], -- GitLab From ed68b28d57a933a0570d61aa9a8a7c8d40ebffb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 15:09:50 +0200 Subject: [PATCH 1085/2133] {system}[intel/2016a] file 5.25 + enhance sanity check --- .../easyconfigs/f/file/file-5.17-GCC-4.8.2.eb | 8 +++--- .../f/file/file-5.25-intel-2016a.eb | 25 +++++++++++++++++++ 2 files changed, 29 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb b/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb index 63db8305d5..bca5d69508 100644 --- a/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb @@ -12,14 +12,14 @@ homepage = 'http://www.darwinsys.com/file/' description = """The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains.""" +toolchain = {'name': 'GCC', 'version': '4.8.2'} + source_urls = ['ftp://ftp.astron.com/pub/file/'] sources = [SOURCE_TAR_GZ] -toolchain = {'name': 'GCC', 'version': '4.8.2'} - sanity_check_paths = { - 'files': ['bin/file'], - 'dirs': [] + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] } moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb b/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb new file mode 100644 index 0000000000..61f8e29397 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.25' + +homepage = 'http://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' -- GitLab From b92eaf3eac50f53ac2b688a53b821a92f797371a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 16:02:50 +0200 Subject: [PATCH 1086/2133] add easyconfig Java-1.8.0_77.eb --- easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb new file mode 100644 index 0000000000..fa48d66cd4 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_77' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 3df8b5b4e3a15448caa4ef4b023b13d4ee1f31a8 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 16:42:55 +0200 Subject: [PATCH 1087/2133] More style edits suggested by @boegel --- .../f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb | 8 ++++---- easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 94cd13bd81..da99f9d5b8 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -24,17 +24,17 @@ builddependencies = [ ('Autotools', '20150215'), ] dependencies = [ - ('GMP', '6.1.0'), + ('GMP', '6.1.0'), ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " -configopts = ('--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' - ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp') +configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' +configopts += ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' sanity_check_paths = { 'files': ['bin/fflas-ffpack-config', 'include/fflas-ffpack/fflas-ffpack.h'], - 'dirs': ['bin', 'include', 'lib'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb index 4f0fbad866..22ad6d392a 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -32,7 +32,7 @@ configopts = "--with-gmp=$EBROOTGMP --enable-inline" sanity_check_paths = { 'files': ['bin/givaro-config', 'include/givaro-config.h'], - 'dirs': ['bin', 'include', 'lib'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index 640a495db8..f0951b2b35 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ ('FFLAS-FFPACK', '2.2.0'), - ('Givaro', '4.0.1'), + ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " @@ -33,7 +33,7 @@ configopts = "--with-givaro=$EBROOTGIVARO --with-fflas-ffpack=$EBROOTFFLASMINFFP sanity_check_paths = { 'files': ['bin/linbox-config', 'include/linbox/linbox-config.h', 'lib/liblinbox.a'], - 'dirs': ['bin', 'include', 'lib'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' -- GitLab From 29197e7d989d93758bf1fb0ee678de15f6d0f592 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 16:47:02 +0200 Subject: [PATCH 1088/2133] add easyconfig NGS-1.2.3-intel-2016a.eb --- .../n/NGS/NGS-1.2.3-intel-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb new file mode 100644 index 0000000000..ed0e37836c --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.2.3' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Java', '1.8.0_77', '', True)] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' -- GitLab From 96afcdd6c2a927d1aaf5e9364af131a34c1e0162 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 22:22:41 +0200 Subject: [PATCH 1089/2133] Use `env` wherever `preconfigopts is used to set environmental variables. Without `env`, we are relying on a syntactical feature of Bourne-type shells; the `env` utility guarantees that the command-line will continue to work even with other shells (e.g., `tcsh`). --- .../easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb | 2 +- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 2 +- .../c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb | 2 +- .../Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb | 2 +- .../g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb | 2 +- .../easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb | 2 +- .../l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb | 2 +- .../l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb | 2 +- .../l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb | 2 +- .../l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb | 2 +- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb | 2 +- .../r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 2 +- .../v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 2 +- 105 files changed, 105 insertions(+), 105 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb index 20c30c8e62..6b5c1c6d52 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb @@ -31,7 +31,7 @@ dependencies = [ ('Boost', '1.58.0', versionsuffix), ] -preconfigopts = 'CPPFLAGS=-I$EBROOTSPARSEHASH/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTSPARSEHASH/include' sanity_check_paths = { 'files': ["bin/ABYSS", "bin/ABYSS-P"], diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb index 13ae69456f..916fcd7e48 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb index 5144a9afc9..97e5c8330b 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb index 3b963e0d7e..74f9dffca6 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb index f6a35a3dc0..efd5845e70 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 608c44a155..35e328daad 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -21,7 +21,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 17ecd5c190..6c55f76694 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -20,7 +20,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 61254037e0..6f9a318360 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -21,7 +21,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index 0007322f1f..ef80ad6bb5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -20,7 +20,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index e6f5a84c78..b8fa0b77ca 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -21,7 +21,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 8efdae380a..9ec199023d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -22,7 +22,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index b6d188a41b..63837a712c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -21,7 +21,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib # further, add the system library path in the rpath: this should 'harden' the # resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' prebuildopts = preconfigopts # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 40e3ccc1a8..cfcfe38d3d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib # further, add the system library path in the rpath: this should 'harden' the # resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' prebuildopts = preconfigopts # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index 501824903b..7b8dca8554 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -34,7 +34,7 @@ patches = [ 'cufflinks-1.x-ldflags.patch' ] -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb index d258537699..2ef873d2da 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb @@ -30,7 +30,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb index 645f94a833..25b9208f0e 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb @@ -32,7 +32,7 @@ dependencies = [ patches = ['Cufflinks_GCC-4.7.patch'] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb index 799e9172ba..9c37cd717b 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb @@ -34,7 +34,7 @@ dependencies = [ configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' configopts += ' --enable-intel64 ' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb index 991b5a4c8b..6751cec530 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb @@ -33,7 +33,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb index d0372e6f70..6ac33d77d4 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb index 2741497a4d..e368245a6c 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb index 0a4b6fa7ab..fe15c228e1 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb @@ -18,7 +18,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb index 43da714323..50fce481a6 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb @@ -19,7 +19,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb index 38e9d1ce03..8360322002 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb @@ -21,7 +21,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I${EBROOTEIGEN}/include' +preconfigopts = 'env CPPFLAGS=-I${EBROOTEIGEN}/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb index ffd2e3a7a6..4bcdb9773b 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb index 8f6396f5b8..7a4d21e078 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb index ee472aa372..4e298ad677 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb index ef2423ee53..4b6a000d12 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb index c0f9f1c6d8..9445690c85 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb index 384aa93ebf..1f66eb79d7 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb index 048ac9570d..8bc580fd82 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb index cc9e86a7d0..8c554c3e24 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb @@ -15,7 +15,7 @@ source_urls = ['http://www.prevanders.net'] dependencies = [('libelf', '0.8.13')] with_configure = True -preconfigopts = 'CFLAGS="-fPIC $CFLAGS" ' +preconfigopts = 'env CFLAGS="-fPIC $CFLAGS" ' configopts = "--enable-shared " # This is dirty but libdwarf cannot find it's own library in the build process... diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb index 6ac9b7d5c3..01c9c7b5d7 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb index a021127537..3c63b87470 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb index 11090d4b7a..437954d342 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb index f66aff6454..f0291301fc 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb index f03e2b9b60..e43c36e89c 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb index 33c34a406a..834a292992 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb index 7e3d115240..c3e51b6854 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb index ce77f3502c..8f259d339a 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb index e28f16cff6..5f22d77a36 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb index 2a5e9c8d05..ea05edcced 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb index 4281029487..1af83efe66 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb index 2ac72299c5..c0a23d9702 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb index 17ca0fce10..084f645370 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb index 8d2ea29b4c..f0751a5aa2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb index aea7099ee4..0ae01c0783 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb index 7216c9ca1c..39cc896311 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb index 6589e3ba7c..9a9c4dd1a0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb index a36ac06d74..245f1b2b64 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb index 4425696364..8e8d97c9af 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb index 8892dfc907..0e2ab07ab0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb index 7778abffff..c6a66c33d9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb index 157a15b6bb..f765c40888 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb index 6a9bcf9cdd..f13cdef958 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb index c5324cbad1..f5f1c5bd47 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb index b07b7634b9..5c9d193cce 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb index 853816b19b..596222a189 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb index 26cadb84b9..2ed024170c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb index 055d457da0..fd8d7fabf0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb index 6f9a153abf..35b967c78d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb index a4bce470a5..54fd902c42 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb index 8003f03676..12e011a8ed 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb index 15a227218e..18ebd1a1e7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb index 9236fd84d0..cdb4bf6f5a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb index 7435fb5029..0f7e912805 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb index a669b4f5be..27560c2cd2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb index a120dd4307..7ca975dc76 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb index 883868add2..b30099a775 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb index d828f262a5..712eabaeda 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb index 252a86c527..667201ed1a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb @@ -17,7 +17,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb index afd0f9f313..55974b6b67 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb index 46e89b5a96..68d5cccacb 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb @@ -19,7 +19,7 @@ builddependencies = [('binutils', '2.25')] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb index 05d8476935..d726fb4329 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb index 362df4f9bd..2745ab8557 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 763ccd9488..c856b61000 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb index d3b76459b6..b5740c5333 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb index 66ecad79ff..4bbd90baa7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb index 037141ab77..e33a1ae239 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb index fb2145ca85..675e8c38cd 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb index 8845b7c009..dbc0087596 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb index 793dcaf0af..cbb20595ce 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb index e594babc96..7ecfe2dc0a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb index ec5413615c..3c009a2b02 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb index 35af50be83..84703a1b03 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb @@ -20,7 +20,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb index 2db2e85326..fdf5247663 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb @@ -20,7 +20,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb index c9c675d484..fb685e3854 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb index 46eef59b19..68d21572c3 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb index 583b41298f..76b828f76d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb index 3e67c20449..9539bb724f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb index 2c8752c400..051672a6f2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb index de76493eec..fa9c58b0b8 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb index 0762f90f29..5b1cb39b0a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb index 5bcb7de6da..b08de1e59f 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb @@ -15,6 +15,6 @@ checksums = ['5dc58ed08fd3142c260b70fe297e127c'] builddependencies = [('Bison', '2.7')] # the hydra launcher start's before LD_LIBRARY_PATH is forwarded, so we provide this hint on where to find some libs -preconfigopts = 'LDFLAGS="-Wl,-rpath,$EBROOTICC/compiler/lib/intel64 $LDFLAGS"' +preconfigopts = 'env LDFLAGS="-Wl,-rpath,$EBROOTICC/compiler/lib/intel64 $LDFLAGS"' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb index 9cac08c076..3b2363cdf9 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb index c6b4f4fabd..b547dd35fb 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb index f3480b9f42..2be6013ea4 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb index a8664f7399..c2a88ca7fa 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index bcf88e98c9..a7caba4fae 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] configopts = ' --enable-unicode=ucs4 ' -preconfigopts = ' LDFLAGS="-lstdc++" ' +preconfigopts = 'env LDFLAGS="-lstdc++" ' # libffi build in python is still broken, see http://bugs.python.org/issue4130 patches = ['python-2.7_libffi-include-xmmintrin.patch'] diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb index 4f0b4fda48..05baffbd16 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb @@ -34,7 +34,7 @@ dependencies = [ ] # use external ZLIB -preconfigopts = 'ZLIB=$EBROOTZLIB ' +preconfigopts = 'env ZLIB=$EBROOTZLIB ' # architecture arch = 'linuxx8664icc' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index 59556c19fd..fc6f18713c 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -32,7 +32,7 @@ dependencies = [ ] # use external ZLIB -preconfigopts = 'ZLIB=$EBROOTZLIB ' +preconfigopts = 'env ZLIB=$EBROOTZLIB ' # architecture arch = 'linuxx8664icc' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb index 740784c812..795671412f 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb @@ -29,7 +29,7 @@ source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 327bd773eb..1e20cf23ec 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -29,7 +29,7 @@ source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb index 375b58016f..b7723d7af3 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb @@ -31,7 +31,7 @@ patches = ['ViennaRNA_ictce-pragma.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index 316c43df98..a66be3332b 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -32,7 +32,7 @@ patches = ['ViennaRNA_ictce-pragma.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index d9a8ebec92..664ec56172 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -31,7 +31,7 @@ patches = ['ViennaRNA-2.1.6_ictce.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', -- GitLab From 53eadadc575930bd0d5729d2239c3df8d70316fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 10:16:47 +0200 Subject: [PATCH 1090/2133] add easyconfig ncbi-vdb-2.5.8-1-intel-2016a.eb --- .../ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb new file mode 100644 index 0000000000..4197805f9e --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.5.8-1' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libxml2', '2.9.3'), + ('file', '5.25'), # provides libmagic + ('HDF5', '1.8.16'), + ('NGS', '1.2.3'), +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-vdb.%s' % SHLIB_EXT, 'lib64/libncbi-vdb.%s' % SHLIB_EXT), + ('lib/libncbi-wvdb.%s' % SHLIB_EXT, 'lib64/libncbi-wvdb.%s' % SHLIB_EXT), + ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a'), ('lib/libncbi-vdb.a', 'lib64/libncbi-vdb.a'), + ('lib/libncbi-wvdb.a', 'lib64/libncbi-wvdb.a')], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 0af7e722e8f3aa0b28b12b62424772425ad587bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 11:57:16 +0200 Subject: [PATCH 1091/2133] add easyconfig HISAT2-2.0.3-beta-intel-2016a.eb --- .../h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb new file mode 100644 index 0000000000..c08c2f92a9 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.3-beta' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +checksums = ['deb29e32e48045b2f970fb999946b411'] + +dependencies = [ + ('NGS', '1.2.3'), + ('ncbi-vdb', '2.5.8-1'), +] + +buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e0707b966ea23e736726488c4039e47960fc9bbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 12:22:31 +0200 Subject: [PATCH 1092/2133] modify easyconfig HISAT2-2.0.3-beta-intel-2016a.eb --- easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb index c08c2f92a9..ab9ee05adb 100644 --- a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncbi-vdb', '2.5.8-1'), ] -buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB" +buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] -- GitLab From 3120311ff75bf2561aa7b6cfee5f6f3456966d47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 12:47:43 +0200 Subject: [PATCH 1093/2133] {bio}[intel/2016a] NGS-Python 1.2.3 --- ...-Python-1.2.3-intel-2016a-Python-2.7.11.eb | 46 +++++++++++++++++++ .../NGS-Python-1.2.3_fix-prefix.patch | 13 ++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..94dc61a1a7 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'NGS-Python' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = ['NGS-Python-%(version)s_fix-prefix.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('NGS', version), + ('ncbi-vdb', '2.5.8-1'), +] + +preconfigopts = "cd ngs-python && " + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS " +configopts += "--with-ncbi-vdb-prefix=$EBROOTNCBIMINVDB" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-python' +installopts = "-C ngs-python" + +parallel = 1 + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python2.7/site-packages', 'share/examples-python'], +} + +sanity_check_commands = [('python', "-c 'import ngs'")] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch new file mode 100644 index 0000000000..60411ef541 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch @@ -0,0 +1,13 @@ +correctly specify prefix to install NGS-Python package to +author: Kenneth Hoste (HPC-UGent) +--- ngs-1.2.3/ngs-python/Makefile.python.orig 2016-03-31 12:34:54.124551782 +0200 ++++ ngs-1.2.3/ngs-python/Makefile.python 2016-03-31 12:37:01.515699327 +0200 +@@ -82,7 +82,7 @@ + + else + @ echo "Installing ngs package..." +- @ python setup.py -q install --user ++ @ python setup.py -q install --prefix $(INST_PYTHONDIR) + endif + + ifneq (, $(NGS_LIBDIR)) -- GitLab From af36210e03039665d0ac97e321a93585e12c0f2a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 12:11:56 +0100 Subject: [PATCH 1094/2133] Add explicit Python dep and rename to reflect that --- ...6.3-foss-2015b.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/r/RSeQC/{RSeQC-2.6.3-foss-2015b.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb} (98%) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb similarity index 98% rename from easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb rename to easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb index c33eb72992..4fc2b27c34 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb @@ -26,6 +26,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('R', '3.2.3'), + (python, pyver), ('numpy', '1.10.1', versionsuffix), ] -- GitLab From 311923d8aa7e6717ee43fa4414580f5e4cf9f605 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Thu, 31 Mar 2016 13:11:59 +0200 Subject: [PATCH 1095/2133] Use `env` wherever `preinstallopts is used to set environmental variables. --- .../p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb index 699eafed53..ab6efabad7 100644 --- a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ skipsteps = ['configure', 'build'] # redefine $HOME to specify installation prefix O_o -preinstallopts = "HOME=%(installdir)s make local &&" +preinstallopts = "env HOME=%(installdir)s make local &&" sanity_check_paths = { 'files': ['p4vasp/bin/p4v', 'p4vasp/lib/libODP.a', 'p4vasp/lib/libp4vasp.a'], -- GitLab From 2fb5725bfc6410ec511fdfa3183ba32d6161dd14 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 12:47:26 +0100 Subject: [PATCH 1096/2133] Fix Subread filename to match version --- ...bread-1.5.0p1-foss-2015b.eb => Subread-1.5.0-p1-foss-2015b.eb} | 0 ...bread-1.5.0p1-foss-2016a.eb => Subread-1.5.0-p1-foss-2016a.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/Subread/{Subread-1.5.0p1-foss-2015b.eb => Subread-1.5.0-p1-foss-2015b.eb} (100%) rename easybuild/easyconfigs/s/Subread/{Subread-1.5.0p1-foss-2016a.eb => Subread-1.5.0-p1-foss-2016a.eb} (100%) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb similarity index 100% rename from easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb rename to easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb similarity index 100% rename from easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb rename to easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb -- GitLab From 476581ab23b45a00bb8d8a5bd7e94fad980ed7be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 14:42:24 +0200 Subject: [PATCH 1097/2133] {tools}[intel/2016a] SCOOP 0.7.1.1 w/ Python 2.7.11 --- ...reenlet-0.4.9-intel-2016a-Python-2.7.11.eb | 30 ++++++++++++++++ .../libsodium/libsodium-1.0.6-intel-2016a.eb | 20 +++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb | 28 +++++++++++++++ ...Q-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb | 28 +++++++++++++++ ...SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb | 27 ++++++++++++++ .../util-linux-2.27.1-intel-2016a.eb | 33 +++++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb | 35 +++++++++++++++++++ 7 files changed, 201 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb create mode 100644 easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..c8fb9489f2 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Greenlet' +version = '0.4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'lib/python%(pyshortver)s/site-packages/greenlet.so'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb new file mode 100644 index 0000000000..8cd02bafe0 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.6' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb new file mode 100644 index 0000000000..7d687c23fb --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb new file mode 100644 index 0000000000..3b84d83e0c --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.2.0' +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..159567d24d --- /dev/null +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'SCOOP' +version = '0.7.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/scoop/' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('Greenlet', '0.4.9', versionsuffix), + ('PyZMQ', '15.2.0', versionsuffix + '-zmq4'), +] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb new file mode 100644 index 0000000000..fa18d8bb1d --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.27.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb new file mode 100644 index 0000000000..5eeb602737 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.1.4' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.27.1'), + ('libsodium', '1.0.6'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 227f6059951a467bb27eecc6f54afda8284eef69 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 14:48:42 +0200 Subject: [PATCH 1098/2133] {tools}[intel/2016a] SCOOP 0.7.1.1 w/ Python 3.5.1 --- ...Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb | 30 +++++++++++++++++++ ...MQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb | 28 +++++++++++++++++ .../SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb | 27 +++++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb create mode 100644 easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..26ba01fae4 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Greenlet' +version = '0.4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'lib/python%(pyshortver)s/site-packages/greenlet.so'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb new file mode 100644 index 0000000000..40389161f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.2.0' +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..8eac309517 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'SCOOP' +version = '0.7.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/scoop/' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('Greenlet', '0.4.9', versionsuffix), + ('PyZMQ', '15.2.0', versionsuffix + '-zmq4'), +] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 31497fc893cc738df14f49f87e60e92868d78313 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:27:31 +0200 Subject: [PATCH 1099/2133] fix sanity check for SCOOP --- .../s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb index 8eac309517..21ced6bf47 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb @@ -20,7 +20,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s-py%(pyshortver)s.egg'], 'dirs': [], } -- GitLab From 43ac5b3c6c64f1f65f61be34acdb65097e0a2ba1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:27:48 +0200 Subject: [PATCH 1100/2133] fix sanity check for SCOOP --- .../s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb index 159567d24d..eb5338d376 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb @@ -20,7 +20,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s-py%(pyshortver)s.egg'], 'dirs': [], } -- GitLab From 7f64fcc96a1ceb19d3f513d26b534cf3e9b36897 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:29:01 +0200 Subject: [PATCH 1101/2133] fix sanity check for Greenlet --- .../g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb index 26ba01fae4..0d6aba002e 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb @@ -22,7 +22,7 @@ patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] dependencies = [('Python', '3.5.1')] sanity_check_paths = { - 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'files': ['include/python%(pyshortver)sm/greenlet/greenlet.h', 'lib/python%(pyshortver)s/site-packages/greenlet.so'], 'dirs': [], } -- GitLab From eb191c8e53282e75113408cb024eb7063c4df418 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:32:28 +0200 Subject: [PATCH 1102/2133] really fix sanity check for Greenlet --- .../g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb index 0d6aba002e..26eafeafb1 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb @@ -22,9 +22,8 @@ patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] dependencies = [('Python', '3.5.1')] sanity_check_paths = { - 'files': ['include/python%(pyshortver)sm/greenlet/greenlet.h', - 'lib/python%(pyshortver)s/site-packages/greenlet.so'], - 'dirs': [], + 'files': ['include/python%(pyshortver)sm/greenlet/greenlet.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'devel' -- GitLab From a671d34e8d9ffcacff21ea8076804301a2e037cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 16:24:05 +0200 Subject: [PATCH 1103/2133] don't hardcode .so in OpenPGM easyconfig --- easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb index 7d687c23fb..d391dfe9fd 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb @@ -21,7 +21,7 @@ configopts = '--with-pic' start_dir = 'pgm' sanity_check_paths = { - 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], 'dirs': ['include'], } -- GitLab From 9771b3cbc1b41f77c6bc468f521a821c3b7c2b1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 18:00:48 +0200 Subject: [PATCH 1104/2133] add zlib as explicit dep in Tk easyconfigs --- easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb | 1 + .../easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb | 1 + 29 files changed, 50 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb index 9ebfd37f5f..ff05f0890c 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb @@ -14,6 +14,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb index 5f035ccbf2..e28fd7a2dc 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb index 16d5293528..cbf7bcb4b2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb index 1415c70f4e..06a1978ba4 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.0.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb index 5c0a6ccd92..4798d6cf81 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb index f65e1a0e09..71f6f47992 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb index 25372ffd8f..11e23b0c07 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb @@ -14,6 +14,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb index 3231de70b9..8b45a8770e 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.5'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb index a79397a5f8..60130e9216 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb @@ -13,7 +13,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb index 602101704a..878cfecf53 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb index 8ff29d34a2..ac0d5ff0bc 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb index c34f24fd99..0cf00324c8 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb index 31e024fb43..aaa247a658 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb index a292e06eb8..0a860475e3 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb index cd4da6afb6..890bfc8cfe 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb index 025f5e6476..6550c8a427 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb index d841e7bd84..4762abfa09 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb index a8245c8580..684f3bddb6 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb index 05eafdb2e8..f077e32cc2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb index da82b39576..9e3efc89f0 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb index c10f179e0c..89ecb3248a 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb index 7aa028f61c..5066a5847c 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb index b3fd0e9714..9419fc66d6 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb index 7feeb34477..60f899a584 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb index 4630a6a0f4..53f70e54d2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb index 6e8ab4a8ff..85504f8688 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb index 6b8350fb20..b7e6c77202 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb index 8ada7cd405..c0f2464a6d 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb @@ -24,6 +24,7 @@ builddependencies = [ dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), (libx11, libxver), ('libXt', '1.1.5'), ('libXext', '1.3.3'), diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb index 9f46cbbff7..9eede49210 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' -- GitLab From ac6e72b23b9ffd5642a04710023df6f515bcfd9a Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Thu, 31 Mar 2016 13:05:24 +0200 Subject: [PATCH 1105/2133] Use `env` wherever `prebuildopts is used to set environmental variables. --- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb | 2 +- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 2 +- .../m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb | 2 +- easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb | 2 +- easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb | 2 +- .../easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb | 2 +- 24 files changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 35e328daad..c3ffc6e24a 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 6c55f76694..418f81f5f1 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -21,7 +21,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 6f9a318360..2e680c9ce3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index ef80ad6bb5..b6d6a68fc6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -21,7 +21,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index b8fa0b77ca..6858b124b1 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 9ec199023d..5378940837 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -23,7 +23,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb index 24f4ba27ec..7278d23d80 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb @@ -23,7 +23,7 @@ start_dir = 'FDS_Compilation' skipsteps = ['configure', 'install'] buildininstalldir = True -prebuildopts = 'FFLAGS="$FFLAGS -fpp"' +prebuildopts = 'env FFLAGS="$FFLAGS -fpp"' modextrapaths = {'PATH': 'FDS_Compilation'} diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 2c72b2e6f5..17513817cb 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -59,7 +59,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl" # package-config files for os dependencies are in an os specific place #preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 1a69d47441..1e7fe202e8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -57,7 +57,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 9d960059a5..43f9b4f3d2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index 73b355c719..7fe4602968 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.so', 'lib/libOSMesa.so', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 72d772f450..3ddc492ea7 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 3ee16e73ea..3fe5e0bc06 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 0cd27019ac..442c4168fe 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index a724cb0c52..82b8af7b4f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -43,7 +43,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb index 70a2816d6b..7c42ab711a 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb index 0371483898..ed80bbbf2f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 7e87cc2bd4..663c38a45e 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 9c7388d824..3df094cda8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb index 3f8c039cdb..0df4d93ef0 100644 --- a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb +++ b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb @@ -15,7 +15,7 @@ sources = ['%(name)s.v%(version)s.tar.gz'] dependencies = [('zlib', '1.2.8')] -prebuildopts = 'CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' +prebuildopts = 'env CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' buildopts = 'CC="$CC" CXX="$CXX" F77="$F77" OPTFLAG_OPT="$CFLAGS"' files_to_copy = [(['bin/Minimac3'], 'bin')] diff --git a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb index e493e1ad48..5bb00f47ad 100644 --- a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb @@ -15,7 +15,7 @@ sources = ['%(name)s.v%(version)s.tar.gz'] dependencies = [('zlib', '1.2.8')] -prebuildopts = 'CFLAGS="$CFLAGS -wd751 -L$EBROOTZLIB/lib"' +prebuildopts = 'env CFLAGS="$CFLAGS -wd751 -L$EBROOTZLIB/lib"' buildopts = 'CC="$CC" CXX="$CXX" F77="$F77" OPTFLAG_OPT="$CFLAGS"' files_to_copy = [(['bin/Minimac3'], 'bin')] diff --git a/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb index 6d97e3c57a..ea8c9d49ac 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb @@ -38,7 +38,7 @@ builddependencies = [ ] # make has problems with utf8 -prebuildopts = "LANG=C " +prebuildopts = "env LANG=C " # motif ships a broken automake and libtool preconfigopts = "rm -f libtool install-sh missing depcomp config.guess config.sub && " diff --git a/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb b/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb index 36d9829a6d..4476f0d922 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb @@ -38,7 +38,7 @@ dependencies = [ ] # make has problems with utf8 -prebuildopts = "LANG=C " +prebuildopts = "env LANG=C " # motif ships a broken automake and libtool preconfigopts = "rm -f libtool install-sh missing depcomp config.guess config.sub && " diff --git a/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb b/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb index e8dddb718d..eb272b1b70 100644 --- a/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb @@ -21,7 +21,7 @@ files_to_copy = [ dependencies = [("ncurses", "5.9")] -prebuildopts = 'DESTDIR=%(installdir)s ' +prebuildopts = 'env DESTDIR=%(installdir)s ' sanity_check_paths = { 'files': ['bin/multitail'], -- GitLab From 27192c656261f1cfaea193869f34d7afdd7a4d81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 18:28:35 +0200 Subject: [PATCH 1106/2133] don't hard overwrite $CPATH in prebuildopts in Mesa easyconfig files --- .../easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 2 +- .../m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 17513817cb..3f895315b2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -59,7 +59,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl" # package-config files for os dependencies are in an os specific place #preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 1e7fe202e8..592c4a1182 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -57,7 +57,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 43f9b4f3d2..2bd0ff0f94 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index 7fe4602968..a22cf02d69 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.so', 'lib/libOSMesa.so', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 3ddc492ea7..171b47710c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 3fe5e0bc06..3282ad740c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 442c4168fe..c47447d239 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index 82b8af7b4f..57483e1d4f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -43,7 +43,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb index 7c42ab711a..fa63661948 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb index ed80bbbf2f..3d2d9d7e93 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 663c38a45e..ac83c1243a 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 3df094cda8..810e10d3bb 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', -- GitLab From 15c44bd734ed1e058bd228a60cd39beab076ee84 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 17:36:49 +0100 Subject: [PATCH 1107/2133] Style fixes for Subread --- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb | 3 +-- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb index 4fd69f051e..4df6c05b5e 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb @@ -14,12 +14,11 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -prebuildopts = 'cd src;' +startdir = 'src &&' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] - sanity_check_paths = { 'files': ['LICENSE', 'README.txt'], 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb index 1312eb0648..f0d2074639 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb @@ -14,12 +14,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -prebuildopts = 'cd src;' +start_dir = 'src &&' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] - sanity_check_paths = { 'files': ['LICENSE', 'README.txt'], 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] -- GitLab From 7fc04b6a034430ccc672bcc4fd954b7efd947704 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 18:53:50 +0200 Subject: [PATCH 1108/2133] use existing libxml2 easyblock, use %(pyver)s --- .../l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb index 0237c8f83b..0df5cbd957 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -1,7 +1,6 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -18,13 +17,9 @@ sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' -pythonver = '2.7.11' -pythonshortver = '.'.join(pythonver.split('.')[:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.11'), ] moduleclass = 'lib' -- GitLab From 0d6511bd1d3ba7dcafa852dc033de9aff737a052 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 18:05:34 +0100 Subject: [PATCH 1109/2133] Use new-style pyver and make sanity_check paths more specific --- .../r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb index 4fc2b27c34..a177369637 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb @@ -6,6 +6,7 @@ easyblock = 'PythonPackage' name = 'RSeQC' version = '2.6.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://rseqc.sourceforge.net/' description = """RSeQC provides a number of useful modules that can @@ -20,21 +21,17 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCE_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] -python = 'Python' -pyver = '2.7.10' -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ ('R', '3.2.3'), - (python, pyver), - ('numpy', '1.10.1', versionsuffix), + ('Python', '2.7.10'), ] runtest = "python setup.py test" sanity_check_paths = { - 'files': [], - 'dirs': ["bin", "lib"] + 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', + 'bin/split_paired_bam.py'], + 'dirs': ['lib'] } options = {'modulename': 'qcmodule'} -- GitLab From e991040ec94fd7b22bab054ff840999434975cd3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 19:06:51 +0200 Subject: [PATCH 1110/2133] consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs --- easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 2 +- 27 files changed, 27 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb index 31c851b3d9..8398e40d06 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.06'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb index 3010711346..b84761b602 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb index b62284872a..b4bb4c955d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb index c2e9e52426..5df1dda5a3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb index 90c7eb9017..f406268a87 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb index a79d153988..560606e07a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb index 372d1c346d..00b1eb05a8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb index 0fa72c61c9..a939e01023 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb index 89984f9baf..64c98aad33 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb index 52fc84e052..745063ebad 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb index e856a3fd43..a95ac9f601 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb index e2764250bf..134d181212 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb index ad83091b2b..25f9aacace 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb index e83b261924..5ca90d16a7 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb index 94ec58056b..4abe05a74f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb index 411820a76b..f58173164e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb index b66775c7a6..6a7048dcf1 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb index 42808d7b77..aa806c1087 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb index 3b4187acd1..304b160de5 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb index e8d95f1f54..46c1b375cb 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb index 68b3d851f6..0289e6c40e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '7.1.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb index d6a8a6e705..857e1b9ffc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb index f842bdc90a..a805266216 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb index 292da57c7e..6746b4b3a4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb index 519be6b6b3..4472772492 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb index 37a6837b2b..104ad6a3bd 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel-para', 'version': '2014.12'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 3f396ce26b..2bc8d9c022 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 2469d572c2a76c37fc5fb46c174678e48b6c85c8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 18:32:03 +0100 Subject: [PATCH 1111/2133] Add R suffix and fix sanity_check style --- ....10.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/r/RSeQC/{RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb} (89%) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb similarity index 89% rename from easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb index a177369637..58d91e5c53 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb @@ -7,6 +7,7 @@ easyblock = 'PythonPackage' name = 'RSeQC' version = '2.6.3' versionsuffix = '-Python-%(pyver)s' +versionsuffix += '-R-%(rver)s' homepage = 'http://rseqc.sourceforge.net/' description = """RSeQC provides a number of useful modules that can @@ -29,8 +30,7 @@ dependencies = [ runtest = "python setup.py test" sanity_check_paths = { - 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', - 'bin/split_paired_bam.py'], + 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', 'bin/split_paired_bam.py'], 'dirs': ['lib'] } -- GitLab From 6027c4ad03cf95b635270fa365e376735c183426 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 31 Mar 2016 13:47:56 -0500 Subject: [PATCH 1112/2133] Renamed Easyconfig file from gtool-0.7.5-linux_x86_64.eb to gtool-0.7.5_linux_x86_64.eb --- .../{gtool-0.7.5-linux_x86_64.eb => gtool-0.7.5_linux_x86_64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/gtool/{gtool-0.7.5-linux_x86_64.eb => gtool-0.7.5_linux_x86_64.eb} (100%) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb similarity index 100% rename from easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb rename to easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb -- GitLab From 61839ae12b5c739ec3e36b4ee971cd5e4da2d3f8 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 31 Mar 2016 14:18:10 -0500 Subject: [PATCH 1113/2133] Renamed Easyconfig file from shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb to shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb --- ...-linux_x86_64.eb => shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/shapeit/{shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb => shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb} (100%) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb rename to easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb -- GitLab From 4df62bb5e637f584d3ebffb56b2fd25d40a94b2b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 22:11:56 +0100 Subject: [PATCH 1114/2133] Use start_dir, not startdir for Subread --- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb index 4df6c05b5e..5192855877 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -startdir = 'src &&' +start_dir = 'src &&' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] -- GitLab From 6dfc122e053950dd94d862cb80be20a6797e4e12 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 22:35:29 +0100 Subject: [PATCH 1115/2133] Style cleanup for versionsuffix --- .../r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb index 58d91e5c53..d3a31d723c 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb @@ -6,8 +6,7 @@ easyblock = 'PythonPackage' name = 'RSeQC' version = '2.6.3' -versionsuffix = '-Python-%(pyver)s' -versionsuffix += '-R-%(rver)s' +versionsuffix = '-Python-%(pyver)s-R-%(rver)s' homepage = 'http://rseqc.sourceforge.net/' description = """RSeQC provides a number of useful modules that can -- GitLab From 37491f387e1a294625a7d71fa72bd06065326dba Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 1 Apr 2016 10:10:53 +0100 Subject: [PATCH 1116/2133] Fix start_dir --- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb | 2 +- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb index 5192855877..612c514399 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -start_dir = 'src &&' +start_dir = 'src' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb index f0d2074639..e525a015c8 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -start_dir = 'src &&' +start_dir = 'src' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] -- GitLab From 2e4f5401e6f65f307bbfced75186d8a0f43aba91 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 1 Apr 2016 11:00:50 -0500 Subject: [PATCH 1117/2133] Converting from 'Binaries' Easyblock to 'Tarball'. --- easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb index 6d1dad133e..bc3ceffb75 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Binary" +easyblock = "Tarball" name = 'gtool' version = '0.7.5' @@ -16,10 +16,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] sources = ['gtool_v%(version)s_x86_64.tgz'] -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " -install_cmd += "cp -a %(builddir)s/* %(installdir)s" - sanity_check_paths = { 'files': ["gtool", "LICENCE"], 'dirs': ["example"] -- GitLab From 163189467710769bcb3fc8785cfc0bc719ab8ac1 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 1 Apr 2016 11:07:32 -0500 Subject: [PATCH 1118/2133] Converting from 'Binaries' Easyblock to 'Tarball'. --- .../s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb index 7441bd58af..75a894a8c8 100644 --- a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb +++ b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Binary" +easyblock = "Tarball" name = 'shapeit' version = '2.r837.GLIBCv2.12' @@ -16,10 +16,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] sources = ['shapeit.v%(version)s.Linux.static.tgz'] -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "tar xzvf shapeit.v%(version)s.Linux.static.tgz && HOME=%(builddir)s && " -install_cmd += "cp -a %(builddir)s/* %(installdir)s" - sanity_check_paths = { 'files': ["bin/shapeit", "LICENCE"], 'dirs': ["example"] -- GitLab From 53eccaea377809af2cf69d87b18ef86843a6cf79 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 00:05:44 -0700 Subject: [PATCH 1119/2133] add easyconfig for LAME MP3 encoder --- .../l/LAME/LAME-3.99.5-foss-2015a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb new file mode 100644 index 0000000000..8ce773805a --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.99.5' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] + +dependencies = [('ncurses', '5.9')] + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.so'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From d07bf5d6c4a52bb9f65d5d8add7c300ce05b084d Mon Sep 17 00:00:00 2001 From: jgp Date: Sat, 2 Apr 2016 09:21:03 +0200 Subject: [PATCH 1120/2133] qt/486 for dummy toolchain --- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb new file mode 100644 index 0000000000..5c83d337b8 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -0,0 +1,15 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] +sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] + +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' +platform = 'linux-g++-64' + +moduleclass = 'devel' -- GitLab From 686957e8a63d021e32cc88fe2a96e09e131651e2 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 00:42:51 -0700 Subject: [PATCH 1121/2133] Pygments: fix homepage URL and description --- .../p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb | 4 ++-- .../p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb index 103bb38998..dc2b7c311c 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb @@ -3,8 +3,8 @@ easyblock = 'PythonPackage' name = 'Pygments' version = '2.0.2' -homepage = 'https://pypi.python.org/pypi/requests/2.6.0' -description = """Python http for humans""" +homepage = 'http://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb index 06251d7872..45a6907cbe 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -3,8 +3,8 @@ easyblock = 'PythonPackage' name = 'Pygments' version = '2.0.2' -homepage = 'https://pypi.python.org/pypi/requests/2.6.0' -description = """Python http for humans""" +homepage = 'http://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" toolchain = {'name': 'intel', 'version': '2015a'} -- GitLab From 9e88f53c5f8c8aa7540c08f84b5c96a77d720fd1 Mon Sep 17 00:00:00 2001 From: jgp Date: Sat, 2 Apr 2016 14:14:43 +0200 Subject: [PATCH 1122/2133] fixing line max length --- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb index 5c83d337b8..48c0604f80 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -9,7 +9,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] -configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' +configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' platform = 'linux-g++-64' moduleclass = 'devel' -- GitLab From 79a0eb02eaac79c6058e84ca25a9326a731c1970 Mon Sep 17 00:00:00 2001 From: jgp Date: Sat, 2 Apr 2016 14:29:52 +0200 Subject: [PATCH 1123/2133] adding -no-webkit for redhat builds --- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb index 48c0604f80..eacf9a8384 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -9,8 +9,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] -configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' -configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' +configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite -no-webkit' platform = 'linux-g++-64' moduleclass = 'devel' -- GitLab From 05a5e0a091c4191a14cac7cf03367874b7e20eae Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 20:53:00 -0700 Subject: [PATCH 1124/2133] add easyconfig for FLAC audio codec --- .../f/FLAC/FLAC-1.3.1-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb new file mode 100644 index 0000000000..72f2e62fcc --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.3.1' + +homepage = 'https://xiph.org/flac/' +description = """Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://downloads.xiph.org/releases/flac/'] + +sanity_check_paths = { + 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.so'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 28b3cea3b180c4b84704914f72a04857aaa980f5 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 21:08:27 -0700 Subject: [PATCH 1125/2133] add easyconfig for SoX (a Torch7 dependency) --- .../s/SoX/SoX-14.4.2-foss-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb new file mode 100644 index 0000000000..8228308a17 --- /dev/null +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'SoX' +version = '14.4.2' + +homepage = 'http://http://sox.sourceforge.net/' +description = """Sound eXchange, the Swiss Army knife of audio manipulation""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sourceforge.net/projects/sox/files/sox/%(version)s'] + +# These are not strictly mandatory but add flac and mp3 support to SoX +dependencies = [ + ('FLAC', '1.3.1'), + ('LAME', '3.99.5') +] + +sanity_check_paths = { + 'files': ['bin/sox', 'include/sox.h', 'lib/libsox.so'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From f42683f08dedc4e4c9980e0d116ef92403cbc805 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 Apr 2016 14:01:34 +0200 Subject: [PATCH 1126/2133] add easyconfig scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb --- ...-learn-0.17.1-intel-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..50d044b41c --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.17.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 65c8245f61d91344b4965fe2f35a153fee92de78 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 09:51:25 -0700 Subject: [PATCH 1127/2133] FLAC: use SHLIB_EXT rather than hardcoding .so --- easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb index 72f2e62fcc..509bb248c0 100644 --- a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://downloads.xiph.org/releases/flac/'] sanity_check_paths = { - 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.so'], + 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From dddf87803d9b9f070568fdefa07f7a2325437c23 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 09:54:55 -0700 Subject: [PATCH 1128/2133] Pygments: keep lines under 120 characters --- .../p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb | 3 ++- .../p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb index dc2b7c311c..bfe92c90eb 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb @@ -4,7 +4,8 @@ name = 'Pygments' version = '2.0.2' homepage = 'http://pygments.org/' -description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb index 45a6907cbe..3c3f9ad92d 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -4,7 +4,8 @@ name = 'Pygments' version = '2.0.2' homepage = 'http://pygments.org/' -description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" toolchain = {'name': 'intel', 'version': '2015a'} -- GitLab From c4186634b8ced2d454d53bad348efcde85150ff3 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 10:11:01 -0700 Subject: [PATCH 1129/2133] use SHLIB_EXT rather than .so --- easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb index 8ce773805a..a1da0d2c90 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb @@ -23,7 +23,7 @@ dependencies = [('ncurses', '5.9')] configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " sanity_check_paths = { - 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.so'], + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From 4505dcb1a2b2ccb0274b3e7dc991244ca376ec8e Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 10:20:21 -0700 Subject: [PATCH 1130/2133] SoX: use SHLIB_EXT rather than hardcoding .so --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb index 8228308a17..a71ba0bca6 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb @@ -24,7 +24,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/sox', 'include/sox.h', 'lib/libsox.so'], + 'files': ['bin/sox', 'include/sox.h', 'lib/libsox.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From a9481ca6559314b4ddf261a8030df7426a7e3251 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Apr 2016 10:57:07 +0200 Subject: [PATCH 1131/2133] add binutils as build dep for FLAC, also run tests --- easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb index 509bb248c0..76be36ffc6 100644 --- a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -17,6 +17,11 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://downloads.xiph.org/releases/flac/'] +# use of assembly routines requires a recent binutils +builddependencies = [('binutils', '2.25', '', ('GCC', '4.9.2'))] + +runtest = 'check' + sanity_check_paths = { 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.%s' % SHLIB_EXT], 'dirs': [], -- GitLab From e20aeaca67693bf5be63cd89953e98b9071642dd Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 10:03:55 -0500 Subject: [PATCH 1132/2133] Changed software name to uppercase (to match the official software name) --- easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb index bc3ceffb75..8b1697e3af 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -4,12 +4,12 @@ easyblock = "Tarball" -name = 'gtool' +name = 'GTOOL' version = '0.7.5' -versionsuffix = '_linux_x86_64' homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' -description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ +description = """ GTOOL is a program for transforming sets of genotype data for use with +the programs SNPTEST and IMPUTE. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From b9707b6147bbd5662971c333ff5a371bf7624483 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 10:13:29 -0500 Subject: [PATCH 1133/2133] Changed the name to SHAPEIT(uppercase), to match the official software name as well as added GLIBCv2.12 part as a versionsuffix --- .../shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb index 75a894a8c8..f2424bbea4 100644 --- a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb +++ b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb @@ -4,17 +4,18 @@ easyblock = "Tarball" -name = 'shapeit' -version = '2.r837.GLIBCv2.12' -versionsuffix = '_linux_x86_64' +name = 'SHAPEIT' +version = '2.r837' +versionsuffix = '.GLIBCv2.12' homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html' -description = """ SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. """ +description = """SHAPEIT is a fast and accurate method for estimation of +haplotypes (aka phasing) from genotype or sequencing data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] -sources = ['shapeit.v%(version)s.Linux.static.tgz'] +sources = ['shapeit.v%(version)s%(versionsuffix)s.Linux.static.tgz'] sanity_check_paths = { 'files': ["bin/shapeit", "LICENCE"], -- GitLab From acd19f1aef37e3efbdc6afb2aa3393f73d6a6e5e Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 10:57:50 -0500 Subject: [PATCH 1134/2133] Renamed the Easyconfig file --- .../g/{gtool/gtool-0.7.5_linux_x86_64.eb => GTOOL-0.7.5.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{gtool/gtool-0.7.5_linux_x86_64.eb => GTOOL-0.7.5.eb} (100%) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/GTOOL-0.7.5.eb similarity index 100% rename from easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb rename to easybuild/easyconfigs/g/GTOOL-0.7.5.eb -- GitLab From e11bdeb3d103cd2b7bfd0538ba674537d47fd89c Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:06:12 -0500 Subject: [PATCH 1135/2133] Renamed the Easyconfig file --- easybuild/easyconfigs/g/{ => gtool}/GTOOL-0.7.5.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{ => gtool}/GTOOL-0.7.5.eb (100%) diff --git a/easybuild/easyconfigs/g/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb similarity index 100% rename from easybuild/easyconfigs/g/GTOOL-0.7.5.eb rename to easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb -- GitLab From 4f08e6223419bd817ec1345de6bf367d0bdccac7 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:10:38 -0500 Subject: [PATCH 1136/2133] Renamed the Easyconfig file --- ...37.GLIBCv2.12_linux_x86_64.eb => SHAPEIT-2.r837.GLIBCv2.12.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/shapeit/{shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb => SHAPEIT-2.r837.GLIBCv2.12.eb} (100%) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb rename to easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb -- GitLab From d21d922f81159e6d35ae23969d32b56797458ac4 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:40:26 -0500 Subject: [PATCH 1137/2133] Renamed the directory from 'gtool' to 'GTOOL' --- easybuild/easyconfigs/g/{gtool => GTOOL}/GTOOL-0.7.5.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{gtool => GTOOL}/GTOOL-0.7.5.eb (100%) diff --git a/easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb similarity index 100% rename from easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb rename to easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb -- GitLab From 03d799432b512447956e6f35f56370817d04b817 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:42:44 -0500 Subject: [PATCH 1138/2133] Renamed the directory from 'shapeit' to 'SHAPEIT' --- .../s/{shapeit => SHAPEIT}/SHAPEIT-2.r837.GLIBCv2.12.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/{shapeit => SHAPEIT}/SHAPEIT-2.r837.GLIBCv2.12.eb (100%) diff --git a/easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb rename to easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb -- GitLab From 64c78cbac01a04a0771040e2cf3ccfa69aa16c14 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 12:44:17 -0500 Subject: [PATCH 1139/2133] Adding 'modextrapaths' parameter to include the root directory in the PATH variable --- easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb index 8b1697e3af..69e22e6cab 100644 --- a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb +++ b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb @@ -16,6 +16,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] sources = ['gtool_v%(version)s_x86_64.tgz'] +modextrapaths = {'PATH': ''} + sanity_check_paths = { 'files': ["gtool", "LICENCE"], 'dirs': ["example"] -- GitLab From 6057e0642b6b7e61c5e68a69c1709d485e17a6c9 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:44:50 -0400 Subject: [PATCH 1140/2133] libxcb-1.11.1 easyconfig for foss-2016a --- .../l/libxcb/libxcb-1.11.1-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb new file mode 100644 index 0000000000..b12be025db --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('pkg-config', '0.29'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), + ('xcb-proto', '1.11', '', True), + ('libpthread-stubs', '0.3'), + +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 3c13fbcd743487e7e4fd7ecc7faa633e07d827d2 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:53:45 -0400 Subject: [PATCH 1141/2133] xproto-7.0.28 easyconfig for foss-2016a --- .../x/xproto/xproto-7.0.28-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb new file mode 100644 index 0000000000..3e787177f0 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 76dbf608ede3b5ec4fc28fb94e93b9ce633e50ad Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:56:17 -0400 Subject: [PATCH 1142/2133] libpthread-stubs-0.3 easyconfig for foss-2016a --- .../libpthread-stubs-0.3-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb new file mode 100644 index 0000000000..fcb767cfdb --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From d9ec15efee75c4133c9b4476d5eca278ee28bfb5 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:59:14 -0400 Subject: [PATCH 1143/2133] libXau-1.0.8 easyconfig for foss-2016a --- .../l/libXau/libXau-1.0.8-foss-2016a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..b6f23c9a07 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('pkg-config', '0.29'), +] + +dependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 0ee9e5f553a8df087774e50b56875a009b0c96b9 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 16:00:39 -0400 Subject: [PATCH 1144/2133] libXdmcp-1.1.2 easyconfig for foss-2016a --- .../l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..9e90ec9775 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('pkg-config', '0.29') +] + +dependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 76339fa83cdd28958c5dd3e44282321dffaa260c Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 16:01:47 -0400 Subject: [PATCH 1145/2133] pkg-config-0.29 easyconfig for foss-2016a --- .../pkg-config/pkg-config-0.29-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb new file mode 100644 index 0000000000..2796515752 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 508d9ac2b09b1bffc86709993300f41fee471478 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 5 Apr 2016 15:23:39 -0500 Subject: [PATCH 1146/2133] Changing the file name and the folder name containing it. --- .../MRIcron-06_22_15.eb} | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/m/{mricron/mricron-062215-linux_x86_64.eb => MRIcron/MRIcron-06_22_15.eb} (60%) diff --git a/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb similarity index 60% rename from easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb rename to easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index a7fb738545..097d50c5b6 100644 --- a/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -4,20 +4,22 @@ easyblock = "Binary" -name = 'mricron' -version = '062215' -versionsuffix = '_linux_x86_64' +name = 'MRIcron' +version = '06_22_15' homepage = 'http://www.mccauslandcenter.sc.edu/mricro/mricron/' -description = """ MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering. """ +description = """ MRIcron allows viewing of medical images. It +includes tools to complement SPM and FSL. Native format is NIFTI +but includes a conversion program (see dcm2nii) for converting DICOM images. +Features layers, ROIs, and volume rendering. """ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] sources = ['lx.zip'] -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "unzip lx.zip && HOME=%(builddir)s && " +# Following commands are used to unzip the files and copy the content to install directory +install_cmd = "unzip lx.zip &&" install_cmd += "cp -a %(builddir)s/* %(installdir)s" sanity_check_paths = { -- GitLab From 030b70a2a075c3b29af339d5210a6569e2d14def Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 6 Apr 2016 11:33:39 +0200 Subject: [PATCH 1147/2133] {vis}[intel-2016a] Pillow 3.2.0 (REVIEW) --- .../Pillow-3.2.0-intel-2016a-Python-2.7.11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..bc1187561f --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '3.2.0' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.11' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('libjpeg-turbo', '1.4.2'), + ('zlib', '1.2.8'), + ('LibTIFF', '4.0.6'), + ('freetype', '2.6.2'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' -- GitLab From e53d9aea980e8a51a012176937fea91cb3cf0255 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 6 Apr 2016 15:41:33 +0200 Subject: [PATCH 1148/2133] Libxslt-1.1.28 for foss-2016a --- .../l/libxslt/libxslt-1.1.28-foss-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb new file mode 100644 index 0000000000..63c3fa7e2d --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), +] + +moduleclass = 'lib' \ No newline at end of file -- GitLab From 2f2d57ae191b8c71b2dd9015965a617f608ddb30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Apr 2016 18:01:14 +0200 Subject: [PATCH 1149/2133] consistently use XORG_LIB_SOURCE constant --- easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb | 2 +- .../l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb | 2 +- .../l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb | 2 +- 34 files changed, 34 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb index bb3839e6a6..ff2702cd71 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.4'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb index 407ce4845d..b63222e9d8 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb index 0fb685525a..1bd7511944 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb index d28d3a6e76..2f28c257c5 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb index 0038b41047..bd5ecc8bcd 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb index a15bba69ef..30a7625681 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.8'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb index 580ce7f28a..a8d0c1fc55 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb index 2a2391d847..c3a28914e6 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb index 641ea44476..503006a89b 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb index b34ef0db33..1bab5701fe 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb index 3522b7de99..3a034255d6 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X11 client-side library""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] pythonversion = '-Python-2.7.8' builddependencies = [ diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb index 8694ab5ad2..96ec24e1fc 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb index 2e88286d07..934e207665 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb index f1bc2bfb36..bd0254a335 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb index 22bf8016cf..afa4166c18 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.26'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb index 408dc4aede..1accebb77f 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb index 9304d0fc79..dafc84e463 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb index 243dbd6f22..8003dc09d5 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb index 735a0391ab..efb7a8e46c 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.26'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb index c12e65e6e8..20f0072ce3 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb index 9233da540e..395760652d 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb index cc513f2315..599620e265 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb index 79416debdd..0912eb0311 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb index 93de3908f0..1639916a6f 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb index 24fc239d5e..6ec7ecf45d 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb index 1eeae06c66..b642948a1b 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libX11', '1.6.1'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb index 9ce9ef676f..388076a498 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb index f5d31320dd..e0c74eaaa7 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb index fea0b330b9..59f66ccd07 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb index c076690abe..3b9f118dec 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb index 23544e2ee3..7c257d0a2f 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb index 93ffb79a95..3751e0a221 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 3e89327b58..2b4eff3bde 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb index 6f79135801..4646632358 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libSM', '1.2.1'), -- GitLab From 1e6a202f0f1415b190d434c94c74464ddccbfc9f Mon Sep 17 00:00:00 2001 From: jrbosch Date: Wed, 6 Apr 2016 12:45:43 -0400 Subject: [PATCH 1150/2133] Update libXdmcp-1.1.2-foss-2016a.eb --- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb index bbe5e2fcc0..dcd4997f9b 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] builddependencies = [ - ('pkg-config', '0.29') + ('pkg-config', '0.29'), ('xproto', '7.0.28'), ] -- GitLab From b9dfd342150f7b28e69e6c96746ab2f2537a5b8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Apr 2016 19:12:21 +0200 Subject: [PATCH 1151/2133] consistently use XORG_*_SOURCE constants --- .../easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb | 2 +- .../easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb | 2 +- easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb | 2 +- .../easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb | 2 +- .../easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb | 2 +- easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb | 2 +- .../easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb | 2 +- 95 files changed, 95 insertions(+), 95 deletions(-) diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb index 88fa55c14d..1deb262347 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb index 80e72c01e5..574d6d02de 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb index c52db08f49..15154dbbea 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb index 06e3d71fba..4df2be2be9 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb index 5d430a5301..8b11789fca 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb index 3fe841d973..fd373c373a 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb index 33951308af..f26ed2df7a 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb index 0719ec51f4..8e577e277b 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb index 6c5ce99387..47f2d3c961 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb index 5c83a62b97..062cfdbcf8 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb index 5b1c1517ba..9c00b32506 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb index f9c5e14a8e..4282ea773f 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb index 06b846c04c..037260e492 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb index 42dc60dd5e..aebc924b14 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb index 8b99a901c9..cb35b32223 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb index 6ccc91bb75..c92de947ba 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb index 2566876879..1f4bad7112 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb index 46b9bdb324..8a7667c002 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb index 4eb87a66ef..b28bfab5ef 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb index a1f9a0b9d2..191cd512ed 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb index c26a1ac08a..5dd250fddb 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb index 3297e8dea0..ce9480d3aa 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb index 1e1be175b1..475b25485e 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb index 56a7e864e0..7ae3e0efff 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb index 75a9c42cf7..9931bbca58 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb index 804a25ce18..19917b0ef7 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb index e307d5deb4..eb95b2f34a 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb index 0437a042db..d652aba387 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb index be4171cde7..cad6b846e6 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb index 1a5db1eefa..b26cb20222 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb index 66fc05b6d4..6a557da522 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb index 21d5d376d5..512fcad715 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb index 83bc32fc03..00ad73c8ec 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb index 323816dd0b..f40968ca7a 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb index 7482053f6f..30967e9fe4 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb index e54e5f74c9..7e3ad5f572 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb index 3790a57f15..ee1d8ab5ad 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb index 664996727e..48cbc77814 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb index 31cb837d0f..2393fe61dc 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb index 2d16cb0b13..295d7b8f94 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb index bca5ddd7ca..86f8eb23de 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb index 050b2bda55..a2add0de30 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb index 62923f260f..13dbd2eb08 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb index d692faf393..9a5a48c480 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb index 29d6a6987a..e5d229774c 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index fc57003279..ce3e6d964e 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb index dacbb816a7..3f72d96af4 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb index db2b6fad94..83069f50b6 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb index ae82f50061..bd1a547705 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb index 0e5bfb142c..38e0bbe3cc 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb index cb2cc76a3b..87f1456d12 100644 --- a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = "Xrandr protocol and ancillary headers" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb index 278cc7bbbf..563fbfcbf2 100644 --- a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb @@ -9,7 +9,7 @@ description = "Xrandr protocol and ancillary headers" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb index 3119cd29b7..a354245bf6 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb index 48199d0511..9f19fc4dfc 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb index c363620cb6..c2eb005cc6 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb index 9d7f0c2a91..c0cb8f56f1 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb index 87042e0e65..59a4298687 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb index b16c201ac1..20a477feb6 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb index 37b516e535..c3ac221b11 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb index 93be023dae..9e6fad7729 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb index 7edd725bb8..6dfd84dd09 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb index 38732656c2..23a639e880 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb index f7d2e42a4b..c294b4f211 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb index 7c6cc82582..4cb4a74155 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb index 222c1cb8a9..c125fc2989 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb index f8d28a6517..658fd35838 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb index 7e5dd65346..a2085627e9 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb index e73a8f9515..6edad56122 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb index 0f74426405..bd75285755 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb index bceed61321..3876294b7f 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb index 9bc6335cdf..53735a84e4 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb index 1800fbf094..beda89b5c6 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb index eb7322e162..82aff3127f 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb index 6156597f8b..4a87699495 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb index 96189817b0..91c591e727 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb index d2b93b5852..c2246d9293 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb index af65fa2a9d..08ca1e412b 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb index b0ee431324..883ec594b7 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb index 797b75e5e7..e582ff06dd 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb index e96e89759a..7e6eb92e97 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb index d198aa80e4..892ed9f5bd 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb index f6c2e0c627..572e38002b 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb index 241268e4a6..6eb06bc7d4 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb index ab202e5075..5054d70df3 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb index e0f4abf144..ddf767b605 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb index 884e64e8dd..06bdb8bc21 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb index 8f17ba5d45..7d12c7f86a 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb index bdb6d9e8c7..76cc9f4a7a 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb index 74b305ce8c..1caa382ace 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb index 4ec0e6221a..4d66b00ecb 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb index f9bd7118c8..a0292fbf8e 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb index 3e787177f0..2a47f2490b 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb index 2591e436f9..8dab7213fb 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb index d3de936da4..6722798efb 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb index 1d3df458a7..9de353786c 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', -- GitLab From c025b26559a8de6353a6e2f64b8a16413b2f1900 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 13:06:53 -0500 Subject: [PATCH 1152/2133] Adhering to the 120 characters per line standard for the description variable --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 097d50c5b6..64d81e0783 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Binary" +easyblock = "PackedBinary" name = 'MRIcron' version = '06_22_15' @@ -19,8 +19,8 @@ source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] sources = ['lx.zip'] # Following commands are used to unzip the files and copy the content to install directory -install_cmd = "unzip lx.zip &&" -install_cmd += "cp -a %(builddir)s/* %(installdir)s" +#install_cmd = "unzip lx.zip &&" +#install_cmd += "cp -a %(builddir)s/* %(installdir)s" sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], -- GitLab From 8be21fa9d9b4d44c566d83c7b8e48cf187d7f4f5 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 13:31:56 -0500 Subject: [PATCH 1153/2133] Removing source_url and adding a comment detailing how to download zip'd files manually from the website --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 64d81e0783..a984af8d3b 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -15,12 +15,10 @@ Features layers, ROIs, and volume rendering. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] -sources = ['lx.zip'] - -# Following commands are used to unzip the files and copy the content to install directory -#install_cmd = "unzip lx.zip &&" -#install_cmd += "cp -a %(builddir)s/* %(installdir)s" +# Automatic Download doesn't work for this software sice you need to accept their +# license, so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ +# and place it in a folder where Easybuild can see it. +sources = [SOURCE.ZIP] sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], -- GitLab From d45ee07c957fb86c3a3794ee2ee8f085ccbf68ec Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 13:57:55 -0500 Subject: [PATCH 1154/2133] Corrected some spell errors --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index a984af8d3b..4c0655294e 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -15,8 +15,8 @@ Features layers, ROIs, and volume rendering. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -# Automatic Download doesn't work for this software sice you need to accept their -# license, so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ +# Automatic Download doesn't work for this software as you need to accept their license, +# so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ # and place it in a folder where Easybuild can see it. sources = [SOURCE.ZIP] -- GitLab From 4c0b59ae9650f557c12569e0085e22f6ec14e1e2 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 14:34:11 -0500 Subject: [PATCH 1155/2133] Adding the source file to the Easyconfig file --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 4c0655294e..daea20393e 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Automatic Download doesn't work for this software as you need to accept their license, # so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ # and place it in a folder where Easybuild can see it. -sources = [SOURCE.ZIP] +sources = ['lx.zip'] sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], -- GitLab From d97b12f986e603dac7e20078dd6db73d79ac709d Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 15:06:42 -0500 Subject: [PATCH 1156/2133] Adding the md5 checksum value for the source --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index daea20393e..69196eb784 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -20,6 +20,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # and place it in a folder where Easybuild can see it. sources = ['lx.zip'] +checksums = ['a2d8b1c053384220953f6b670d0fd4df'] + sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], 'dirs': ["example", "lut", "templates"] -- GitLab From 29f2c6b09b5e6b7d871d0da26aab6597c5c52163 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 18:05:56 -0400 Subject: [PATCH 1157/2133] libXrandr-1.5.0 easyconfig for foss-2016a --- .../l/libXrandr/libXrandr-1.5.0-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..b6614e79e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXrandr' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Resize, Rotate and Reflection extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('randrproto', '1.5.0'), + ('renderproto', '0.11'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrandr.%s' % SHLIB_EXT, 'lib/libXrandr.a'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From a7a61c9d0568c5d4f59df08abb5aae85f3def8f4 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 18:08:32 -0400 Subject: [PATCH 1158/2133] randrproto-1.5.0 easyconfig for foss-2016a --- .../randrproto/randrproto-1.5.0-foss-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..d480848616 --- /dev/null +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'randrproto' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrandr protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 44cf756826c8e52b397447b030e627360e7c5bdf Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:38:57 -0400 Subject: [PATCH 1159/2133] libXi-1.7.6 for foss-2016a toolchain --- .../l/libXi/libXi-1.7.6-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb new file mode 100644 index 0000000000..bd92d68db6 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' +name = 'libXi' +version = '1.7.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('inputproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From a5dd9bfb4552cf157384fbccf9b9538e771453f7 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:39:56 -0400 Subject: [PATCH 1160/2133] libXfixes-5.0.1 for foss-2016a toolchain --- .../l/libXfixes/libXfixes-5.0.1-foss-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb new file mode 100644 index 0000000000..aa11951f76 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From fd70a1bdd1a84da2729aa341abe5e8262512e767 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:41:19 -0400 Subject: [PATCH 1161/2133] xorg-macros-1.19.0 for foss-2016a toolchain --- .../xorg-macros-1.19.0-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 285276c385c90279c966915beba4bb24fbc1aae1 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:44:31 -0400 Subject: [PATCH 1162/2133] fixesproto-5.0 for foss-2016a toolchain --- .../f/fixesproto/fixesproto-5.0-foss-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb new file mode 100644 index 0000000000..b04efa3b3a --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From 03e17713072089963a0bceb1a92e343f650ef664 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Thu, 7 Apr 2016 00:21:05 -0400 Subject: [PATCH 1163/2133] libGLU for foss-2016a toolchain --- .../l/libGLU/libGLU-9.0.0-foss-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb new file mode 100644 index 0000000000..087bd589cb --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '11.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 6db2fe08a4d22e3e21471bca3ae1eb74e3bc437d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 7 Apr 2016 09:37:09 +0200 Subject: [PATCH 1164/2133] use of %(pyver)s --- .../p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb index bc1187561f..e08e25c6bb 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'Pillow' version = '3.2.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. @@ -12,12 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = 'Python' -pyver = '2.7.11' -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.11'), ('libjpeg-turbo', '1.4.2'), ('zlib', '1.2.8'), ('LibTIFF', '4.0.6'), -- GitLab From f5cca74c3cae5b9e3e51677a37cc33fd0e25993d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:02:48 +0200 Subject: [PATCH 1165/2133] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig GLib-2.47.5-foss-2016a.eb, modify easyconfig freetype-2.6.2-foss-2016a.eb, modify easyconfig pixman-0.34.0-foss-2016a.eb, modify easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig libX11-1.6.3-foss-2016a.eb, add easyconfig libxcb-1.11.1-foss-2016a.eb, add easyconfig libXrender-0.9.9-foss-2016a.eb, add easyconfig libXext-1.3.3-foss-2016a.eb, add easyconfig renderproto-0.11-foss-2016a.eb, add easyconfig xextproto-7.3.0-foss-2016a.eb, add easyconfig xproto-7.0.28-foss-2016a.eb, add easyconfig libffi-3.2.1-foss-2016a.eb, add easyconfig gettext-0.19.7-foss-2016a.eb, add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb, add easyconfig PCRE-8.38-foss-2016a.eb, add easyconfig inputproto-2.3.1-foss-2016a.eb, add easyconfig libpthread-stubs-0.3-foss-2016a.eb, add easyconfig kbproto-1.0.7-foss-2016a.eb, add easyconfig xtrans-1.3.5-foss-2016a.eb, add easyconfig xorg-macros-1.19.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 30 ++++++++++++++- .../g/GLib/GLib-2.47.5-foss-2016a.eb | 33 +++++++++++++++++ .../g/gettext/gettext-0.19.7-foss-2016a.eb | 23 ++++++++++++ .../inputproto/inputproto-2.3.1-foss-2016a.eb | 19 ++++++++++ .../k/kbproto/kbproto-1.0.7-foss-2016a.eb | 19 ++++++++++ .../l/libX11/libX11-1.6.3-foss-2016a.eb | 37 +++++++++++++++++++ .../l/libXext/libXext-1.3.3-foss-2016a.eb | 34 +++++++++++++++++ .../libXrender/libXrender-0.9.9-foss-2016a.eb | 32 ++++++++++++++++ .../l/libffi/libffi-3.2.1-foss-2016a.eb | 23 ++++++++++++ .../libpthread-stubs-0.3-foss-2016a.eb | 20 ++++++++++ .../l/libxcb/libxcb-1.11.1-foss-2016a.eb | 33 +++++++++++++++++ .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++ .../p/PCRE/PCRE-8.38-foss-2016a.eb | 20 ++++++++++ .../renderproto-0.11-foss-2016a.eb | 20 ++++++++++ .../x/xextproto/xextproto-7.3.0-foss-2016a.eb | 24 ++++++++++++ .../xorg-macros-1.19.0-foss-2016a.eb | 22 +++++++++++ .../x/xproto/xproto-7.0.28-foss-2016a.eb | 23 ++++++++++++ .../x/xtrans/xtrans-1.3.5-foss-2016a.eb | 22 +++++++++++ 18 files changed, 462 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index 4afe79dcce..ab395e2001 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = "cairo" +name = 'cairo' version = '1.14.6' homepage = 'http://cairographics.org' @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_XZ] +glibver = '2.47.5' + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), @@ -21,9 +23,33 @@ dependencies = [ ('pixman', '0.34.0'), ('fontconfig', '2.11.94'), ('expat', '2.1.0'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), +] + +builddependencies = [ + ('renderproto', '0.11'), + ('libXext', '1.3.3'), + ('xextproto', '7.3.0'), + ('libX11', '1.6.3'), + ('xproto', '7.0.28'), + ('libxcb', '1.11.1') ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -configopts = "--enable-symbol-lookup=no" +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb new file mode 100644 index 0000000000..fb0fcbff8c --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb new file mode 100644 index 0000000000..168b2490e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb new file mode 100644 index 0000000000..be4171cde7 --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb new file mode 100644 index 0000000000..bca5ddd7ca --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb new file mode 100644 index 0000000000..7bbdcf2dc4 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000..b53c0d9a18 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb new file mode 100644 index 0000000000..12b8caece2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), + ('libX11', '1.6.3'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28') +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb new file mode 100644 index 0000000000..c7c638b6fa --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb new file mode 100644 index 0000000000..fcb767cfdb --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb new file mode 100644 index 0000000000..d818b47843 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb new file mode 100644 index 0000000000..1fe2fcb26c --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.38' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb new file mode 100644 index 0000000000..48199d0511 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb new file mode 100644 index 0000000000..9bc6335cdf --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb new file mode 100644 index 0000000000..3e787177f0 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb new file mode 100644 index 0000000000..1d32cb1ae6 --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From f73937858cb1ce3028affcc9f53f79f287f9a3af Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:21:22 +0200 Subject: [PATCH 1166/2133] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig libXau-1.0.8-foss-2016a.eb, add easyconfig libXdmcp-1.1.2-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 4 ++- .../l/libXau/libXau-1.0.8-foss-2016a.eb | 25 +++++++++++++++++++ .../l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 25 +++++++++++++++++++ 3 files changed, 53 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index ab395e2001..5cf49b60d8 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -25,9 +25,11 @@ dependencies = [ ('expat', '2.1.0'), ('GLib', glibver), ('libX11', '1.6.3'), + ('libXau', '1.0.8'), ('libxcb', '1.11.1'), - ('libXrender', '0.9.9'), + ('libXdmcp', '1.1.2'), ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..8694ab5ad2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c12e65e6e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 3f8d502c4b072f4e045c7ed18628e219a304cd24 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:46:56 +0200 Subject: [PATCH 1167/2133] modify easyconfig Blitz++-0.10-foss-2016a.eb, add easyconfig Blitz++-0.10-goolf-1.5.16.eb --- .../b/Blitz++/Blitz++-0.10-foss-2016a.eb | 9 ++------- .../b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb | 20 +++++++++++++++++++ 2 files changed, 22 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb index 03886c8db9..f91bad5dd3 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb @@ -10,16 +10,11 @@ description = """Blitz++ is a (LGPLv3+) licensed meta-template library for array toolchain = {'name': 'foss', 'version': '2016a'} sources = ['blitz-%(version)s.tar.gz'] -source_urls = ['https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', - 'download'] +source_urls = [('https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', 'download')] sanity_check_paths = { 'files': ['lib/libblitz.a'], - 'dirs': ['include/blitz/array', - 'include/blitz/gnu', - 'include/blitz/meta', - 'include/random', - 'lib/pkgconfig'], + 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb new file mode 100644 index 0000000000..f75014e6f2 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'Blitz++' +version = '0.10' + +homepage = 'http://blitz.sourceforge.net/' +description = """Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ + with a speed comparable to Fortran implementations, while preserving an object-oriented interface""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +sources = ['blitz-%(version)s.tar.gz'] +source_urls = [('https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', 'download')] + +sanity_check_paths = { + 'files': ['lib/libblitz.a'], + 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 9f9d4d40dcff4c9109de8ce909ca0e950a386531 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:53:06 +0200 Subject: [PATCH 1168/2133] modify easyconfig Saxon-HE-9.7.0.4-Java-1.7.0_79.eb --- .../easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb index eed56a9078..d38576ab53 100644 --- a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -2,6 +2,7 @@ easyblock = 'Tarball' name = 'Saxon-HE' version = '9.7.0.4' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://saxon.sourceforge.net' description = """Open Source SAXON XSLT processor developed by Saxonica Limited.""" @@ -9,11 +10,8 @@ description = """Open Source SAXON XSLT processor developed by Saxonica Limited. toolchain = {'name': 'dummy', 'version': ''} sources = ['SaxonHE%sJ.zip' % version.replace(".","-")] - source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s' , 'download'] -versionsuffix = '-Java-%(javaver)s' - dependencies = [('Java', '1.7.0_79')] jarfiles = ['saxon%(version_major)she.jar', 'saxon%(version_major)s-test.jar', 'saxon%(version_major)s-xqj.jar'] -- GitLab From 4c3641259118bc70d74b75893f2c24e348a1d661 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 7 Apr 2016 11:40:45 +0200 Subject: [PATCH 1169/2133] 1 --- .../g/GConf/GConf-3.2.6-intel-2016a.eb | 39 ++++++++++++++++ ...Python-3.0.2.0-intel-2016-Python-2.7.11.eb | 45 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb new file mode 100644 index 0000000000..118e97695c --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +homepage = 'https://projects.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('dbus-glib', '0.106'), + ('GLib', '2.47.5'), + ('GObject-Introspection', '1.47.1'), + ('libxml', '2.9.3'), + ('GTK+', '2.24.28'), +] + +configopts = '--disable-orbit ' + +sanity_check_paths = { + 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + + ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + + ['lib/libgconf-2.%s' % x for x in['a', 'so']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb new file mode 100644 index 0000000000..2bca75979e --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -0,0 +1,45 @@ +name = 'wxPython' +version = '3.0.2.0' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://www.wxpython.org' +description = """wxPython is a GUI toolkit for the Python programming language. + It allows Python programmers to create programs with a robust, + highly functional graphical user interface, simply and easily. + It is implemented as a Python extension module (native code) + that wraps the popular wxWidgets cross platform GUI library, + which is written in C++.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] + +patches = ['%(name)s_%(version)s_intel.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('expat', '2.1.0'), + ('GTK+', '2.24.28'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '0.10.36'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/wxrc'] + + ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + + ['lib/lib%s-3.0.so' % x for x in ['wx_baseu', 'wx_gtk2u_core']], + 'dirs': ['include', 'share', 'lib/python%(pyshortver)s/site-packages'] +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/wx-3.0-gtk2'], +} + +moduleclass = 'vis' -- GitLab From fb1feec5cb73661660cfa839cf2ff6aa193a2b5c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 7 Apr 2016 15:42:40 +0200 Subject: [PATCH 1170/2133] removed newline --- easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb index 63c3fa7e2d..6b593148b4 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb @@ -21,4 +21,4 @@ dependencies = [ ('libxml2', '2.9.3'), ] -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' -- GitLab From 7b27041bb0c383832ffb63e6f205c1f091a3934a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 15:59:16 +0200 Subject: [PATCH 1171/2133] add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb --- .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' -- GitLab From 690b3dbdd43db476033b8e56facd240268975327 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 16:45:13 +0200 Subject: [PATCH 1172/2133] add easyconfig MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb, add easyconfig libxml2-2.9.2-goolf-1.5.16.eb, add easyconfig HDF5-1.8.9-goolf-1.5.16.eb, add easyconfig Szip-2.1-goolf-1.5.16.eb --- .../h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb | 22 ++++++++++++++ .../l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb | 29 ++++++++++++++++++ ...goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 30 +++++++++++++++++++ .../s/Szip/Szip-2.1-goolf-1.5.16.eb | 23 ++++++++++++++ 4 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb new file mode 100644 index 0000000000..755c2cc7f9 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb @@ -0,0 +1,22 @@ +# Built with EasyBuild version 2.1.1 on 2015-08-05_14-22-07 +name = 'HDF5' +version = '1.8.9' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb new file mode 100644 index 0000000000..54c5dad803 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb new file mode 100644 index 0000000000..a5aa488ebe --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus' +version = '7.0.67' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a methodology + for management of complex scientific data.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['stable_release-%s.zip' % version.replace('.','-')] + +dependencies = [ + ('Java', '1.7.0_79', '', True), + ('Python', '2.7.9'), + ('HDF5', '1.8.9'), + ('libxml2', '2.9.2'), + ('zlib', '1.2.8') +] + +configopts = '--with-jdk=$JAVA_HOME' + +preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' + +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb new file mode 100644 index 0000000000..73e27f5f6c --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From ec8c9fd7d0dadd4dd1c5089f6135a0e87a76e244 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 8 Apr 2016 09:26:38 +0200 Subject: [PATCH 1173/2133] add easyconfig Python-2.7.9-goolf-1.5.16.eb, add easyconfig bzip2-1.0.6-goolf-1.5.16.eb, add easyconfig libreadline-6.3-goolf-1.5.16.eb, add easyconfig ncurses-5.9-goolf-1.5.16.eb, add easyconfig SQLite-3.8.8.1-goolf-1.5.16.eb, add easyconfig Tk-8.6.3-goolf-1.5.16-no-X11.eb, add easyconfig OpenSSL-1.0.1k-goolf-1.5.16.eb --- .../b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb | 15 +++ .../libreadline-6.3-goolf-1.5.16.eb | 30 +++++ .../n/ncurses/ncurses-5.9-goolf-1.5.16.eb | 36 ++++++ .../o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb | 24 ++++ .../p/Python/Python-2.7.9-goolf-1.5.16.eb | 116 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb | 38 ++++++ .../t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb | 25 ++++ 7 files changed, 284 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb new file mode 100644 index 0000000000..1f608a116f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically +compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical +compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s/'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb new file mode 100644 index 0000000000..9a2a57c200 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb new file mode 100644 index 0000000000..0d4841191f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, +and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and +function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb new file mode 100644 index 0000000000..895b5bd87b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1k' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb new file mode 100644 index 0000000000..dee7cd4fdf --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -0,0 +1,116 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), + ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb new file mode 100644 index 0000000000..6946daaee7 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb new file mode 100644 index 0000000000..b383831c92 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 2b8706a0b067912224fda3a480f910701fe0cbe4 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:19:45 +0200 Subject: [PATCH 1174/2133] add easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig freetype-2.6.2-foss-2016a.eb, add easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig pixman-0.34.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 29 +++++++++++++++++++ .../f/freetype/freetype-2.6.2-foss-2016a.eb | 3 +- .../p/pixman/pixman-0.34.0-foss-2016a.eb | 20 +++++++++++++ 3 files changed, 50 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb new file mode 100644 index 0000000000..4afe79dcce --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb index 41c2f0204e..3111a314be 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -14,8 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, - 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb new file mode 100644 index 0000000000..896aab1550 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 2fb7134c01aa47664c480fb407f7242b41013d51 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 8 Apr 2016 03:45:51 -0400 Subject: [PATCH 1175/2133] support for Yade but it's not yet completed --- .../y/Yade/Yade-1.20.0-foss-2016a.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb new file mode 100644 index 0000000000..3711be5fc1 --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb @@ -0,0 +1,88 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '1.20.0' + +homepage = 'www.yade-dem.org' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] + +pyver = '2.7.11' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('git', '2.8.0'), + ('freeglut', '3.0.0'), + ('loki', '-------'), + ('Boost', '1.60.0'), + ('fakeroot', '-------'), + ('dpkg', '-------'), + ('IPython', '3.2.3', versionsuffix), + ('matplotlib', '1.5.1'), + ('SQLite', '3.9.2'), + ('numpy', '1.10.4', versionsuffix) + ('TK', '8.6.4', 'no-X11'), + ('gnuplot', '5.0.3'), + ('gts', '0.7.6'), + ('Graphviz', '2.38'), + ('ScientificPython', '2.9.4', versionsuffix), + ('Eigen', '3.2.7'), + ('Qt', '4.8.7'), + ('gtk+', '2.24.28'), + ('libqglviewer-dev', '-------'), + ('libjs-jquery', '---------'), + ('Sphinx', '1.3.3'), + ('bibtexparser', '0.6.0'), + ('libXmu', '1.1.2'), + ('libXi', '1.7.6'), + ('help2man', '--------'), + ('bzip2', '1.0.6'), + ('ziblg-dev', '---------------'), + ('GDB', '7.10.1',versionsuffix), + # optional + ('VTK', '6.3.0'), + ('CGAL', '4.7'), + ('SuiteSparse', '4.5.1'), + ('OpenBLAS', '0.2.15'), + ('METIS', '5.1.0'), +] + +builddependencies = [('CMake', '3.2.3')] + +separate_build_dir = True + +# In case you want disable some Yade features +# configopts = '-OPTION_1 = OFF -OPTION_2 = OFF ...' + +# options available, +# ENABLE_GUI: enable GUI option (ON by default) +# ENABLE_CGAL: enable CGAL option (ON by default) +# ENABLE_VTK: enable VTK-export option (ON by default) +# ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default) +# ENABLE_GTS: enable GTS-option (ON by default) +# ENABLE_GL2PS: enable GL2PS-option (ON by default) +# ENABLE_LINSOLV: enable LINSOLV-option (ON by default) +# ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default) +# ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default) +# ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default) +# ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013] for details (OFF by default) +# ENABLE_MASK_ARBITRARY: enable MASK_ARBITRARY option (OFF by default) +# ENABLE_PROFILING: enable profiling, e.g., shows some more metrics, which can define bottlenecks of the code (OFF by default) +# runtimePREFIX: used for packaging, when install directory is not the same as runtime directory (/usr/local by default) +# CHUNKSIZE: specifiy the chunk size if you want several sources to be compiled at once. Increases compilation speed but RAM-consumption during compilation as well (1 by default) +# VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) +# USE_QT5: use QT5 for GUI, experimental (OFF by default) + +sanity_check_paths = { + 'files': ['bin/%s-%s' %(namelower, version), 'bin/%s-%s-batch' %(namelower, version)], + 'dirs': ['lib/x86_64-linux-gnu'] +} + +moduleclass = 'devel' -- GitLab From 821479d0f1049f642b3f2ff7cfb9a2fca8f9206b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 10:18:48 +0200 Subject: [PATCH 1176/2133] 2 --- .../d/DBus/DBus-1.10.8-intel-2016a.eb | 24 +++++++++++ .../dbus-glib/dbus-glib-0.106-intel-2016a.eb | 25 +++++++++++ .../g/GConf/GConf-3.2.6-intel-2016a.eb | 5 ++- .../GST-plugins-base-0.10.36-intel-2016a.eb | 37 +++++++++++++++++ .../GStreamer-0.10.36-intel-2016a.eb | 41 +++++++++++++++++++ ...intltool-0.51.0-intel-2016a-Perl-5.22.1.eb | 25 +++++++++++ ...Python-3.0.2.0-intel-2016-Python-2.7.11.eb | 6 +++ ...XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb | 27 ++++++++++++ 8 files changed, 188 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb new file mode 100644 index 0000000000..f322881382 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.10.8' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb new file mode 100644 index 0000000000..321204b244 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.106' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GLib', '2.47.5'), + ('DBus', '1.10.8'), + ('expat', '2.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb index 118e97695c..ec87efba55 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -8,7 +8,7 @@ description = """GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.""" -toolchain = {'name': 'intel', 'version': '2014b'} +toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] @@ -17,8 +17,9 @@ dependencies = [ ('dbus-glib', '0.106'), ('GLib', '2.47.5'), ('GObject-Introspection', '1.47.1'), - ('libxml', '2.9.3'), + ('libxml2', '2.9.3'), ('GTK+', '2.24.28'), + ('intltool', '0.51.0', '-Perl-5.22.1'), ] configopts = '--disable-orbit ' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb new file mode 100644 index 0000000000..914e875639 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '0.10.36')] + +#Does not work with Bison 3 +builddependencies = [ +# ('Bison', '2.7', '', True), + ('Bison', '3.0.4'), + ('flex', '2.6.0'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-0.10' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-0.10.so' % x for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb new file mode 100644 index 0000000000..6c81f735d4 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.47.5'), + ('GObject-Introspection', '1.47.1'), + ('zlib', '1.2.8'), +] + +#Does not work with Bison 3 +builddependencies = [ +# ('Bison', '2.7', '', True), + ('Bison', '3.0.4'), + ('flex', '2.6.0'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-0.10' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-0.10.so' % x for x in ['reamer', 'base', 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..4c3bc089de --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.22.1' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.44', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb index 2bca75979e..439291d7b0 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -1,3 +1,6 @@ +easyblock = 'ConfigureMake' +#easyblock = 'PythonPackage' + name = 'wxPython' version = '3.0.2.0' versionsuffix = "-Python-%(pyver)s" @@ -31,6 +34,9 @@ dependencies = [ parallel = 1 +#options = {'modulename': 'wx'} +#skipsteps = ['install_step', 'make_installdir' ] + sanity_check_paths = { 'files': ['bin/wxrc'] + ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..5cb19baa1c --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.44' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1'), + ('expat', '2.1.0') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], +} + +moduleclass = 'data' -- GitLab From 0263a7c1eae14b20cf0d549b928a77037cdc15ce Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 10:39:37 +0200 Subject: [PATCH 1177/2133] Builddependencies fixed for GObject-introspection --- .../GObject-Introspection-1.42.0-intel-2014b.eb | 4 +++- .../GObject-Introspection-1.44.0-intel-2015a.eb | 3 +++ .../GObject-Introspection-1.47.1-intel-2015b.eb | 3 +++ .../GObject-Introspection-1.47.1-intel-2016a.eb | 8 +++++--- 4 files changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb index 7ae4e4f769..1f246a9bfc 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb @@ -18,9 +18,11 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.8'), ('GLib', '2.40.0'), - ('Bison', '3.0.2'), ] +builddependencies = [ + ('Bison', '3.0.2'), +] sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb index 0461a34f5f..835de46b5b 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb @@ -18,6 +18,9 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.44.1'), +] + +builddependencies = [ ('Bison', '3.0.4', '', ('GCC', '4.9.2')), ] diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb index 7bff362648..3e1f37f646 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb @@ -18,6 +18,9 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.47.1'), +] + +builddependencies = [ ('Bison', '3.0.4'), ] diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb index eaa343080d..360f641464 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -20,14 +20,16 @@ pyver = '2.7.11' dependencies = [ ('Python', pyver), ('GLib', '2.47.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), ('flex', '2.6.0'), ('Bison', '3.0.4'), ('cairo', '1.14.6'), - ('libffi', '3.2.1'), ] -builddependencies = [('Autotools', '20150215')] - preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts -- GitLab From 7b8ff1272ac3332e3a75cb50cf751cb568ae4ea2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 10:44:38 +0200 Subject: [PATCH 1178/2133] fixed gobject-intro builddep --- .../GObject-Introspection-1.47.1-foss-2016a.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb index 3c83530c29..2ea4584a28 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -20,14 +20,16 @@ pyver = '2.7.11' dependencies = [ ('Python', pyver), ('GLib', '2.47.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), ('flex', '2.6.0'), ('Bison', '3.0.4'), ('cairo', '1.14.6'), - ('libffi', '3.2.1'), ] -builddependencies = [('Autotools', '20150215')] - preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts -- GitLab From ab78bd9b77913e4fc297e3a80c01225d559b051b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:02:48 +0200 Subject: [PATCH 1179/2133] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig GLib-2.47.5-foss-2016a.eb, modify easyconfig freetype-2.6.2-foss-2016a.eb, modify easyconfig pixman-0.34.0-foss-2016a.eb, modify easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig libX11-1.6.3-foss-2016a.eb, add easyconfig libxcb-1.11.1-foss-2016a.eb, add easyconfig libXrender-0.9.9-foss-2016a.eb, add easyconfig libXext-1.3.3-foss-2016a.eb, add easyconfig renderproto-0.11-foss-2016a.eb, add easyconfig xextproto-7.3.0-foss-2016a.eb, add easyconfig xproto-7.0.28-foss-2016a.eb, add easyconfig libffi-3.2.1-foss-2016a.eb, add easyconfig gettext-0.19.7-foss-2016a.eb, add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb, add easyconfig PCRE-8.38-foss-2016a.eb, add easyconfig inputproto-2.3.1-foss-2016a.eb, add easyconfig libpthread-stubs-0.3-foss-2016a.eb, add easyconfig kbproto-1.0.7-foss-2016a.eb, add easyconfig xtrans-1.3.5-foss-2016a.eb, add easyconfig xorg-macros-1.19.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 30 +++++++++++++++-- .../g/GLib/GLib-2.47.5-foss-2016a.eb | 33 +++++++++++++++++++ .../g/gettext/gettext-0.19.7-foss-2016a.eb | 23 +++++++++++++ .../l/libXext/libXext-1.3.3-foss-2016a.eb | 1 + .../libXrender/libXrender-0.9.9-foss-2016a.eb | 4 +++ .../l/libffi/libffi-3.2.1-foss-2016a.eb | 23 +++++++++++++ .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++ .../xorg-macros-1.19.0-foss-2016a.eb | 22 +++++++++++++ 8 files changed, 164 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index 4afe79dcce..ab395e2001 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = "cairo" +name = 'cairo' version = '1.14.6' homepage = 'http://cairographics.org' @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_XZ] +glibver = '2.47.5' + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), @@ -21,9 +23,33 @@ dependencies = [ ('pixman', '0.34.0'), ('fontconfig', '2.11.94'), ('expat', '2.1.0'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), +] + +builddependencies = [ + ('renderproto', '0.11'), + ('libXext', '1.3.3'), + ('xextproto', '7.3.0'), + ('libX11', '1.6.3'), + ('xproto', '7.0.28'), + ('libxcb', '1.11.1') ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -configopts = "--enable-symbol-lookup=no" +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb new file mode 100644 index 0000000000..fb0fcbff8c --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb new file mode 100644 index 0000000000..168b2490e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index ce3e6d964e..0a0acbe42b 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -15,6 +15,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index eee347a314..12b8caece2 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -14,6 +14,10 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), + ('libX11', '1.6.3'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28') ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb new file mode 100644 index 0000000000..c7c638b6fa --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 23d49b344a3159cf6e1b84a0e873754b08789e41 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:21:22 +0200 Subject: [PATCH 1180/2133] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig libXau-1.0.8-foss-2016a.eb, add easyconfig libXdmcp-1.1.2-foss-2016a.eb --- easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index ab395e2001..5cf49b60d8 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -25,9 +25,11 @@ dependencies = [ ('expat', '2.1.0'), ('GLib', glibver), ('libX11', '1.6.3'), + ('libXau', '1.0.8'), ('libxcb', '1.11.1'), - ('libXrender', '0.9.9'), + ('libXdmcp', '1.1.2'), ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), ] builddependencies = [ -- GitLab From 3dcbdd98222ef584623e17fe698cf4f602897cdc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 8 Apr 2016 12:02:01 +0100 Subject: [PATCH 1181/2133] Update IGVTools to 2.3.72 --- .../IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb new file mode 100644 index 0000000000..af0616b491 --- /dev/null +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'IGVTools' +version = '2.3.72' + +homepage = 'http://www.broadinstitute.org/software/igv/' +description = """ This package contains command line utilities for preprocessing, + computing feature count density (coverage), sorting, and indexing data files. + See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] +sources = ['%(namelower)s_%(version)s.zip'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["igvtools.jar", "igvtools"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 4dab0a4ea3bcc8e35b8f22daab6ba0ebe764a781 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 14:42:42 +0200 Subject: [PATCH 1182/2133] {vis}[intel-2016a] wxPython 3.0.2.0 (REVIEW) --- .../GST-plugins-base-0.10.36-intel-2016a.eb | 4 +-- .../GStreamer-0.10.36-intel-2016a.eb | 4 +-- .../libXxf86vm-1.1.4-intel-2016a.eb | 30 +++++++++++++++++++ ...Python-3.0.2.0-intel-2016-Python-2.7.11.eb | 12 ++++---- .../w/wxPython/wxPython_3.0.2.0_intel.patch | 12 ++++++++ .../xf86vidmodeproto-2.3.1-intel-2016a.eb | 19 ++++++++++++ 6 files changed, 69 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch create mode 100644 easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index 914e875639..af962689d7 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -18,9 +18,7 @@ dependencies = [('GStreamer', '0.10.36')] #Does not work with Bison 3 builddependencies = [ -# ('Bison', '2.7', '', True), - ('Bison', '3.0.4'), - ('flex', '2.6.0'), + ('Bison', '2.7', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index 6c81f735d4..178e012daf 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -22,9 +22,7 @@ dependencies = [ #Does not work with Bison 3 builddependencies = [ -# ('Bison', '2.7', '', True), - ('Bison', '3.0.4'), - ('flex', '2.6.0'), + ('Bison', '2.7', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000..873ae3da80 --- /dev/null +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXxf86vm' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 XFree86 video mode extension library""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xf86vidmodeproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xf86vmode.h']+ + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb index 439291d7b0..4d7ba463bd 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -1,6 +1,3 @@ -easyblock = 'ConfigureMake' -#easyblock = 'PythonPackage' - name = 'wxPython' version = '3.0.2.0' versionsuffix = "-Python-%(pyver)s" @@ -30,12 +27,15 @@ dependencies = [ ('GTK+', '2.24.28'), ('GConf', '3.2.6'), ('GST-plugins-base', '0.10.36'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('libSM', '1.2.2'), + ('libXxf86vm', '1.1.4'), ] -parallel = 1 +options = {'modulename': 'wx'} -#options = {'modulename': 'wx'} -#skipsteps = ['install_step', 'make_installdir' ] +parallel = 1 sanity_check_paths = { 'files': ['bin/wxrc'] + diff --git a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch new file mode 100644 index 0000000000..ac58f0c1ac --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch @@ -0,0 +1,12 @@ +# Intel compiler have problems with precompiled headers (cannot mix C and C++ precompiled headers, like in GNU compilers) +# B. Hajgato (VUB) April 8th 2016 +--- wxPython-src-3.0.2.0/build/tools/build-wxwidgets.py.org 2014-11-27 21:49:59.000000000 +0100 ++++ wxPython-src-3.0.2.0/build/tools/build-wxwidgets.py 2016-04-08 13:03:01.362591062 +0200 +@@ -268,6 +268,7 @@ + configure_opts.append("--with-gtk=3") + + wxpy_configure_opts = [ ++ "--disable-precomp-headers", + "--with-opengl", + "--enable-sound", + "--enable-graphics_ctx", diff --git a/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb b/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb new file mode 100644 index 0000000000..3665e42444 --- /dev/null +++ b/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xf86vidmodeproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 XFree86 video mode extension protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xf86vm%s.h' % x for x in ['', 'proto', 'str']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 556b6294cd2ae5229d67cc4986caa48b4a0bcb33 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 8 Apr 2016 15:52:14 -0400 Subject: [PATCH 1183/2133] add ScientificPython 2.9.4 and numpy 1.10.4 for foss 2016a toolchain --- .../numpy-1.10.4-foss-2016a-Python-2.7.11.eb | 26 ++++++++++++++ ...icPython-2.9.4-foss-2016a-Python-2.7.11.eb | 35 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f2c859648a --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.10.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%(version)s-sse42.patch', +] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a597bd3eff --- /dev/null +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'ScientificPython' +version = '2.9.4' + +homepage = 'https://sourcesup.cru.fr/projects/scientific-py/' +description = """ScientificPython is a collection of Python modules for scientific computing. + It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, + and parallelization.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + # older version of numpy than the one included in Python module required + # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for + ('numpy', '1.10.4', versionsuffix), +] + +options = {'modulename': 'Scientific'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Scientific' % pyshortver], +} + +moduleclass = 'math' -- GitLab From 2f44609dc27711bf4292e2b9101d2cbac77061f1 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 8 Apr 2016 16:38:14 -0400 Subject: [PATCH 1184/2133] Update source_urls parameter in ScientificPython easyconfig files --- .../ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb | 2 +- .../ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb | 2 +- .../ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb index b783e38692..c1aca8b5ad 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'gmpolf', 'version': '1.4.8'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f3c253971b..65204949fb 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb index ed6a708c5f..25d50d354e 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb @@ -10,7 +10,7 @@ and parallelization.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb index 20336396df..9274b5b9ad 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb index fcc68a81ed..5aa3dd118d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'ictce', 'version': '5.2.0'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb index 997b8a1673..89a12d0943 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb index 2446abe86f..b745e7f0a4 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4411'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb index 0170615e9c..876a244102 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb index 47671f1164..857fd95a08 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] pyver = '2.7.11' -- GitLab From c74b00de25ab3199f39cde3c889c01383f1ef871 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 11:21:50 +0200 Subject: [PATCH 1185/2133] use XORG_LIB_SOURCE everywhere --- easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb index fa49f6c97c..78420c88a5 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb index fe3df1bbcf..289966eec9 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), -- GitLab From 1a9927879a743d52c447108463b62b095a6d15ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 12:19:03 +0200 Subject: [PATCH 1186/2133] add checksums in SuiteSparse easyconfigs --- .../ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb | 2 ++ .../ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb | 2 ++ .../ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb | 2 ++ 9 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb index b783e38692..ce094bf25b 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'gmpolf', 'version': '1.4.8'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f3c253971b..a89c80a516 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb index ed6a708c5f..51bacf787c 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb index 20336396df..a889a4de4d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb index fcc68a81ed..2c70b32004 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '5.2.0'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb index 997b8a1673..e0938abda4 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb index 2446abe86f..feb8f56c9d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2014b'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['73ee0df19c7b58cdf2954261f0763c77'] + python = "Python" pythonversion = '2.7.8' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb index 0170615e9c..01aca5b107 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] sources = [SOURCE_TAR_GZ] +checksums = ['dc2987089e106cb807b4ccecf7adc071'] + python = 'Python' pythonversion = '2.7.9' pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb index 47671f1164..20da6ee305 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] sources = [SOURCE_TAR_GZ] +checksums = ['dc2987089e106cb807b4ccecf7adc071'] + pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[:2]) -- GitLab From ff6955fedb6d0c154f4ab0b3d8f057f986c215d7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 9 Apr 2016 12:10:39 +0100 Subject: [PATCH 1187/2133] Initial version of bam-readcount --- ...readcount-0.7.4-cmake_install_prefix.patch | 12 +++++++ .../bam-readcount-0.7.4-foss-2015b.eb | 35 +++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch create mode 100644 easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch new file mode 100644 index 0000000000..2916d1f5e7 --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch @@ -0,0 +1,12 @@ +diff -u bam-readcount-0.7.4/CMakeLists.txt bam-readcount-0.7.4.new/CMakeLists.txt +--- bam-readcount-0.7.4/CMakeLists.txt 2014-12-07 19:45:03.000000000 +0000 ++++ bam-readcount-0.7.4.new/CMakeLists.txt 2016-04-06 22:06:12.336807391 +0100 +@@ -2,7 +2,7 @@ + + project(bam-readcount) + +-set(CMAKE_INSTALL_PREFIX "/usr") ++#set(CMAKE_INSTALL_PREFIX "/usr") + set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake;${CMAKE_SOURCE_DIR}/build-common/cmake") + include(TestHelper) + include(VersionHelper) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb new file mode 100644 index 0000000000..b19ba9482c --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'CMakeMake' + +name = 'bam-readcount' +version = '0.7.4' + +homepage = 'https://github.com/genome/bam-readcount' +description = """Count DNA sequence reads in BAM files""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/genome/%(name)s/archive'] + +patches = ['%(name)s-%(version)s-cmake_install_prefix.patch'] + +builddependencies = [ + ('SAMtools', '1.3'), + ('CMake', '3.4.1'), +] + +configopts = " -DCMAKE_INSTALL_PREFIX=%(installdir)s " + +prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&" + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/bam-readcount"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 09e71b456c69f7db1a62915a145b1dab23b5e952 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 15:21:46 +0200 Subject: [PATCH 1188/2133] use XORG_PROTO_SOURCE + 'env' in preconfigopts --- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb index 0d7fd4a4a2..1fbffb2758 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb index d26077ac1e..850097aee1 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb index 75924f159f..c39482e40c 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index c9dd66c1c1..fb2151e5df 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, -- GitLab From 68db97d838656d94d12133f292533dc2670c42f0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 9 Apr 2016 14:51:56 +0100 Subject: [PATCH 1189/2133] Remove obsolete configopts and add explanation/authorship to patch --- .../bam-readcount-0.7.4-cmake_install_prefix.patch | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch index 2916d1f5e7..aecba22db8 100644 --- a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch @@ -1,3 +1,7 @@ +# patch to remove hard-coded installation prefix +# Adam Huffman +# The Francis Crick Institute + diff -u bam-readcount-0.7.4/CMakeLists.txt bam-readcount-0.7.4.new/CMakeLists.txt --- bam-readcount-0.7.4/CMakeLists.txt 2014-12-07 19:45:03.000000000 +0000 +++ bam-readcount-0.7.4.new/CMakeLists.txt 2016-04-06 22:06:12.336807391 +0100 -- GitLab From 86e08e86be0bf0b7717a15b4bd15b9ace3b60c60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 16:37:07 +0200 Subject: [PATCH 1190/2133] sync preconfigopts/buildopts in GObject-Introspection 1.47.1 easyconfigs --- .../GObject-Introspection-1.47.1-intel-2015b.eb | 5 +++++ .../GObject-Introspection-1.47.1-intel-2016a.eb | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb index 3e1f37f646..42f9c4f97f 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb @@ -24,6 +24,11 @@ builddependencies = [ ('Bison', '3.0.4'), ] +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb index 360f641464..7606731e75 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -30,7 +30,7 @@ builddependencies = [ ('cairo', '1.14.6'), ] -preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -- GitLab From ebb1e4c1d3f91f420161ddacb12c4270b9380e84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 16:39:35 +0200 Subject: [PATCH 1191/2133] sync (build) deps in GObject-Introspection 1.47.1 easyconfigs --- .../GObject-Introspection-1.47.1-intel-2015b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb index 42f9c4f97f..b1d634cd35 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb @@ -18,10 +18,14 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.47.1'), + ('libffi', '3.2.1'), ] builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), ('Bison', '3.0.4'), + ('cairo', '1.14.4'), ] preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " -- GitLab From d0eedfe69ed10024cd995cb170fddb0d1467732d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 17:27:10 +0200 Subject: [PATCH 1192/2133] various small style fixes --- .../GObject-Introspection-1.47.1-foss-2016a.eb | 6 ++---- easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb | 1 + .../l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb | 1 + easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb | 1 + easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb | 1 + easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb | 1 + .../m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb | 2 +- .../m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb | 2 +- .../m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb | 2 +- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 2 +- .../m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb | 2 +- .../m/makedepend/makedepend-1.0.5-intel-2015a.eb | 2 +- .../m/makedepend/makedepend-1.0.5-intel-2015b.eb | 2 +- .../m/makedepend/makedepend-1.0.5-intel-2016a.eb | 2 +- 19 files changed, 20 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb index 2ea4584a28..ef2d0a1446 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -15,10 +15,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -pyver = '2.7.11' - dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ('GLib', '2.47.5'), ('libffi', '3.2.1'), ] @@ -30,7 +28,7 @@ builddependencies = [ ('cairo', '1.14.6'), ] -preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb index 6943d3e084..68589245d1 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb index eaa232fe89..cd973d2ea0 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' versionsuffix = '-Python-2.7.11' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb index 0ed8e42a20..60cd626d31 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb index bd92d68db6..c94df236e0 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.6' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb index 265985f5e5..5e9d4cb87a 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.6' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb index 3b30e0e1d5..6fb02db3e5 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb index 393090c994..00c6dd2232 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb index f5f634beae..82ed5ca658 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] patches = ['makedepend_icc-sigaction.patch'] diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb index 25ba8c0849..c4b315a1b7 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb index 858f7c2608..255cd2ad52 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb index 808282ac91..49f692fd43 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb index 873b6391a2..ece06f94eb 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb index 07b6b524bf..50e1707937 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] patches = ['makedepend_icc-sigaction.patch'] diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index 8bd95eee91..863911703e 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb index c92d8634e2..38d76d37d2 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb index 0b36b37c50..282179280a 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb index 77541afc67..ca6025105b 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb index 1158bd68be..e38d07d26e 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], -- GitLab From 25115093469d2add35217998147dd08a68ce16aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 18:34:13 +0200 Subject: [PATCH 1193/2133] use XORG_PROTO_SOURCE --- .../x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb index a40280e419..fdbb9a1f7d 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], -- GitLab From 6e3de4adfa74be7ef5b164931fa37c5dba22be68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 20:23:28 +0200 Subject: [PATCH 1194/2133] clean up wxPython easyconfig according to enhancements to wxPython easyblock --- .../wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb index 4d7ba463bd..803388b88a 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -33,19 +33,4 @@ dependencies = [ ('libXxf86vm', '1.1.4'), ] -options = {'modulename': 'wx'} - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/wxrc'] + - ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + - ['lib/lib%s-3.0.so' % x for x in ['wx_baseu', 'wx_gtk2u_core']], - 'dirs': ['include', 'share', 'lib/python%(pyshortver)s/site-packages'] -} - -modextrapaths = { - 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/wx-3.0-gtk2'], -} - moduleclass = 'vis' -- GitLab From 71405555deacf3b3a4280055e2b11d53317629f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 20:35:55 +0200 Subject: [PATCH 1195/2133] style fixes --- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb | 1 - .../GST-plugins-base-0.10.36-intel-2016a.eb | 6 +++--- .../g/GStreamer/GStreamer-0.10.36-intel-2016a.eb | 9 +++++---- .../intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb index ec87efba55..89fe1cefe2 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -37,4 +37,3 @@ modextrapaths = { } moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index af962689d7..f2d1e756a5 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -16,14 +16,14 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [('GStreamer', '0.10.36')] -#Does not work with Bison 3 +# does not work with Bison 3.x builddependencies = [ ('Bison', '2.7', '', True), ] sanity_check_paths = { - 'files': ['bin/gst-%s-0.10' % x for x in ['discoverer', 'visualise']] + - ['lib/libgst%s-0.10.so' % x for x in ['app', 'audio', 'video']], + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index 178e012daf..ccd3a73617 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -20,15 +20,16 @@ dependencies = [ ('zlib', '1.2.8'), ] -#Does not work with Bison 3 +# does not work with Bison 3.x builddependencies = [ ('Bison', '2.7', '', True), ] sanity_check_paths = { - 'files': ['bin/gst-%s-0.10' % x for x in ['inspect', 'typefind', 'launch']] + - ['lib/libgst%s-0.10.so' % x for x in ['reamer', 'base', 'controller', 'check']], - 'dirs': ['include', 'share', 'libexec'] + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['reamer', 'base', + 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'], } modextrapaths = { diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb index 4c3bc089de..0b9db08cff 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb @@ -10,7 +10,7 @@ description = """intltool is a set of tools to centralize translation of toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] dependencies = [ -- GitLab From 9fe4ba351aca7af665bb92fb5ce3a5220bb630a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Apr 2016 10:47:20 +0200 Subject: [PATCH 1196/2133] fix typo in filename for wxPython --- ...on-2.7.11.eb => wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/w/wxPython/{wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb => wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb rename to easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb -- GitLab From 8ac5aefb82cd2237cd679ba3c103e973ee3f9581 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 10 Apr 2016 16:00:31 +0200 Subject: [PATCH 1197/2133] Fix build/runtime dependencies --- .../easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index 12b8caece2..1e63340752 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -14,7 +14,6 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), - ('libX11', '1.6.3'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28') -- GitLab From 75e2d85779aa974e7c506e0a95547fa6618ddc73 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 10 Apr 2016 21:26:14 +0100 Subject: [PATCH 1198/2133] Really remove the obsolete configopts this time --- .../b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb index b19ba9482c..a786a5b208 100644 --- a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -21,8 +21,6 @@ builddependencies = [ ('CMake', '3.4.1'), ] -configopts = " -DCMAKE_INSTALL_PREFIX=%(installdir)s " - prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&" separate_build_dir = True -- GitLab From e3800389846428f835f7674d1e3a9d31923189c2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 10 Apr 2016 23:17:21 +0100 Subject: [PATCH 1199/2133] Port GROMACS 5.1.2 to foss-2016a --- .../GROMACS-5.1.2-foss-2016a-hybrid.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb new file mode 100644 index 0000000000..5b189abdbd --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +# +# Version 5.1.2 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.2' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.4.1'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.60.0')] + +moduleclass = 'bio' -- GitLab From 0382afb4bd7cb2f5c50dd5364d7090eb238747df Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 10 Apr 2016 23:50:25 +0100 Subject: [PATCH 1200/2133] Update libxml2 to 2.9.3 for foss-2016a --- .../easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb index 5b189abdbd..e699b7dd9b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb @@ -31,7 +31,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.4.1'), - ('libxml2', '2.9.2') + ('libxml2', '2.9.3') ] dependencies = [('Boost', '1.60.0')] -- GitLab From 22adb35c727a98b0064b959c40b49d646e055e9b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 11 Apr 2016 09:27:41 +0100 Subject: [PATCH 1201/2133] Add missing zlib dep and change samtools to normal, not build dep --- .../b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb index a786a5b208..9f5b2f295c 100644 --- a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -17,10 +17,14 @@ source_urls = ['https://github.com/genome/%(name)s/archive'] patches = ['%(name)s-%(version)s-cmake_install_prefix.patch'] builddependencies = [ - ('SAMtools', '1.3'), ('CMake', '3.4.1'), ] +dependencies = [ + ('SAMtools', '1.3'), + ('zlib', '1.2.8'), +] + prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&" separate_build_dir = True -- GitLab From a7b47e4ad40b160fb4989ad4cf48697e6006e266 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 10:34:28 +0200 Subject: [PATCH 1202/2133] foss 2016a version for sparsehash --- .../sparsehash/sparsehash-2.0.2-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb new file mode 100644 index 0000000000..062c5abe5e --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.2' + +homepage = 'https://code.google.com/p/sparsehash/' +description = """An extremely memory-efficient hash_map + implementation. 2 bits/entry overhead! The SparseHash library + contains several hash-map implementations, including + implementations that optimize for space or speed.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sparsehash.googlecode.com/files/'] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' \ No newline at end of file -- GitLab From 52b1c35a20d08cd618263ffe10d9108548360361 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 10:37:50 +0200 Subject: [PATCH 1203/2133] removed newline --- .../easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb index 062c5abe5e..d835154d86 100644 --- a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb @@ -20,4 +20,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'devel' \ No newline at end of file +moduleclass = 'devel' -- GitLab From 8cf5d34294607fb7c056c4c581f26444a3152e68 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 10:45:57 +0200 Subject: [PATCH 1204/2133] foss 2016a version for ABySS --- .../a/ABySS/ABySS-1.9.0-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb new file mode 100644 index 0000000000..1aff3781e1 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Maxime Schmitt , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.9.0' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] + +dependencies = [('Boost', '1.60.0')] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From f7ac943a2ff6f9d2719bd0ca4d704cbf3af38622 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Apr 2016 11:52:51 +0200 Subject: [PATCH 1205/2133] add easyconfig pandas-0.18.0-intel-2016a-Python-2.7.11.eb, add easyconfig pandas-0.18.0-intel-2016a-Python-3.5.1.eb --- ...pandas-0.18.0-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ .../pandas-0.18.0-intel-2016a-Python-3.5.1.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..69e84f6fa3 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..a3d2dbb5d1 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 446c86fc8446d9ceff2641644de5b40c79318f99 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 12:33:47 +0200 Subject: [PATCH 1206/2133] Dependency of sparsehash --- easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb index 1aff3781e1..46ae6d041a 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -22,7 +22,10 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] -dependencies = [('Boost', '1.60.0')] +dependencies = [ + ('Boost', '1.60.0'), + (sparsehash, '2.0.2') +] sanity_check_paths = { 'files': ["bin/ABYSS", "bin/ABYSS-P"], -- GitLab From 807626f4d5d2ea884882a3fd8da582245e8726ee Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 14:44:56 +0200 Subject: [PATCH 1207/2133] add easyconfig Tcl-8.6.3-goolf-1.5.16.eb --- .../t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb new file mode 100644 index 0000000000..a8f55caa25 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From 100f5c6abb616bfeb897c14a99b9023787f0ff6f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 14:52:11 +0200 Subject: [PATCH 1208/2133] Remove comment from HDF5-1.8.9-goolf-1.5.16.eb --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb index 755c2cc7f9..46dd3d15ad 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.1 on 2015-08-05_14-22-07 name = 'HDF5' version = '1.8.9' -- GitLab From c65cce06d6b0a92d173c96e87a6161f06a4b0a74 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 14:53:58 +0200 Subject: [PATCH 1209/2133] Comment out OpenSSL dependency in Python-2.7.9-goolf-1.5.16.eb --- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index dee7cd4fdf..d726f06367 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -21,7 +21,7 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), - ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -- GitLab From 2d01f15bc0ff258e333b4110d1e60ba413e6dbb3 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:03:51 +0200 Subject: [PATCH 1210/2133] Use https where possible in Python-2.7.9-goolf-1.5.16.eb --- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index d726f06367..70860e49fa 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -40,16 +40,16 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'source_urls': [('https://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], }), ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + 'source_urls': [('https://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], -- GitLab From 8acce97e99dd80a6fdad06c62cdc1f01b396b3fc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:04:46 +0200 Subject: [PATCH 1211/2133] Correct preconfigopts in libreadline-6.3-goolf-1.5.16.eb --- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb index 9a2a57c200..a11e7823ed 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + -- GitLab From 3752406eadac2b7d4b7f5b2f98a206b441b0d5de Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:14:10 +0200 Subject: [PATCH 1212/2133] Restrict parallel build in MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index a11de24d4f..5af25d6b8e 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -23,6 +23,6 @@ configopts = '--with-jdk=$JAVA_HOME' preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' -buildopts = '-j 1' +parallel = 1 moduleclass = 'data' -- GitLab From 179a5fc322d8db28072e25ddf7c30851a389f14e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:18:20 +0200 Subject: [PATCH 1213/2133] Wrap description to <120 characters in MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 5af25d6b8e..6a1d121ef8 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -5,7 +5,8 @@ version = '7.0.67' versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' homepage = 'http://mdsplus.org/' -description = """MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.""" +description = """MDSplus is a set of software tools for data acquisition and storage and a + methodology for management of complex scientific data.""" toolchain = {'name': 'foss', 'version': '2016a'} -- GitLab From 472992ac0f7f131dcd519fa2fed53114f1a27e0f Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 11 Apr 2016 16:01:43 +0200 Subject: [PATCH 1214/2133] Beast latest version using foss-2016a --- .../b/Beast/Beast-2.4.0-foss-2016a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb new file mode 100644 index 0000000000..68cf147acc --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'Beast' +version = '2.4.0' + +homepage = 'http://beast2.org/' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%(version)s.Linux.tgz'] + + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '2_1_2', '', ('foss', '2016a')), +] + +sanity_check_paths = { + 'files': ["bin/beast"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From a6397ef10bccd4aa65c1bc309b57c3a3cc40321d Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 11 Apr 2016 16:06:53 +0200 Subject: [PATCH 1215/2133] latest beagle-lib support foss2016a --- .../beagle-lib/beagle-lib-2_1_2-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb new file mode 100644 index 0000000000..033afea4f8 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '2_1_2' + +homepage = 'http://code.google.com/p/beagle-lib/' +description = """ +beagle-lib is a high-performance library that can perform the core +calculations at the heart of most Bayesian and Maximum Likelihood +phylogenetics packages. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['beagle_release_%(version)s.tar.gz'] + +dependencies = [('Java', '1.7.0_15', '', True)] + +# parallel build does not work (to test) +parallel = 1 + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From edeed474f2fd36ab442256811a34bc917853649b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 17:27:04 +0200 Subject: [PATCH 1216/2133] quickfix quotes for sparsehash dependency --- easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb index 46ae6d041a..442c127432 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -24,7 +24,7 @@ source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] dependencies = [ ('Boost', '1.60.0'), - (sparsehash, '2.0.2') + ('sparsehash', '2.0.2') ] sanity_check_paths = { -- GitLab From e2ca621fcc6de9d3d7acd6a59c8f150370f1c588 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 14:48:56 -0400 Subject: [PATCH 1217/2133] using numpy 1.8.2 that support oldnumeric and makes compatible with Scientificpython --- ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 44 +++++++++++++++++++ ...icPython-2.9.4-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..182905c4bb --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index a597bd3eff..ef29eaf445 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ ('Python', pyver), # older version of numpy than the one included in Python module required # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for - ('numpy', '1.10.4', versionsuffix), + ('numpy', '1.8.2', versionsuffix), ] options = {'modulename': 'Scientific'} -- GitLab From a947b9c9d89fc88a92ac4a55183a037922b70dad Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 15:04:46 -0400 Subject: [PATCH 1218/2133] add easyconfig numpy 1.8.2 for foss --- ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 44 ------------------- ...> numpy-1.8.2-foss-2016a-Python-2.7.11.eb} | 14 +++--- 2 files changed, 7 insertions(+), 51 deletions(-) delete mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb rename easybuild/easyconfigs/n/numpy/{numpy-1.10.4-foss-2016a-Python-2.7.11.eb => numpy-1.8.2-foss-2016a-Python-2.7.11.eb} (82%) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index 182905c4bb..0000000000 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'Bundle' - -name = 'matplotlib' -version = '1.5.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - -dependencies = [ - ('Python', '2.7.11'), - ('freetype', '2.6.2'), - ('libpng', '1.6.21'), -] - -exts_list = [ - ('Cycler', '0.9.0', { - 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], - 'source_tmpl': 'cycler-%(version)s.tar.gz', - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), -] - -# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module -full_sanity_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb similarity index 82% rename from easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb index f2c859648a..e591de8fe1 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb @@ -1,6 +1,5 @@ name = 'numpy' -version = '1.10.4' -versionsuffix = '-Python-%(pyver)s' +version = '1.8.2' homepage = 'http://www.numpy.org' description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: @@ -14,13 +13,14 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = [ - 'numpy-1.8.0-mkl.patch', - 'numpy-%(version)s-sse42.patch', -] +patches = ['numpy-1.8.1-mkl.patch'] + +python = 'Python' +pyver = '2.7.11' +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('Python', '2.7.11'), + (python, pyver), ] moduleclass = 'math' -- GitLab From af9773821329739f983ee9983353627e0b1d673c Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 16:06:16 -0400 Subject: [PATCH 1219/2133] matplotlib 1.5.1 for foss 2016a --- ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..182905c4bb --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From d297900bdcad241d8e042b2c8136cd5f3044995b Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 17:42:22 -0400 Subject: [PATCH 1220/2133] add easyconfig files for git 2.8.0 foss toolchain --- .../g/gettext/gettext-0.19.7-foss-2016a.eb | 23 +++++++++++++ .../easyconfigs/g/git/git-2.8.0-foss-2016a.eb | 33 +++++++++++++++++++ .../p/Perl/Perl-5.22.1-foss-2016a-bare.eb | 17 ++++++++++ 3 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb new file mode 100644 index 0000000000..168b2490e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb b/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb new file mode 100644 index 0000000000..37fb210f88 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.8.0' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +dependencies = [ + ('cURL', '7.47.0'), + ('expat', '2.1.0'), + ('gettext', '0.19.7'), + ('Perl', '5.22.1', '-bare'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb new file mode 100644 index 0000000000..9234ed61fa --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.22.1' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' -- GitLab From 48839f3594a14f4b645de4e827294b8ee99ae24b Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 12 Apr 2016 16:57:34 +1200 Subject: [PATCH 1221/2133] New EasyConfig for Boost-1.60.0 with the foss-2015a toolchain --- .../b/Boost/Boost-1.60.0-foss-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb new file mode 100644 index 0000000000..76d7cbc284 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.60.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From c35baf4c311b0abecf3fb9e6942386f6bca79b0e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:35:06 +0200 Subject: [PATCH 1222/2133] correctly specify Perl location in git easyconfig --- easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index 6a03e95dba..d8dcaa74d8 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -36,7 +36,7 @@ preconfigopts = 'make configure && ' # Work around git build system bug. If LIBS contains -lpthread, then configure # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--with-perl=${EBPERLROOT} --enable-pthreads='-lpthread'" +configopts = "--with-perl=${EBPERLROOT}/bin/perl --enable-pthreads='-lpthread'" sanity_check_paths = { 'files': ['bin/git'], -- GitLab From 3ab69db466b5c4491146598c3e23f17c9fc52191 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:39:03 +0200 Subject: [PATCH 1223/2133] add easyconfig MultiNest-3.10-intel-2016a.eb --- .../m/MultiNest/MultiNest-3.10-intel-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb b/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb new file mode 100644 index 0000000000..78d3266bf6 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'MultiNest' +version = '3.10' + +homepage = 'https://ccpforge.cse.rl.ac.uk/gf/project/multinest/' +description = """MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space + which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# download via https://ccpforge.cse.rl.ac.uk/gf/project/multinest/frs (requires registration) +sources = ['MultiNest_v%(version)s_CMake.tar.gz'] +checksums = ['a4ed7c15f2fbbf7f859f565734fc5296'] + +builddependencies = [('CMake', '3.4.3')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ackley', 'eggboxC', 'eggboxC++', 'gaussian', 'gauss_shell', 'himmelblau', + 'obj_detect', 'rosenbrock']] + + ['lib/lib%s' % x for x in ['multinest.a', 'multinest_mpi.a', 'multinest_mpi.%s' % SHLIB_EXT, + 'multinest.%s' % SHLIB_EXT]] + + ['include/multinest.h'], + 'dirs': ['modules'], +} + +moduleclass = 'tools' -- GitLab From 04e53f7a24ab360a3f3812526116aafc8a73a421 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:39:58 +0200 Subject: [PATCH 1224/2133] fix typo --- easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index d8dcaa74d8..1da07f9d58 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -36,7 +36,7 @@ preconfigopts = 'make configure && ' # Work around git build system bug. If LIBS contains -lpthread, then configure # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--with-perl=${EBPERLROOT}/bin/perl --enable-pthreads='-lpthread'" +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" sanity_check_paths = { 'files': ['bin/git'], -- GitLab From fbb3f0cd75ab28fb77e3c558f35ab2a8c6117da8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:42:31 +0200 Subject: [PATCH 1225/2133] add easyconfig CMake-3.5.1-intel-2016a.eb --- .../c/CMake/CMake-3.5.1-intel-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb new file mode 100644 index 0000000000..a70441375c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From d2dbcc47e9b38f23d53272986bfbc28aa15faaaf Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 12 Apr 2016 11:32:03 +0200 Subject: [PATCH 1226/2133] fix beagle-lib dependency --- easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb index 68cf147acc..484da63909 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb @@ -21,12 +21,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] sources = ['BEAST.v%(version)s.Linux.tgz'] - dependencies = [ # this is not mandatory but beagle-lib is recommended by developers # beagle-lib will also load the required java dependency # if you remove this you should add the java dependency - ('beagle-lib', '2_1_2', '', ('foss', '2016a')), + ('beagle-lib', '2.1.2'), ] sanity_check_paths = { -- GitLab From 2b7c6d3f7ccd97633b3f77e36d3083ecc8135c8f Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 12 Apr 2016 11:34:32 +0200 Subject: [PATCH 1227/2133] fix java version, naming, builddependencies --- .../beagle-lib/beagle-lib-2.1.2-foss-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb new file mode 100644 index 0000000000..29785ed5e6 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '2.1.2' +homepage= 'https://github.com/beagle-dev/beagle-lib' +description = """ +beagle-lib is a high-performance library that can perform the core +calculations at the heart of most Bayesian and Maximum Likelihood +phylogenetics packages. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] + +dependencies = [('Java', '1.8.0_74', '', True)] + +builddependencies = [('Autotools', '20150215')] + +# parallel build does not work (to test) +parallel = 1 + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 18e01e189a43b9ad3c3f6c356919cb8808dd7f39 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 12 Apr 2016 13:25:43 +0200 Subject: [PATCH 1228/2133] removed bad beagle-lib --- .../beagle-lib/beagle-lib-2_1_2-foss-2016a.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb deleted file mode 100644 index 033afea4f8..0000000000 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'beagle-lib' -version = '2_1_2' - -homepage = 'http://code.google.com/p/beagle-lib/' -description = """ -beagle-lib is a high-performance library that can perform the core -calculations at the heart of most Bayesian and Maximum Likelihood -phylogenetics packages. -""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz -source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] -sources = ['beagle_release_%(version)s.tar.gz'] - -dependencies = [('Java', '1.7.0_15', '', True)] - -# parallel build does not work (to test) -parallel = 1 - -preconfigopts = "./autogen.sh && " - -sanity_check_paths = { - 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile - for includefile in ["beagle.h", "platform.h"]] + - ["lib/libhmsbeagle%s.so" % libfile - for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], - 'dirs': [] -} - -moduleclass = 'numlib' -- GitLab From 4a944ea2fd093c34ea0941a39499c694fd26d6b0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 14:32:26 +0200 Subject: [PATCH 1229/2133] dependency for SQLite --- easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb index 442c127432..aa09a6e789 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -23,8 +23,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] dependencies = [ - ('Boost', '1.60.0'), - ('sparsehash', '2.0.2') + ('Boost', '1.60.0'), + ('sparsehash', '2.0.2'), + ('SQLite', '3.9.2'), ] sanity_check_paths = { -- GitLab From 7724b2dfaa1a7cfb474d0c1c7b188dd796ce53b3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 15:42:21 +0200 Subject: [PATCH 1230/2133] ANTLR with foss 2016a --- .../ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a69233b272 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = "2.7.7" + +homepage = 'http://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_includes.patch'] + +pythonversion = '2.7.11' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ + ('Java', '1.8.0_74', '', True), + ('Python', pythonversion), +] + +configopts = '--disable-examples --disable-csharp ' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' -- GitLab From 2b1307343774ae1202878dfafa731a4a6d2f09d0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 16:46:02 +0200 Subject: [PATCH 1231/2133] BayesAss with foss 2016a --- .../b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb new file mode 100644 index 0000000000..3e78699b7f --- /dev/null +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'BayesAss' +version = '3.0.3' + +homepage = 'http://www.rannala.org/?page_id=245' description = """ +BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +sources = ['BA3-%(version)s.tar.gz'] +source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%s/src/' % +version] +dependencies = [ + ('GSL','1.16') +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["BA3"]], + 'dirs' : ['bin','include'] +} + +moduleclass = 'bio' -- GitLab From 4a1fe16ac37a29bdf91da0c140fc6b92f3e7809d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 16:54:33 +0200 Subject: [PATCH 1232/2133] newline added --- easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 3e78699b7f..9f74a15dd0 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -3,7 +3,8 @@ easyblock = 'ConfigureMake' name = 'BayesAss' version = '3.0.3' -homepage = 'http://www.rannala.org/?page_id=245' description = """ +homepage = 'http://www.rannala.org/?page_id=245' +description = """ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes """ -- GitLab From 441d862ecefdf2adc6222a07a7b2129f618ec502 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:09:00 +0200 Subject: [PATCH 1233/2133] HTSlib for foss 2016a --- .../h/HTSlib/HTSlib-1.3-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb new file mode 100644 index 0000000000..7f85666c7d --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.3' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' \ No newline at end of file -- GitLab From 6e446908e5bb57328bccdb45bc08d8e751ec8fa9 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:11:17 +0200 Subject: [PATCH 1234/2133] removed newline --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb index 7f85666c7d..93d7d3c6df 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb @@ -24,4 +24,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From bd6af2e81b9f53060da3ebb1a51fc7abdd4f69ae Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:13:57 +0200 Subject: [PATCH 1235/2133] BCFtools for foss 2016a --- .../b/BCFtools/BCFtools-1.3-foss-2016a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb new file mode 100644 index 0000000000..fe8eabe029 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.3' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [ + ('HTSlib', '1.3'), + ('zlib', '1.2.8'), + ('GSL', '1.16'), +] + +parallel = 1 + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/plugins', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['lib/plugins'], +} + +moduleclass = 'bio' -- GitLab From 0330bcc156ccb9096c94cdee4b1c7c9c479577db Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:23:53 +0200 Subject: [PATCH 1236/2133] quickfix version number --- .../easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 9f74a15dd0..b10287dfdd 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -1,14 +1,14 @@ easyblock = 'ConfigureMake' name = 'BayesAss' -version = '3.0.3' +version = '3.0.4' homepage = 'http://www.rannala.org/?page_id=245' description = """ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes """ -toolchain = {'name': 'foss', 'version': '2016a'} +toolchain = {'name': 'foss','version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%s/src/' % version] @@ -19,7 +19,7 @@ dependencies = [ runtest = 'check' sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["BA3"]], + 'files': [bin/BA3], 'dirs' : ['bin','include'] } -- GitLab From da26578e66c29d9448e012483a1af10a2166b073 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 17:26:13 +0200 Subject: [PATCH 1237/2133] add missing 'easyblock' spec in libunwind easyconfig file --- .../l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb index 5a47aa7676..cdac53c708 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb @@ -6,6 +6,8 @@ # This work is based from experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## +easyblock = 'ConfigureMake' + name = 'libunwind' version = '1.1' @@ -18,13 +20,9 @@ description = """The primary goal of this project is to define a portable and ef toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://download.savannah.gnu.org/releases/libunwind/libunwind-1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] -# --- BM LIB64 --- -# -# On some systems libraries end up in lib/ sanity_check_paths = { 'files': ['include/libunwind.h', ('lib/libunwind.a', 'lib64/libunwind.a')], 'dirs': [], -- GitLab From b824736fb1f0ecb20854c4d1f6cb09a463413246 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 17:29:47 +0200 Subject: [PATCH 1238/2133] add missing 'easyblock' line in Extrae easyconfig + comments in Extrae patch file --- .../Extra-2.4.1_configure-no-shared-binutils.patch | 2 ++ .../e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb | 10 ++++++---- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch b/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch index 8b712760c3..c2fc719e06 100644 --- a/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch +++ b/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch @@ -1,3 +1,5 @@ +fix configure tests for libbfd.a +author: Bernd Mohr (Juelich Supercomputing Centre, Germany) --- configure.orig 2013-11-11 16:38:11.872367495 +0100 +++ configure 2013-11-11 16:38:32.872767289 +0100 @@ -27477,9 +27477,9 @@ diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb index d8500be6ba..a73fcf181f 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb @@ -6,6 +6,8 @@ # This work is based from experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## +easyblock = 'ConfigureMake' + name = "Extrae" version = "2.4.1" @@ -24,7 +26,7 @@ toolchainopts = {"usempi": True} # Requires input of email address for download sources = [SOURCELOWER_TAR_BZ2] -patches = ['Extra-2.4.1_configure-no-shared-binutils.patch'] +patches = ['Extra-%(version)s_configure-no-shared-binutils.patch'] # compiler toolchain depencies dependencies = [ @@ -35,6 +37,9 @@ dependencies = [ ('PAPI', '5.2.0'), ] +# make sure libbfd.a/libiberty.a provided by binutils is used rather than the ones provided by GCC +preconfigopts = 'export LDFLAGS="-L${EBROOTBINUTILS}/lib -L${EBROOTBINUTILS}/lib64 $LDFLAGS" && ' + configopts = ' --with-mpi=${EBROOTOPENMPI}' configopts += ' --with-papi=${EBROOTPAPI} --enable-sampling' configopts += ' --enable-xml --enable-merge-in-trace' @@ -42,11 +47,8 @@ configopts += ' --with-unwind=${EBROOTLIBUNWIND}' configopts += ' --without-dwarf --without-dyninst' configopts += ' --with-boost=${EBROOTBOOST}' configopts += ' --with-binutils=${EBROOTBINUTILS}' -# make sure libbfd.a/libiberty.a provided by binutils is used rather than the ones provided by GCC -preconfigopts = 'export LDFLAGS="-L${EBROOTBINUTILS}/lib -L${EBROOTBINUTILS}/lib64 $LDFLAGS" && ' # --- BM EXTENSIONS --- -# # Extrae also supports CUDA measurements - not yet tested # configopts += ' --with-cuda=${EBROOTCUDA} --with-cupti=${EBROOTCUDA}/extras/CUPTI' -- GitLab From 63ddc7705a012695122cc6a7b58db2d13618d9d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 17:30:54 +0200 Subject: [PATCH 1239/2133] minor change to osdeps in Boost easyconfig --- .../easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb index 3e994ae064..621e1934a4 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = ['zlib-devel'] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' -- GitLab From 0387f648baf38ac56a0ac5b9f41ff9851ba879e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 17:54:38 +0200 Subject: [PATCH 1240/2133] fix name of Boost serial easyconfig --- ....53.0-serial-GCC-4.7.3.eb => Boost-1.53.0-GCC-4.7.3-serial.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/Boost/{Boost-1.53.0-serial-GCC-4.7.3.eb => Boost-1.53.0-GCC-4.7.3-serial.eb} (100%) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-GCC-4.7.3-serial.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb rename to easybuild/easyconfigs/b/Boost/Boost-1.53.0-GCC-4.7.3-serial.eb -- GitLab From e4b84a2bc7e5e6f95e21523fb6b05320e33780a9 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 12 Apr 2016 15:29:39 -0500 Subject: [PATCH 1241/2133] Changing the version (Date Format) and also adding instructions to rename the downloaded file to lx-%(version)s.zip --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 69196eb784..9830a06815 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -5,7 +5,7 @@ easyblock = "PackedBinary" name = 'MRIcron' -version = '06_22_15' +version = '20150601' homepage = 'http://www.mccauslandcenter.sc.edu/mricro/mricron/' description = """ MRIcron allows viewing of medical images. It @@ -17,8 +17,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Automatic Download doesn't work for this software as you need to accept their license, # so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ -# and place it in a folder where Easybuild can see it. -sources = ['lx.zip'] +# and place it in a folder where Easybuild can see it. +# Also rename the zip file to lx-20150601.zip +sources = ['lx-%(version)s.zip'] checksums = ['a2d8b1c053384220953f6b670d0fd4df'] -- GitLab From d25771501a9f87623f013f7f34c643b824846f50 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 12 Apr 2016 15:51:36 -0500 Subject: [PATCH 1242/2133] Renaming the Easyconfig from easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb -> easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb --- .../m/MRIcron/{MRIcron-06_22_15.eb => MRIcron-20150601.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MRIcron/{MRIcron-06_22_15.eb => MRIcron-20150601.eb} (100%) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb similarity index 100% rename from easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb rename to easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb -- GitLab From 428e635f7c6c76b6e89bba45dc64e263930df681 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 12 Apr 2016 23:01:13 +0200 Subject: [PATCH 1243/2133] Add missing zlib dependency to MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 6a1d121ef8..b1dbee0965 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -17,7 +17,8 @@ dependencies = [ ('Java', '1.7.0_79', '', True), ('Python', '2.7.11'), ('HDF5', '1.8.16'), - ('libxml2', '2.9.3', '-Python-%(pyver)s') + ('libxml2', '2.9.3', '-Python-%(pyver)s'), + ('zlib', '1.2.8') ] configopts = '--with-jdk=$JAVA_HOME' -- GitLab From 2a277f236dbba0ad4e31f680f65d5ac4f5d4da27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Apr 2016 07:35:25 +0200 Subject: [PATCH 1244/2133] fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender --- easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb | 4 ++++ easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 1 + .../easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb | 3 +++ 3 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb index 2966a85fa7..a289e5fb02 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb @@ -28,9 +28,13 @@ dependencies = [ ('libxcb', '1.11.1'), ('libXrender', '0.9.9'), ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), ] builddependencies = [ ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 2b4eff3bde..2d93058e5e 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -15,6 +15,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index eee347a314..1e63340752 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -14,6 +14,9 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28') ] dependencies = [ -- GitLab From b9067f93645bb3e7ac817334393b612f4d21ad47 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 10:50:26 +0200 Subject: [PATCH 1245/2133] fix (pyver)s --- .../a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb index a69233b272..ddbfe7c092 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'ANTLR' version = "2.7.7" +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.antlr2.org/' description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) @@ -16,12 +17,9 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] -pythonversion = '2.7.11' -versionsuffix = "-Python-%s" % pythonversion - dependencies = [ ('Java', '1.8.0_74', '', True), - ('Python', pythonversion), + ('Python', '2.7.11'), ] configopts = '--disable-examples --disable-csharp ' -- GitLab From 46471130a735bf0c4bcc673d57e4f92dc0128e01 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 13 Apr 2016 10:19:44 +0100 Subject: [PATCH 1246/2133] Update rtracklayer to 1.30.4 --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 2 +- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 78a36e128c..60ddc2ec31 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -80,7 +80,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.3', bioconductor_options), + ('rtracklayer', '1.30.4', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index 42093e636a..75d2568589 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -79,7 +79,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.3', bioconductor_options), + ('rtracklayer', '1.30.4', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), -- GitLab From b38448a86b6ed9d38ab6d5653d2582a50ddbae0d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:39:21 +0200 Subject: [PATCH 1247/2133] quickfixes, but still needs GSL-2.1 dependency --- .../easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index b10287dfdd..ba5608e32b 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -10,8 +10,9 @@ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes toolchain = {'name': 'foss','version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] -source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%s/src/' % -version] + +source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/'] + dependencies = [ ('GSL','1.16') ] @@ -20,7 +21,7 @@ runtest = 'check' sanity_check_paths = { 'files': [bin/BA3], - 'dirs' : ['bin','include'] + 'dirs' : ['bin', 'include'] } moduleclass = 'bio' -- GitLab From 49bf25ee263585f62beec59942007be8f3dbce47 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:39:49 +0200 Subject: [PATCH 1248/2133] GSL-2.1 dependency --- easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index ba5608e32b..97b9dbe142 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -14,7 +14,7 @@ sources = ['BA3-%(version)s.tar.gz'] source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/'] dependencies = [ - ('GSL','1.16') + ('GSL','2.1') ] runtest = 'check' -- GitLab From 2de7a18c82c6442ebb2bc246fbb2964a4c4ce511 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:42:36 +0200 Subject: [PATCH 1249/2133] GSL for foss 2016a --- .../easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb new file mode 100644 index 0000000000..f4a28c0d8f --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = "2.1" + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'version': '2016a', 'name': 'foss'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' -- GitLab From db2effc74e8f575a3632e68206455bab132a3fcd Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:49:49 +0200 Subject: [PATCH 1250/2133] missing quotes --- easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 97b9dbe142..0dc4a540af 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -20,7 +20,7 @@ dependencies = [ runtest = 'check' sanity_check_paths = { - 'files': [bin/BA3], + 'files': ['bin/BA3'], 'dirs' : ['bin', 'include'] } -- GitLab From 84b85cd3604256e9af2be975196276df1bf66c5c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 12:04:52 +0200 Subject: [PATCH 1251/2133] GSL dependency from 1.16 -> 2.1 --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb index fe8eabe029..3e9dc817b1 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -18,7 +18,7 @@ patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] dependencies = [ ('HTSlib', '1.3'), ('zlib', '1.2.8'), - ('GSL', '1.16'), + ('GSL', '2.1'), ] parallel = 1 -- GitLab From f8941af3095fdf106df4e80d4a7e56ee8d96fde2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 16:30:15 +0200 Subject: [PATCH 1252/2133] dos newlines to unix --- .../BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..c3ca739024 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.6.924' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.tar.gz' % version.replace('.', '-')] + +dependencies = [ + ('Perl', '5.22.1'), + ('DB_File', '1.835', versionsuffix), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' -- GitLab From 2d8bab7056a653924682ff0c75bed5b2b9eb77f9 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 16:57:19 +0200 Subject: [PATCH 1253/2133] DB_File for foss 2016a --- .../DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..b280622820 --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.835' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1'), + ('DB', '4.8.30'), +] + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From e65dfd7e88dc147706ce2f11c886b93549b6862e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 16:59:20 +0200 Subject: [PATCH 1254/2133] DB with foss 2016a --- .../easyconfigs/d/DB/DB-4.8.30-foss2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb new file mode 100644 index 0000000000..0db26d6d7e --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '4.8.30' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'tools' -- GitLab From 9c45c9617c8e9beeb9bf697457d644b33c664b3d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 17:02:48 +0200 Subject: [PATCH 1255/2133] biopython with foss 2016a --- .../Biopython-1.65-foss-2016a-2.7.11.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb new file mode 100644 index 0000000000..fc337c6c52 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = "PythonPackage" + +name = 'Biopython' +version = '1.65' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://biopython.org/DIST'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, + 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ + pyshortver), + 'lib/python%s/site-packages/BioSQL' % pyshortver] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' -- GitLab From f41070db77f5eec9d76f3d28e9ff2fbbab6cc607 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 13 Apr 2016 11:56:18 -0400 Subject: [PATCH 1256/2133] PGI: add easyconfig for version 16.3. --- .../p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..def0637f0b --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '16.3' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['618cb7ddbc57d4e4ed1f21a0ab25f427'] + +gccver = '4.9.3' +binutilsver = '2.25' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") + +moduleclass = 'compiler' -- GitLab From d4aba5b03e694f4e89d23260d4aaf6625dcb2c82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Apr 2016 18:53:09 +0200 Subject: [PATCH 1257/2133] fix bitstring 3.1.3 download URL --- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 6 ++++-- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 6 ++++-- .../easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb | 6 ++++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 6 ++++-- .../p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 6 ++++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 6 ++++-- 6 files changed, 24 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index b360b95e8c..51bd3f9ff0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -123,8 +123,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 2556554c13..80212964f1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -123,8 +123,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index 9c41844d2f..a99feb7078 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -126,8 +126,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index 3976e80bf2..bce00fd447 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -126,8 +126,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 62884700e2..0965b7d1e9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -128,8 +128,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 1ecb34bdf1..1468388148 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -126,8 +126,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], -- GitLab From ea5d4a30da2d8caaede51155c211321b3817f9c7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 21:06:48 +0200 Subject: [PATCH 1258/2133] buildopts added --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb index 3e9dc817b1..6d469bdd3b 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -25,6 +25,7 @@ parallel = 1 skipsteps = ['configure'] +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1' installopts = ' prefix=%(installdir)s' postinstallcmds = [ -- GitLab From 3aed66b4731165b057fa9396425c15ab63f5971a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 14 Apr 2016 11:07:18 +0800 Subject: [PATCH 1259/2133] initial support for ABINIT-7.10.5 with intel-2016.02-GCC-4.9 toolchain --- .../ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..d59f27574e --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,24 @@ +# initially generated with eb ABINIT-7.10.4-intel-2015a.eb --try-software-version=7.10.5 +# --try-toolchain=intel,2016.02-GCC-4.9, worked but it seems to at least lack mpi support +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = "7.10.5" + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' + -- GitLab From 81be1a45da8cdbe335fe23b0a0a6cf396c8512d2 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 22:29:10 -0700 Subject: [PATCH 1260/2133] OptiX 3.8.0: fix easyconfig issues --- .../o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb index db096d2117..a4d1d070ca 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb @@ -3,6 +3,7 @@ # Authors:: Stephane Thiell ## easyblock = 'Binary' + name = 'OptiX' version = '3.8.0' @@ -13,21 +14,26 @@ description = """OptiX is NVIDIA SDK for easy ray tracing performance. toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} -#source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] - +# Registration required. Download links: +# https://developer.nvidia.com/designworks/optix/download +# https://developer.nvidia.com/designworks/optix/downloads/legacy sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.run'] checksums = [ 'ecf63cf32b87defa36d3cd283d085314', # NVIDIA-OptiX-SDK-3.8.0-linux64.run + '73eb689d6247e3d406cf3a38e80ec473', # NVIDIA-OptiX-SDK-3.7.0-linux64.run ] install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" sanity_check_paths = { - 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.so", "lib64/liboptixu.so"], + 'files': ["include/optix.h", + "include/optix_cuda.h", + "lib64/liboptix.%s" % SHLIB_EXT, + "lib64/liboptixu.%s" % SHLIB_EXT], 'dirs': [] } -modextravars = { 'OPTIX_HOME': '%(installdir)s' } +modextravars = {'OPTIX_HOME': '%(installdir)s'} moduleclass = 'vis' -- GitLab From 83165bc9263c9bd20569d013fda4c8b7c68a3711 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 22:29:41 -0700 Subject: [PATCH 1261/2133] add Nvidia OptiX 3.9.0 easyconfig --- .../o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..c8c1772071 --- /dev/null +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors:: Stephane Thiell +## +easyblock = 'Binary' + +name = 'OptiX' +version = '3.9.0' + +homepage = 'https://developer.nvidia.com/optix' +description = """OptiX is NVIDIA SDK for easy ray tracing performance. + It provides a simple framework for accessing the GPU’s massive ray tracing + power using state-of-the-art GPU algorithms.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +# Registration required. Download links: +# https://developer.nvidia.com/designworks/optix/download +# https://developer.nvidia.com/designworks/optix/downloads/legacy +sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.sh'] + +checksums = [ + '13b1953af766b82e0a4aaa28766a05a1', # NVIDIA-OptiX-SDK-3.9.0-linux64.sh +] + +install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ["include/optix.h", + "include/optix_cuda.h", + "lib64/liboptix.%s" % SHLIB_EXT, + "lib64/liboptixu.%s" % SHLIB_EXT], + 'dirs': [] +} + +modextravars = {'OPTIX_HOME': '%(installdir)s'} + +moduleclass = 'vis' -- GitLab From 0a8d27bcbf785078454859c00a483c64a99cd40b Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 22:54:42 -0700 Subject: [PATCH 1262/2133] add easyconfig for CUDA 7.0.28 --- easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb new file mode 100644 index 0000000000..e6b47b55c2 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -0,0 +1,18 @@ +name = 'CUDA' +version = '7.0.28' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux.run'] + +modextravars = {'CUDA_HOME': '%(installdir)s'} + +moduleclass = 'system' -- GitLab From e1f57b8fb0e64c025494208f50636c69c0cd6797 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 14 Apr 2016 07:25:03 +0100 Subject: [PATCH 1263/2133] Updates for limma, edgeR, Gviz, Rsubread --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 8 ++++---- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 60ddc2ec31..13ad83c774 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -62,7 +62,7 @@ exts_list = [ ('preprocessCore', '1.32.0', bioconductor_options), ('affy', '1.48.0', bioconductor_options), ('GO.db', '3.2.2', bioconductor_options), - ('limma', '3.26.8', bioconductor_options), + ('limma', '3.26.9', bioconductor_options), ('RBGL', '1.46.0', bioconductor_options), ('org.Hs.eg.db', '3.2.3', bioconductor_options), ('AnnotationForge', '1.12.2', bioconductor_options), @@ -70,7 +70,7 @@ exts_list = [ ('annaffy', '1.42.0', bioconductor_options), ('gcrma', '2.42.0', bioconductor_options), ('oligoClasses', '1.32.0', bioconductor_options), - ('edgeR', '3.12.0', bioconductor_options), + ('edgeR', '3.12.1', bioconductor_options), ('PFAM.db', '3.2.2', bioconductor_options), ('perm', '1.0-0.0', ext_options), ('baySeq', '2.4.1', bioconductor_options), @@ -126,13 +126,13 @@ exts_list = [ ('Mfuzz', '2.30.0', bioconductor_options), ('maSigPro', '1.42.0', bioconductor_options), ('SPIA', '2.22.0', bioconductor_options), - ('Gviz', '1.14.4', bioconductor_options), + ('Gviz', '1.14.7', bioconductor_options), ('cummeRbund', '2.12.1', bioconductor_options), ('GenomicFiles', '1.6.2', bioconductor_options), ('derfinderHelper', '1.4.1', bioconductor_options), ('derfinder', '1.4.4', bioconductor_options), ('polyester', '1.6.0', bioconductor_options), - ('Rsubread', '1.20.3', bioconductor_options), + ('Rsubread', '1.20.5', bioconductor_options), ('pcaMethods', '1.60.0', bioconductor_options), ('marray', '1.48.0', bioconductor_options), ('CGHbase', '1.30.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index 75d2568589..64a35be205 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -61,7 +61,7 @@ exts_list = [ ('preprocessCore', '1.32.0', bioconductor_options), ('affy', '1.48.0', bioconductor_options), ('GO.db', '3.2.2', bioconductor_options), - ('limma', '3.26.8', bioconductor_options), + ('limma', '3.26.9', bioconductor_options), ('RBGL', '1.46.0', bioconductor_options), ('org.Hs.eg.db', '3.2.3', bioconductor_options), ('AnnotationForge', '1.12.2', bioconductor_options), @@ -69,7 +69,7 @@ exts_list = [ ('annaffy', '1.42.0', bioconductor_options), ('gcrma', '2.42.0', bioconductor_options), ('oligoClasses', '1.32.0', bioconductor_options), - ('edgeR', '3.12.0', bioconductor_options), + ('edgeR', '3.12.1', bioconductor_options), ('PFAM.db', '3.2.2', bioconductor_options), ('perm', '1.0-0.0', ext_options), ('baySeq', '2.4.1', bioconductor_options), @@ -125,13 +125,13 @@ exts_list = [ ('Mfuzz', '2.30.0', bioconductor_options), ('maSigPro', '1.42.0', bioconductor_options), ('SPIA', '2.22.0', bioconductor_options), - ('Gviz', '1.14.4', bioconductor_options), + ('Gviz', '1.14.7', bioconductor_options), ('cummeRbund', '2.12.1', bioconductor_options), ('GenomicFiles', '1.6.2', bioconductor_options), ('derfinderHelper', '1.4.1', bioconductor_options), ('derfinder', '1.4.4', bioconductor_options), ('polyester', '1.6.0', bioconductor_options), - ('Rsubread', '1.20.3', bioconductor_options), + ('Rsubread', '1.20.5', bioconductor_options), ('pcaMethods', '1.60.0', bioconductor_options), ('marray', '1.48.0', bioconductor_options), ('CGHbase', '1.30.0', bioconductor_options), -- GitLab From 52f5d1c9486f961db52a9ec2ff4373b760e0d539 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 23:34:11 -0700 Subject: [PATCH 1264/2133] add easyconfig for cuDNN 4.0 and 5.0 --- easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb | 32 ++++++++++++++++++++++ easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb | 32 ++++++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb new file mode 100644 index 0000000000..5bcd0e1aa3 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '4.0' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-7.0-linux-x64-v%(version)s-prod.tgz'] + +dependencies = [('CUDA', '7.5.18')] + +checksums = [ + '845ead4b37f1a2a243d7d1b4d42d1d8b', # cudnn-7.0-linux-x64-v4.0-prod.tgz +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb new file mode 100644 index 0000000000..fcf816c8fb --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '5.0' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-7.5-linux-x64-v%(version)s-rc.tgz'] + +dependencies = [('CUDA', '7.5.18')] + +checksums = [ + '0febee3f11276218668857191514b7e0', # cudnn-7.5-linux-x64-v5.0-rc.tgz +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' -- GitLab From 0de0c65aa8aee81d2dbb094481227bf4976ca9dd Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 23:52:00 -0700 Subject: [PATCH 1265/2133] OptiX: fix a few issues --- easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb | 5 +---- easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb | 4 +--- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb index a4d1d070ca..69dec5c347 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb @@ -21,15 +21,12 @@ sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.run'] checksums = [ 'ecf63cf32b87defa36d3cd283d085314', # NVIDIA-OptiX-SDK-3.8.0-linux64.run - '73eb689d6247e3d406cf3a38e80ec473', # NVIDIA-OptiX-SDK-3.7.0-linux64.run ] install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" sanity_check_paths = { - 'files': ["include/optix.h", - "include/optix_cuda.h", - "lib64/liboptix.%s" % SHLIB_EXT, + 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.%s" % SHLIB_EXT, "lib64/liboptixu.%s" % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb index c8c1772071..7960265e87 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb @@ -26,9 +26,7 @@ checksums = [ install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" sanity_check_paths = { - 'files': ["include/optix.h", - "include/optix_cuda.h", - "lib64/liboptix.%s" % SHLIB_EXT, + 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.%s" % SHLIB_EXT, "lib64/liboptixu.%s" % SHLIB_EXT], 'dirs': [] } -- GitLab From 278865b55584db402d5cbe24ffd599c6b90a0d0e Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 23:59:34 -0700 Subject: [PATCH 1266/2133] remove CUDA_HOME modext as it is already handled by easyblock --- easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb index e6b47b55c2..87e535776e 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -13,6 +13,4 @@ source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_majo sources = ['%(namelower)s_%(version)s_linux.run'] -modextravars = {'CUDA_HOME': '%(installdir)s'} - moduleclass = 'system' -- GitLab From 4a4426f75304e17e6e10c50200e4527aa4f8fd32 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 09:37:21 +0200 Subject: [PATCH 1267/2133] Add ALPS --- .../ALPS-2.2b4-intel-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..27a5876ff2 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'ALPS' +version = '2.2b4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.example.com' +description = """ The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort +aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ +libraries for simplifying the development of such code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://alps.comp-phys.org/static/software/releases'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('HDF5', '1.8.16'), + ('matplotlib', '1.5.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'phys' -- GitLab From c972ef56ffd0e56fa124971f5ef54666cf5b5bae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 10:16:24 +0200 Subject: [PATCH 1268/2133] add easyconfig Perl-5.20.3-intel-2015a.eb --- .../p/Perl/Perl-5.20.3-intel-2015a.eb | 909 ++++++++++++++++++ 1 file changed, 909 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb new file mode 100644 index 0000000000..e4d3b47d6f --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb @@ -0,0 +1,909 @@ +name = 'Perl' +version = '5.20.3' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.58', { + 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('TAP::Harness::Env', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.021', { + 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '0.46', { + 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.93', { + 'source_tmpl': 'DateTime-TimeZone-1.93.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.22', { + 'source_tmpl': 'Try-Tiny-0.22.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Params::Validate', '1.21', { + 'source_tmpl': 'Params-Validate-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.20', { + 'source_tmpl': 'DateTime-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Module::Build', '0.4214', { + 'source_tmpl': 'Module-Build-0.4214.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Readonly', '2.00', { + 'source_tmpl': 'Readonly-2.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.27', { + 'source_tmpl': 'Tree-DAG_Node-1.27.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.48', { + 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.72', { + 'source_tmpl': 'Shell-0.72.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.47', { + 'source_tmpl': 'PathTools-3.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::WrapTie', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.40', { + 'source_tmpl': 'Test-Exception-0.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.11', { + 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.69', { + 'source_tmpl': 'URI-1.69.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.00', { + 'source_tmpl': 'Pod-POM-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.43', { + 'source_tmpl': 'Text-Diff-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.020', { + 'source_tmpl': 'IO-Socket-SSL-2.020.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Getopt::Long', '2.47', { + 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '0.117', { + 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.000002', { + 'source_tmpl': 'Moo-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.05', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.63', { + 'source_tmpl': 'Test-Differences-0.63.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.14', { + 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9912', { + 'source_tmpl': 'version-0.9912.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD/'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.30', { + 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.11', { + 'source_tmpl': 'AnyEvent-7.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0609', { + 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], 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('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('LWP', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000001', { + 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.19', { + 'source_tmpl': 'File-Which-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.39', { + 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.42', { + 'source_tmpl': 'Scalar-List-Utils-1.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('IO::Scalar', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.87', { + 'source_tmpl': 'Log-Handler-0.87.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Devel::StackTrace', '2.00', { + 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1603', { + 'source_tmpl': 'Moose-2.1603.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.33', { + 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9154', { + 'source_tmpl': 'CPANPLUS-0.9154.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Harness', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.04', { + 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.14', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' -- GitLab From 5baa6d14a4f0a16626d4317e433b63f618984f40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 10:22:07 +0200 Subject: [PATCH 1269/2133] fix Perl dependency in worker, it required non-standard Perl modules --- easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index e3023d8f2c..cdf0174497 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('Perl', '5.20.1', '-bare') + ('Perl', '5.20.3') ] # adjust worker configuration file -- GitLab From c8354ece8ecb261c40e561951d32c1d0c002684f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 13:10:24 +0200 Subject: [PATCH 1270/2133] add easyconfig dask-0.8.2-intel-2016a-Python-2.7.11.eb --- .../dask-0.8.2-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..10a9f3bf36 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From 15df4db6a6f422c44e7f33a2f203776aca51fd47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 13:16:45 +0200 Subject: [PATCH 1271/2133] add easyconfig dask-0.8.2-intel-2016a-Python-3.5.1.eb --- .../dask-0.8.2-intel-2016a-Python-3.5.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..7dcf741ab4 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From a34e72227fe18a01ef50128de64d8b9dd7aab7ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 13:41:02 +0200 Subject: [PATCH 1272/2133] add easyconfig worker-1.6.4-intel-2016a.eb --- .../w/worker/worker-1.6.4-intel-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb new file mode 100644 index 0000000000..3c373e597a --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.4' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.22.1') +] + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', # tweak this (maybe) + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', # tweak this (maybe) +] + +moduleclass = 'tools' -- GitLab From 942d3126ede0f528f12f643439eab5b7d96d7043 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 14:35:01 +0200 Subject: [PATCH 1273/2133] add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma --- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 1 + easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index 782d02fe62..c11711336f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), + ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index 5dcd8c848b..f0600eefc0 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), + ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -- GitLab From c9dd68acf5e40c1f285cc47073077135a7c24887 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 14 Apr 2016 08:38:54 -0400 Subject: [PATCH 1274/2133] PGI: adjust license file (suggested by @boegel) and add numactl-GCCcore dependency. --- .../n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb | 25 +++++++++++++++++++ .../p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb | 4 +-- 2 files changed, 27 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..e54c32859f --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('binutils', '2.25')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb index def0637f0b..1b4b9a4866 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb @@ -16,10 +16,10 @@ versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ ('GCCcore', gccver), ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), ] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") +license_file = HOME + '/licenses/pgi/license.dat' moduleclass = 'compiler' -- GitLab From e913f23e064c6018bcd09084aebc10d61b54e7ea Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 14:51:53 +0200 Subject: [PATCH 1275/2133] Almost there for ALPS --- ...1.eb => ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb} | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/a/ALPS/{ALPS-2.2b4-intel-2016a-Python-2.7.11.eb => ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb} (73%) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb similarity index 73% rename from easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb index 27a5876ff2..cf98c0aae4 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'ALPS' -version = '2.2b4' +version = '2.2.b4' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.example.com' @@ -17,12 +17,20 @@ source_urls = ['http://alps.comp-phys.org/static/software/releases'] builddependencies = [('CMake', '3.4.3')] dependencies = [ + ('zlib', '1.2.8'), ('Python', '2.7.11'), - ('Boost', '1.60.0', versionsuffix), + ('Boost', '1.58.0', versionsuffix), ('HDF5', '1.8.16'), ('matplotlib', '1.5.1', versionsuffix), ] +configopts = '-DSZIP_INCLUDE_DIR=$EBROOTSZIP/include -DSZIP_LIBRARY=$EBROOTSZIP/lib ' +configopts += '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' + +separate_build_dir = True + +maxparallel = 1 + sanity_check_paths = { 'files': [], 'dirs': ["."] -- GitLab From 8e87dab94667a21f1e994e7548b7bfc681751c91 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:12:02 +0200 Subject: [PATCH 1276/2133] Add Boost 1.58 for intel/2016a --- .../Boost-1.58.0-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f392ae7ad4 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.58.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From e9dedd35e4fdb96140766e12e25dc1be849b8708 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:35:32 +0200 Subject: [PATCH 1277/2133] Add MariaDB 10.1.13 --- .../j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 23 +++++++++++++++ .../m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 29 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb new file mode 100644 index 0000000000..76daf74962 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.1.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.canonware.com/download/jemalloc/'] +sources = [SOURCE_TAR_BZ2] + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.1']} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb new file mode 100644 index 0000000000..e373db06bd --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.1.13' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('ncurses', '6.0'), + ('jemalloc', '4.1.0'), +] + +builddependencies = [('CMake', '3.4.3')] + +#configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'data' -- GitLab From f1eefdcb7cbdca66815ced46a8c94986afd8e219 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:37:25 +0200 Subject: [PATCH 1278/2133] jemalloc: use github --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 76daf74962..840d6b9d2e 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -9,8 +9,8 @@ description = """jemalloc is a general purpose malloc(3) implementation that emp toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://www.canonware.com/download/jemalloc/'] -sources = [SOURCE_TAR_BZ2] +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] sanity_check_paths = { 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, -- GitLab From 9b6344d8e154a27ab11b607c9fe36330c4c4d291 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:44:15 +0200 Subject: [PATCH 1279/2133] Use autogen for jemalloc --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 840d6b9d2e..26a2f81a65 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://github.com/jemalloc/jemalloc/archive'] sources = ['%(version)s.tar.gz'] +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " + sanity_check_paths = { 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], -- GitLab From 57391a12530ca3fde36656478ed248ed9ecd0b3f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:49:35 +0200 Subject: [PATCH 1280/2133] Fix jemalloc build --- easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 26a2f81a65..59c52ac8e4 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -15,6 +15,7 @@ sources = ['%(version)s.tar.gz'] builddependencies = [('Autotools', '20150215')] preconfigopts = "./autogen.sh && " +prebuildopts = "make dist && " sanity_check_paths = { 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, -- GitLab From 87d301508772d255d769f48a01cc79b066c30236 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:53:00 +0200 Subject: [PATCH 1281/2133] Fix sanity check of jemalloc --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 59c52ac8e4..e13485c431 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -18,11 +18,11 @@ preconfigopts = "./autogen.sh && " prebuildopts = "make dist && " sanity_check_paths = { - 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, - 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'lib/libjemalloc.so.2', 'include/jemalloc/jemalloc.h'], 'dirs': ['share'], } -modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.1']} +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.2']} moduleclass = 'lib' -- GitLab From 494835b0f6103687cafe2ccb67e54767058a8651 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 16:20:47 +0200 Subject: [PATCH 1282/2133] Add options to MariaDB --- .../easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index e373db06bd..dc6e52c840 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -15,11 +15,13 @@ dependencies = [ ('zlib', '1.2.8'), ('ncurses', '6.0'), ('jemalloc', '4.1.0'), + ('PCRE', '8.38'), + ('XZ', '5.2.2'), ] builddependencies = [('CMake', '3.4.3')] -#configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DWITH_INNODB_LZMA=on" sanity_check_paths = { 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], -- GitLab From b1e18a3183cb74b9ad3de414a1610cadfb7a7f98 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 16:54:14 +0200 Subject: [PATCH 1283/2133] Even more deps for MariaDB --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index dc6e52c840..68f736cb1a 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -17,6 +17,8 @@ dependencies = [ ('jemalloc', '4.1.0'), ('PCRE', '8.38'), ('XZ', '5.2.2'), + ('Boost', '1.60.0'), + ('libxml2', '2.9.3'), ] builddependencies = [('CMake', '3.4.3')] -- GitLab From e8ddbaeb437dc2dd0d5f91184e5872522e2a5aee Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 17:37:34 +0200 Subject: [PATCH 1284/2133] Add PostgreSQL 9.5.2 --- .../PostgreSQL-9.5.2-intel-2016a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb new file mode 100644 index 0000000000..eef652753d --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.5.2' + +homepage = 'http://www.mysql.com/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +java = 'Java' +javaver = '1.8.0_77' + +dependencies = [ + (java, javaver, '', True), + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.22.1'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 9a687e50ddb2431600853fa58e563c3b7b54fcf1 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 14 Apr 2016 17:44:10 +0200 Subject: [PATCH 1285/2133] Add easyconfig for latest PAPI version --- .../p/PAPI/PAPI-5.4.3-foss-2016a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb new file mode 100644 index 0000000000..e76514b4cc --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.4.3' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' +description = """PAPI provides the tool designer and application engineer with a consistent interface and + methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables + software engineers to see, in near real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and software stack.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = [ + '3211b5a5bb389fe692370f5cf4cc2412', # papi-5.4.3.tar.gz +] + +start_dir = 'src' + +# parallel build doesn't always work +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", "version", + "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 2c9d18f3b8b4ad7726e68f266d51a22177c755d5 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Thu, 14 Apr 2016 10:21:58 -0700 Subject: [PATCH 1286/2133] Fix source_urls for CUDA 7.0.28 --- easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb index 87e535776e..ab24e09cd3 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -9,7 +9,9 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] +source_urls = [ + 'http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/Prod/local_installers/', +] sources = ['%(namelower)s_%(version)s_linux.run'] -- GitLab From 62c7d9239f1252566faf69b865a3107bd4c10bfb Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 14 Apr 2016 19:26:33 +0200 Subject: [PATCH 1287/2133] Add easyconfig for latest PDT version --- .../easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb new file mode 100644 index 0000000000..a48bf0f63e --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'PDT' +version = '3.21' + +homepage = 'http://www.cs.uoregon.edu/research/pdt/' +description = """Program Database Toolkit (PDT) is a framework for analyzing source + code written in several programming languages and for making rich program knowledge + accessible to developers of static and dynamic analysis tools. PDT implements a standard + program representation, the program database (PDB), that can be accessed in a uniform way + through a class library supporting common PDB operations.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +checksums = [ + '3092ca0d8833b69992c17e63ae66c263', # pdtoolkit-3.21.tar.gz +] + +moduleclass = 'perf' -- GitLab From d9c5268a398def93fbee7c1ca43a024c433394b7 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 14 Apr 2016 19:34:55 +0200 Subject: [PATCH 1288/2133] Add easyconfig for OPARI2 2.0 --- .../o/OPARI2/OPARI2-2.0-foss-2016a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb new file mode 100644 index 0000000000..2f3c2cf421 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb @@ -0,0 +1,38 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0' + +homepage = 'http://www.score-p.org' +description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, + is a source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls to + the POMP2 measurement interface.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] + +checksums = [ + '72350dbdb6139f2e68a5055a4f0ba16c', # opari2-2.0.tar.gz +] + +sanity_check_paths = { + 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From bb3faf23369c5cb5c69f998022a92109f0a88487 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Thu, 14 Apr 2016 10:42:39 -0700 Subject: [PATCH 1289/2133] cuDNN: use 5.0-rc instead of 5.0 (RC version) --- .../easyconfigs/c/cuDNN/{cuDNN-5.0.eb => cuDNN-5.0-rc.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/cuDNN/{cuDNN-5.0.eb => cuDNN-5.0-rc.eb} (91%) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb similarity index 91% rename from easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb rename to easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb index fcf816c8fb..536c2f33c6 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb @@ -6,7 +6,7 @@ easyblock = 'Tarball' name = 'cuDNN' -version = '5.0' +version = '5.0-rc' homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for @@ -16,7 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download -sources = ['%(namelower)s-7.5-linux-x64-v%(version)s-rc.tgz'] +sources = ['%(namelower)s-7.5-linux-x64-v%(version)s.tgz'] dependencies = [('CUDA', '7.5.18')] -- GitLab From 08549d2371151ec00e4332545557bbc407b77f12 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 15 Apr 2016 14:12:41 +1200 Subject: [PATCH 1290/2133] Added zlib configopt per request --- easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb index 7c1a817fb6..59e0331739 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [ ('zlib', '1.2.8'), -- GitLab From e737838f230f762c730bab0ac0c156d886cb7fb6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 15 Apr 2016 10:29:05 +0800 Subject: [PATCH 1291/2133] ensure intel mpi and fft in ABINIT-7.10.5 with intel-2016.02-GCC-4.9 toolchain --- .../ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 25 +++++++++++++------ 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index d59f27574e..003543ca3f 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -1,24 +1,35 @@ -# initially generated with eb ABINIT-7.10.4-intel-2015a.eb --try-software-version=7.10.5 -# --try-toolchain=intel,2016.02-GCC-4.9, worked but it seems to at least lack mpi support +# initially generated with eb ABINIT-7.10.4-intel-2015a.eb --try-software-version=7.10.5 +# --try-toolchain=intel,2016.02-GCC-4.9, then added intel mpi and fft support easyblock = 'ConfigureMake' name = 'ABINIT' version = "7.10.5" homepage = 'http://www.abinit.org/' -description = """ABINIT is a package whose main program allows one to find the total energy, charge density and - electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional - Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} source_urls = ['http://ftp.abinit.org/'] sources = [SOURCELOWER_TAR_GZ] checksums = [] + +# ensure mpi and intel toolchain +configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' \ + '--with-fft-flavor=fftw3-mkl ' \ + '--with-fft-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core"' + +# there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? +# eb --try-amend can be used to install those variants from the same easyconfig file... + sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', + 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], } moduleclass = 'chem' - -- GitLab From a97102970f055a0393f3c52d072bd3f55aed02cc Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 15 Apr 2016 16:47:05 +1200 Subject: [PATCH 1292/2133] Update checksum --- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 3ea34a9824..99e680c26d 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -14,8 +14,10 @@ source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] # tarballs with the same version number can have different checksums. For this # reason, it is suggested to manually download and rename the tarball. The # checksum may also need updating from time to time. +# Checksum last updated: 15 April 2016 +# Date tarball was reported to have been modified: 11 January 2016 sources = ['dftd3-%(version)s.tgz'] -checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] +checksums = [('md5', 'c9d6a92c43bb2ba71ad75f388fdce216')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From cffac5f722257a77ce6ef8b6a705c3f67ab81d8e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 15 Apr 2016 13:03:39 +0800 Subject: [PATCH 1293/2133] files generated with "eb Python-2.7.11-intel-2016a.eb --try-toolchain=intel,2016.02-GCC-4.9 -r" --- .../Autoconf-2.69-intel-2016.02-GCC-4.9.eb | 26 ++++ .../Automake-1.15-intel-2016.02-GCC-4.9.eb | 33 +++++ ...utotools-20150215-intel-2016.02-GCC-4.9.eb | 17 +++ .../bzip2-1.0.6-intel-2016.02-GCC-4.9.eb | 15 ++ .../g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb | 30 ++++ .../libreadline-6.3-intel-2016.02-GCC-4.9.eb | 30 ++++ .../libtool-2.4.6-intel-2016.02-GCC-4.9.eb | 17 +++ .../m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb | 23 +++ .../ncurses-6.0-intel-2016.02-GCC-4.9.eb | 34 +++++ .../Python-2.7.11-intel-2016.02-GCC-4.9.eb | 139 ++++++++++++++++++ .../SQLite-3.9.2-intel-2016.02-GCC-4.9.eb | 40 +++++ .../t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb | 25 ++++ .../Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb | 26 ++++ .../zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb | 22 +++ 14 files changed, 477 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..e627b672b4 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..84750fffa9 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..65fd1e93a3 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..d048641ea5 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..70b7019537 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..c3f437ac8a --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..857c0faabb --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..b3bc79e1fe --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..7c1c8c34c6 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..b8a12d273e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,139 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%s-sse42.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..3555a7ac4c --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..c2af97cc03 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb new file mode 100644 index 0000000000..ed76be27b6 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..a389aa72f5 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From e43d75237ef71c7f231673f9c189e1bdafdf0fcf Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 15 Apr 2016 13:11:17 +0800 Subject: [PATCH 1294/2133] adapted from ASE-3.9.1.4567-intel-2016a-Python-2.7.11.eb --- ...0.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb new file mode 100644 index 0000000000..95f2c7f4a5 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.10.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase/' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ['https://pypi.python.org/packages/source/a/ase/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], +} + +moduleclass = 'chem' -- GitLab From 213c16a9d14446e594d1873b334a7427e51dcf0f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 15 Apr 2016 11:40:36 +0200 Subject: [PATCH 1295/2133] DB-6.2.23 for foss 2016a --- .../easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb new file mode 100644 index 0000000000..fcf1bd7696 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '6.2.23' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["include/db.h"], + 'dirs': [], +} + +moduleclass = 'tools' \ No newline at end of file -- GitLab From 5561b2936134e5e5c2583218364d104f37419971 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 15 Apr 2016 11:46:08 +0200 Subject: [PATCH 1296/2133] Drop java and add Python suffix to PostgreSQL --- ...016a.eb => PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb} | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) rename easybuild/easyconfigs/p/PostgreSQL/{PostgreSQL-9.5.2-intel-2016a.eb => PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb} (95%) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb similarity index 95% rename from easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb rename to easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index eef652753d..a7590c6580 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'PostgreSQL' version = '9.5.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.mysql.com/' description = """PostgreSQL is a powerful, open source object-relational database system. @@ -20,11 +21,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} osdependencies = [('openssl-devel', 'libssl-dev')] -java = 'Java' -javaver = '1.8.0_77' - dependencies = [ - (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), -- GitLab From 9c90718ca8b5ffefc190be503c2e997aeead2c5b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 15 Apr 2016 12:09:27 +0200 Subject: [PATCH 1297/2133] Added MADlib --- .../MADlib-1.9-intel-2016a-Python-2.7.11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..35ae5d23c5 --- /dev/null +++ b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'MADlib' +version = '1.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://madlib.incubator.apache.org' +description = """MADlib: Big Data Machine Learning in SQL for Data Scientists""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['apache-madlib-%(version)s-incubating-source.tar.gz'] +source_urls = ['https://dist.apache.org/repos/dist/release/incubator/madlib/%(version)s-incubating'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('Python', '2.7.11'), + ('PostgreSQL', '9.5.2', versionsuffix), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/madpack'], + 'dirs': [] +} + +moduleclass = 'data' -- GitLab From f0a0f612b846ea753245c4d73fc78f0ea1325c99 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 15 Apr 2016 13:52:48 +0200 Subject: [PATCH 1298/2133] Biopython with foss 2016a --- ...Biopython-1.65-foss-2016a-Python-2.7.11.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..fc337c6c52 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = "PythonPackage" + +name = 'Biopython' +version = '1.65' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://biopython.org/DIST'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, + 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ + pyshortver), + 'lib/python%s/site-packages/BioSQL' % pyshortver] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' -- GitLab From 55e6a328a624cb037bf7a70e9d70fe3e2d8982a2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 15 Apr 2016 14:15:34 +0200 Subject: [PATCH 1299/2133] numpy dependency --- .../b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index fc337c6c52..8730db898f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -30,6 +30,7 @@ versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ (python, pyver), + ('numpy', '1.10.1', versionsuffix) ] sanity_check_paths = { -- GitLab From 9e097a1ed69abae68f558a85caa3128c44b78077 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 14:42:37 +0200 Subject: [PATCH 1300/2133] add easyconfig ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb, add easyconfig freetype-2.6.3-intel-2016a.eb --- .../f/freetype/freetype-2.6.3-intel-2016a.eb | 22 ++++++++ ...ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 55 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb new file mode 100644 index 0000000000..6245460dc2 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.3' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..2cea64ddb8 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,55 @@ +name = 'ROOT' +version = 'v5.34.36' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', + 'ROOT-v5.34.26_libX.patch', +] + +dependencies = [ + ('GSL', '2.1'), + ('Mesa', '11.1.2'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), + ('CFITSIO', '3.38'), + ('freetype', '2.6.3'), + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('libXft', '2.3.2'), + ('libXpm', '3.5.11'), + ('libXext', '1.3.3'), +] + +# use external ZLIB +preconfigopts = 'env ZLIB=$EBROOTZLIB ' + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xrootd --disable-mysql --disable-krb5 --disable-odbc ' +configopts += ' --disable-oracle --disable-pgsql --disable-qt --disable-sqlite' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +configopts += ' --with-cfitsio-incdir=$EBROOTCFITSIO/include --with-cfitsio-libdir=$EBROOTCFITSIO/lib' +configopts += ' --with-opengl-incdir=$EBROOTMESA/include --with-opengl-libdir=$EBROOTMESA/lib' +configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLIBXEXT/lib' +configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' +configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' + +moduleclass = 'data' -- GitLab From 523361945d9181f98ac685afa9cebcd16a0644bb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 14:46:28 +0200 Subject: [PATCH 1301/2133] modernise libxml2 2.9.1 easyconfig --- .../l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb index d68ae2eaee..ae7f22f7a4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -13,15 +14,11 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' - -pythonver = '2.7.5' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.5'), ] moduleclass = 'lib' -- GitLab From 1ac2352b2d011c437af9827b9518b29f661e467e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 14:55:52 +0200 Subject: [PATCH 1302/2133] downgrade back to freetype 2.9.3 due to conflicts in dep graph --- .../r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb index 2cea64ddb8..7d1106317b 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ dependencies = [ ('libxml2', '2.9.3'), ('PCRE', '8.38'), ('CFITSIO', '3.38'), - ('freetype', '2.6.3'), + ('freetype', '2.6.2'), ('Python', '2.7.11'), ('zlib', '1.2.8'), ('libXft', '2.3.2'), -- GitLab From 88eb3bb5814e86288fa54bc8ab85b04733c72eea Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 15 Apr 2016 09:02:06 -0400 Subject: [PATCH 1303/2133] PGI: add OpenMPI and pompi toolchain easyconfigs. --- .../OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 40 +++++++++++++++++++ .../easyconfigs/p/pompi/pompi-2016.03.eb | 19 +++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/p/pompi/pompi-2016.03.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..8cd6dea646 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify + +dependencies = [('hwloc', '1.11.2')] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +#sanity_check_commands = [ +# ('mpicc --version | grep pgcc', ''), +# ('mpicxx --version | grep pgc++', ''), +# ('mpifort --version | grep pgfortran', ''), +#] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb b/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb new file mode 100644 index 0000000000..0bf9bb7552 --- /dev/null +++ b/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'pompi' +version = '2016.03' +pgisuffix = '-GCC-4.9.3-2.25' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.3' + +dependencies = [ + ('PGI', compver, pgisuffix), + ('OpenMPI', '1.10.2', '', ('PGI', '%s%s' % (compver, pgisuffix))), +] + +moduleclass = 'toolchain' -- GitLab From a6b0c16f90bac68dbde7a849e551b15cce6130cb Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 15 Apr 2016 09:57:14 -0400 Subject: [PATCH 1304/2133] PGI: add pomkl-2016.03 toolchain + imkl-11.3.2.181-pompi + HPL --- .../h/HPL/HPL-2.1-pomkl-2016.03.eb | 23 ++++++++++++ .../i/imkl/imkl-11.3.2.181-pompi-2016.03.eb | 36 +++++++++++++++++++ .../easyconfigs/p/pomkl/pomkl-2016.03.eb | 20 +++++++++++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb create mode 100644 easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb new file mode 100644 index 0000000000..73bc06cddb --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb @@ -0,0 +1,23 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'pomkl', 'version': '2016.03'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +# needs to include -ldl or else we get +# .../libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' +import os +os.environ['LIBS'] = '-ldl' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb new file mode 100644 index 0000000000..ac3a95728c --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.2.181' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'pompi', 'version': '2016.03'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb b/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb new file mode 100644 index 0000000000..6b7d80bf52 --- /dev/null +++ b/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'pomkl' +version = '2016.03' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.3' +gccsuff = '-GCC-4.9.3-2.25' + +dependencies = [ + ('PGI', compver, gccsuff), + ('OpenMPI', '1.10.2', '', ('PGI', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.2.181', '', ('pompi', '%s' % (version))), +] + +moduleclass = 'toolchain' -- GitLab From dc578361e24586f76539339d6624d11163d73cfb Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 15 Apr 2016 10:27:01 -0400 Subject: [PATCH 1305/2133] Move checksum under sources. --- .../easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb index e54c32859f..91b7fa73b1 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb @@ -3,8 +3,6 @@ easyblock = 'ConfigureMake' name = 'numactl' version = '2.0.11' -checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] - homepage = 'http://oss.sgi.com/projects/libnuma/' description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. @@ -15,6 +13,8 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] sources = [SOURCE_TAR_GZ] +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + builddependencies = [('binutils', '2.25')] sanity_check_paths = { -- GitLab From 63e171985e5db8c4347f3689c19e473fb2302667 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 22:34:37 +0200 Subject: [PATCH 1306/2133] add easyconfig Singularity-1.0-GCC-4.9.3-2.25.eb --- .../Singularity-1.0-GCC-4.9.3-2.25.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..8d785f5395 --- /dev/null +++ b/easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Singularity' +version = '1.0' + +homepage = 'http://gmkurtzer.github.io/singularity' +description = """Singularity is a portable application stack packaging and runtime utility.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/sapprun', 'bin/singularity'], + 'dirs': ['libexec/singularity'], +} + +moduleclass = 'tools' -- GitLab From 80fdf0a80881156c27cf8f1758b4fa29498ec00e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:10:04 +0800 Subject: [PATCH 1307/2133] removed empty checksums line --- .../easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index 003543ca3f..457e0344c7 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -16,7 +16,6 @@ toolchainopts = {'usempi': True} source_urls = ['http://ftp.abinit.org/'] sources = [SOURCELOWER_TAR_GZ] -checksums = [] # ensure mpi and intel toolchain configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' \ -- GitLab From 4699a7ded9ba555502560808128af5ff10ff9ef7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:31:45 +0800 Subject: [PATCH 1308/2133] use --- .../easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index 457e0344c7..670f55a3aa 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -20,7 +20,7 @@ sources = [SOURCELOWER_TAR_GZ] # ensure mpi and intel toolchain configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' \ '--with-fft-flavor=fftw3-mkl ' \ - '--with-fft-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core"' + '--with-fft-libs="$LIBFFT"' # there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? # eb --try-amend can be used to install those variants from the same easyconfig file... -- GitLab From 2d346147e65a1c386ed640277af77b2570fb42a6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:32:31 +0800 Subject: [PATCH 1309/2133] drop initial comments --- .../easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index 670f55a3aa..56d9801a74 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -1,5 +1,3 @@ -# initially generated with eb ABINIT-7.10.4-intel-2015a.eb --try-software-version=7.10.5 -# --try-toolchain=intel,2016.02-GCC-4.9, then added intel mpi and fft support easyblock = 'ConfigureMake' name = 'ABINIT' -- GitLab From 1cc58270bcf50313de5768625c59b4bdfa7a910e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:33:55 +0800 Subject: [PATCH 1310/2133] fix code style --- .../a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index 56d9801a74..ebe9e262ac 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -18,14 +18,13 @@ sources = [SOURCELOWER_TAR_GZ] # ensure mpi and intel toolchain configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' \ '--with-fft-flavor=fftw3-mkl ' \ - '--with-fft-libs="$LIBFFT"' + '--with-fft-libs="$LIBFFT"' # there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? # eb --try-amend can be used to install those variants from the same easyconfig file... sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', - 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], } -- GitLab From 79992eb03a7801afb1cfb8775b8082eb86d49e9f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:45:14 +0800 Subject: [PATCH 1311/2133] fix code style --- .../a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index ebe9e262ac..049507e41f 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -16,9 +16,9 @@ source_urls = ['http://ftp.abinit.org/'] sources = [SOURCELOWER_TAR_GZ] # ensure mpi and intel toolchain -configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' \ - '--with-fft-flavor=fftw3-mkl ' \ - '--with-fft-libs="$LIBFFT"' +configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' +configopts += '--with-fft-flavor=fftw3-mkl ' +configopts += '--with-fft-libs="$LIBFFT"' # there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? # eb --try-amend can be used to install those variants from the same easyconfig file... -- GitLab From ea458d6c6e4761e35835c3a85f1b25894dc9eab0 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:54:18 +0800 Subject: [PATCH 1312/2133] add CPPFLAGS=-fgnu89-inline to M4 eb --- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb index b3bc79e1fe..899804b18f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 2a5b19d02f135381c0d70b5bddb092400cc9a867 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:55:24 +0800 Subject: [PATCH 1313/2133] use env in libreadline eb --- .../l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb index c3f437ac8a..9c5b9b6279 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + -- GitLab From 21ad457a50367bae49fcabae0713cddf08c4fcfa Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 08:01:55 +0800 Subject: [PATCH 1314/2133] use pyver template --- .../ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 95f2c7f4a5..3592b22134 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'ASE' version = '3.10.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://wiki.fysik.dtu.dk/ase/' description = """ASE is a python package providing an open source Atomic Simulation Environment @@ -12,17 +13,15 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = ['https://pypi.python.org/packages/source/a/ase/'] sources = ['%(namelower)s-%(version)s.tar.gz'] -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ] sanity_check_paths = { 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], - 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } moduleclass = 'chem' -- GitLab From 4a9dbd98c864d90586d41615b289cb2b617d348d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 08:03:41 +0800 Subject: [PATCH 1315/2133] use PYPI_LOWER_SOURCE and SOURCELOWER_TAR_GZ --- .../a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 3592b22134..96dd7193cd 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -10,8 +10,8 @@ description = """ASE is a python package providing an open source Atomic Simulat toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -source_urls = ['https://pypi.python.org/packages/source/a/ase/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] versionsuffix = '-Python-%s' % pyver -- GitLab From 559166337d94b390123c8fd3858e990479bb3851 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 08:05:29 +0800 Subject: [PATCH 1316/2133] remove duplicated versionsuffix --- .../a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 96dd7193cd..ca4b5697db 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -13,8 +13,6 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -versionsuffix = '-Python-%s' % pyver - dependencies = [ ('Python', '2.7.11'), ] -- GitLab From d1ac97c1d17a194f4da66b1863e98566298b9a5b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 15:01:14 +0800 Subject: [PATCH 1317/2133] add variant with libxc support --- ...INIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb new file mode 100644 index 0000000000..113a1ca853 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = "7.10.5" +versionsuffix = "_libxc" + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# ensure mpi and intel toolchain +configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' +configopts += '--with-fft-flavor=fftw3-mkl ' +configopts += '--with-fft-libs="$LIBFFT" ' + +# there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? +# eb --try-amend can be used to install those variants from the same easyconfig file... + +# libxc variant +configopts += '--with-dft-flavor=libxc ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' -- GitLab From ec81d7170848d183f52d41ddb7ed37146662f282 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Sat, 16 Apr 2016 15:47:40 +0200 Subject: [PATCH 1318/2133] Add easyconfig for Cube 4.3.4 --- .../c/Cube/Cube-4.3.4-foss-2016a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb new file mode 100644 index 0000000000..2ac3b5a935 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb @@ -0,0 +1,44 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Cube' +version = '4.3.4' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + '50f73060f55311cb12c5b3cb354d59fa', # cube-4.3.4.tar.gz +] + +dependencies = [ + ('Qt', '4.8.7'), +] + +sanity_check_paths = { + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), + ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' -- GitLab From bd7a5f04e9f9fc8c4125d84c29da5cdec5bbf590 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Sat, 16 Apr 2016 15:57:14 +0200 Subject: [PATCH 1319/2133] Add easyconfig for OTF2 2.0 --- .../easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb new file mode 100644 index 0000000000..42ee5fa840 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb @@ -0,0 +1,38 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '2.0' + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +checksums = [ + '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib/libotf2.a", "lib64/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 08d30a3a12bdcc7a0e31d1a478ec81ea6cedd253 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Sat, 16 Apr 2016 17:31:31 +0200 Subject: [PATCH 1320/2133] Add easyconfig for Score-P 2.0.1 --- .../s/Score-P/Score-P-2.0.1-foss-2016a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb new file mode 100644 index 0000000000..1657f1511e --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Score-P' +version = '2.0.1' + +homepage = 'http://www.score-p.org' +description = """The Score-P measurement infrastructure is a highly scalable and + easy-to-use tool suite for profiling, event tracing, and online analysis of HPC + applications.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['scorep-%(version)s.tar.gz'] +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] + +checksums = [ + '031a82fa26e2c9412e55d964f92fc9e9', # scorep-2.0.1.tar.gz +] + +dependencies = [ + # binutils is implicitly available via GCC toolchain + # ('binutils', '2.25', '', ('GCCcore', '4.9.3')), + ('Cube', '4.3.4'), + ('OPARI2', '2.0'), + ('OTF2', '2.0'), + ('PAPI', '5.4.3'), + ('PDT', '3.21'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ["bin/scorep", "include/scorep/SCOREP_User.h", + ("lib/libscorep_adapter_mpi_event.a", "lib64/libscorep_adapter_mpi_event.a"), + ("lib/libscorep_adapter_mpi_event.%s" % SHLIB_EXT, "lib64/libscorep_adapter_mpi_event.%s" % SHLIB_EXT)], + 'dirs': [], +} + +# Ensure that local metric documentation is found by Cube GUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' -- GitLab From d9bbb9563527681c5ae947bd520e25ff1cadf9ea Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 16 Apr 2016 17:42:07 +0200 Subject: [PATCH 1321/2133] Fix packmol eb and add newest version --- .../p/packmol/packmol-13.243-ictce-4.1.13.eb | 4 ++-- .../p/packmol/packmol-16.103-intel-2016a.eb | 23 +++++++++++++++++++ 2 files changed, 25 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb b/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb index 29c565eb8d..669406175c 100644 --- a/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb @@ -3,13 +3,13 @@ easyblock = "MakeCp" name = 'packmol' version = '13.243' -homepage = 'http://www.cmbi.ru.nl/molden/' +homepage = 'http://www.ime.unicamp.br/~martinez/packmol/' description = "Packing Optimization for Molecular Dynamics Simulations" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['https://packmol.googlecode.com/files'] +source_urls = ['http://leandro.iqm.unicamp.br/packmol/versionhistory'] buildopts = 'FORTRAN="$F90"' diff --git a/easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb b/easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb new file mode 100644 index 0000000000..a5ed58eedd --- /dev/null +++ b/easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = "MakeCp" + +name = 'packmol' +version = '16.103' + +homepage = 'http://www.ime.unicamp.br/~martinez/packmol/' +description = "Packing Optimization for Molecular Dynamics Simulations" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://leandro.iqm.unicamp.br/packmol/versionhistory'] + +buildopts = 'FORTRAN="$F90"' + +files_to_copy = [(['packmol'], 'bin'), 'COPYING', 'AUTHORS', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/packmol', 'COPYING', 'AUTHORS', 'LICENSE'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From fdf27805329e819e54f906f4f8d0efc4ad1298ab Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Sat, 16 Apr 2016 18:29:22 +0200 Subject: [PATCH 1322/2133] Add easyconfig for Scalasca 2.3 --- .../s/Scalasca/Scalasca-2.3-foss-2016a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb new file mode 100644 index 0000000000..250c8ea829 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb @@ -0,0 +1,45 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Scalasca' +version = '2.3' + +homepage = 'http://www.scalasca.org/' +description = """Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The analysis identifies + potential performance bottlenecks -- in particular those concerning communication and + synchronization -- and offers guidance in exploring their causes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] + +checksums = [ + 'de782c8b6ecfce0e16a4b143ba7a9b5a', # scalasca-2.3.tar.gz +] + +dependencies = [ + ('Cube', '4.3.4'), + ('OTF2', '2.0'), +] + +sanity_check_paths = { + 'files': ["bin/scalasca", ("lib/libpearl.replay.a", "lib64/libpearl.replay.a")], + 'dirs': [], +} + +# Ensure that local metric documentation is found by Cube GUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scalasca/patterns'} + +moduleclass = 'perf' -- GitLab From 2bd9fac7ab90a4cb83e0a5c77cfd85273eb56e91 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Sat, 16 Apr 2016 14:11:16 -0400 Subject: [PATCH 1323/2133] Using %(pyver)s and %(pyshortver)s template for ScientificPython and numpy easyconfig --- .../n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb | 8 +++----- .../ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb | 9 +++------ 2 files changed, 6 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb index e591de8fe1..eeb3a0e326 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb @@ -13,14 +13,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['numpy-1.8.1-mkl.patch'] +versionsuffix = '-Python-%(pyver)s' -python = 'Python' -pyver = '2.7.11' -versionsuffix = '-%s-%s' % (python, pyver) +patches = ['numpy-1.8.1-mkl.patch'] dependencies = [ - (python, pyver), + ('Python', '2.7.11'), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index ef29eaf445..c1b4e8f39a 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -13,13 +13,10 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = '-Python-%s' % pyver +versionsuffix = '-Python-%(pyver)s' dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), # older version of numpy than the one included in Python module required # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for ('numpy', '1.8.2', versionsuffix), @@ -29,7 +26,7 @@ options = {'modulename': 'Scientific'} sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/Scientific' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Scientific'], } moduleclass = 'math' -- GitLab From ee958027b6ebcc5c2ee4a0161c16e773e52aa5f9 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Sat, 16 Apr 2016 15:02:52 -0400 Subject: [PATCH 1324/2133] adjust position versionsuffix --- .../n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb | 3 +-- .../ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb index eeb3a0e326..b9ddbc1927 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'numpy' version = '1.8.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.numpy.org' description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: @@ -13,8 +14,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' - patches = ['numpy-1.8.1-mkl.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index c1b4e8f39a..1c40ab4f4d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'ScientificPython' version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://sourcesup.cru.fr/projects/scientific-py/' description = """ScientificPython is a collection of Python modules for scientific computing. @@ -13,7 +14,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' dependencies = [ ('Python', '2.7.11'), -- GitLab From f2412f0594a35ca854a7aa07266a8278ef60fb4a Mon Sep 17 00:00:00 2001 From: jrbosch Date: Sat, 16 Apr 2016 15:05:37 -0400 Subject: [PATCH 1325/2133] Update ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb --- .../ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index 1c40ab4f4d..267282ee97 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -14,7 +14,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.11'), # older version of numpy than the one included in Python module required -- GitLab From 7f3237cc029b0d1f089f80a06e6f764807f8e8f7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 17 Apr 2016 16:16:22 +0200 Subject: [PATCH 1326/2133] preinstall opts --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index b280622820..efd22bd922 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -3,6 +3,9 @@ easyblock = 'PerlModule' name = 'DB_File' version = '1.835' versionsuffix = '-Perl-%(perlver)s' +preinstallopts = 'export DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib' + + homepage = 'http://perldoc.perl.org/DB_File.html' description = """Perl5 access to Berkeley DB version 1.x.""" @@ -14,7 +17,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Perl', '5.22.1'), - ('DB', '4.8.30'), + ('DB', '6.2.23'), ] sanity_check_paths = { -- GitLab From b2ba3820d14534216925834905539bb6153994b9 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 17 Apr 2016 17:25:37 +0200 Subject: [PATCH 1327/2133] Bowtie with foss 2016a --- .../b/Bowtie/Bowtie-1.1.2-foss-2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..7979ba4e23 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb @@ -0,0 +1,18 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +moduleclass = 'bio' -- GitLab From 0e80dac7141e79a117e7674230156c9f66204fc1 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 12:36:43 +1200 Subject: [PATCH 1328/2133] New EasyConfig for binutils 2.26 with the GCC core 4.9.2 --- .../b/binutils/binutils-2.26-GCCcore-4.9.2.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..75c194bc7b --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c6e1b054ff4644003954ba0dbe6ac7dab8a525d9 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:25:07 +1200 Subject: [PATCH 1329/2133] New EasyConfig for binutils 2.25 with GCC core 4.9.2 --- .../b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..a9d4815d89 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From a0283d931e8b0133cca0e511484f4ddb825824d0 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:29:50 +1200 Subject: [PATCH 1330/2133] New EasyConfig for zlib with the GCCcore 4.9.2 compiler --- .../z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..a7b3977bb9 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 74fa24f980d83f4c0bfed691b837d5137a807a0d Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:30:25 +1200 Subject: [PATCH 1331/2133] New EasyConfig for the GCC core -- GCC 4.9.2 compiler --- .../easyconfigs/g/GCCcore/GCCcore-4.9.2.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb new file mode 100644 index 0000000000..01f4776c64 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb @@ -0,0 +1,48 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '4.9.2' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.2' +gcc_name = 'GCC' + +source_urls = [ + 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + '%s-%s.tar.bz2' % (gcc_name.lower(), version), + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('binutils', '2.25'), +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' -- GitLab From 1d9edaed048b05f78f4c52c6c7e8b8985cd9dcd5 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:36:06 +1200 Subject: [PATCH 1332/2133] New EasyConfig for flex 2.5.39 with the GCCcore 4.9.2 toolchain --- .../f/flex/flex-2.5.39-GCCcore-4.9.2.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..71675a8b5c --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb @@ -0,0 +1,19 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.25', '', True) +] + +moduleclass = 'lang' -- GitLab From f0a867d2f56b99b4233ad60709796e966a1d9db7 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:40:26 +1200 Subject: [PATCH 1333/2133] New EasyConfig for M4 1.4.17 with the GCCcore 4.9.2 toolchain --- .../m/M4/M4-1.4.17-GCCcore-4.9.2.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..5551b81d85 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 6b51bde2d6ac315665b0bfe4c83df85a81bbd617 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 15:29:53 +1200 Subject: [PATCH 1334/2133] New EasyConfig for Bison 3.0.4 with the GCCcore 4.9.2 toolchain --- .../b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..159751eac5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From f055ab3a57d7eea9846742e9507bfc302ec8db05 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 15:39:05 +1200 Subject: [PATCH 1335/2133] New EasyConfig for numactl 2.0.11 with the GCCcore toolchain --- .../n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..49ba8f9bf3 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +builddependencies = [('binutils', '2.25')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' -- GitLab From d5737cc4992c7571f25173d5cabd1b68e76560d5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 18 Apr 2016 15:20:26 +0800 Subject: [PATCH 1336/2133] initial commit for BerkeleyGW-1.0.6 using intel-2016.02-GCC-4.9 toolchain (not working) --- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..6b0669dd87 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'BerkeleyGW' +version = "1.0.6" + +homepage = 'http://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk + periodic crystals to nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] +sources = ['BGW-%(version)s.tar.gz'] +checksums = ['8740562da41e87a62eb8d457675e4bfd'] + +files_to_copy = ['*'] + +prebuildopts = 'touch arch.mk; ' + +buildopts = 'all-flavors' + +parallel = 1 -- GitLab From 39fe8799dc0bf5b5332674dc40ea04a4b452d54c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 10:02:22 +0200 Subject: [PATCH 1337/2133] Bonnie++ with foss 2016a --- .../b/Bonnie++/Bonnie++-1.97-foss-2016a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb new file mode 100644 index 0000000000..4d9f9e29d3 --- /dev/null +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'Bonnie++' +version = '1.97' + +homepage = 'http://www.coker.com.au/bonnie++/' +description = """Bonnie++-1.97: Enhanced performance Test of Filesystem I/O""" + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://www.coker.com.au/bonnie++/experimental'] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['sbin/bonnie++'], + 'dirs': [] +} + +moduleclass = 'tools' + -- GitLab From b1c9ec39190cbd12d599b1f0df233e09bb29d230 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 10:25:51 +0200 Subject: [PATCH 1338/2133] remove DB eb file --- .../easyconfigs/d/DB/DB-4.8.30-foss2016a.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb deleted file mode 100644 index 0db26d6d7e..0000000000 --- a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'DB' -version = '4.8.30' - -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' -description = """Berkeley DB enables the development of custom data management solutions, - without the overhead traditionally associated with such custom projects.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['http://download.oracle.com/berkeley-db/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], - 'dirs': ['bin'], -} - -moduleclass = 'tools' -- GitLab From 23b49aa5020cb896337ae7875a886c2d51b0456d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 10:27:59 +0200 Subject: [PATCH 1339/2133] removed DB eb file --- .../easyconfigs/d/DB/DB-4.8.30-foss2016a.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb deleted file mode 100644 index 0db26d6d7e..0000000000 --- a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'DB' -version = '4.8.30' - -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' -description = """Berkeley DB enables the development of custom data management solutions, - without the overhead traditionally associated with such custom projects.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['http://download.oracle.com/berkeley-db/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], - 'dirs': ['bin'], -} - -moduleclass = 'tools' -- GitLab From 9a01d8b691c5da8fdda8188a18eb4a83458bb119 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 11:23:40 +0200 Subject: [PATCH 1340/2133] export path --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index efd22bd922..19d6de4aa0 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -3,7 +3,6 @@ easyblock = 'PerlModule' name = 'DB_File' version = '1.835' versionsuffix = '-Perl-%(perlver)s' -preinstallopts = 'export DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib' @@ -20,6 +19,8 @@ dependencies = [ ('DB', '6.2.23'), ] +preinstallopts = 'export DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" && ' + sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], -- GitLab From 29a97dd8e9370b38c0947ec500a17f4ef87b2997 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 18 Apr 2016 17:24:34 +0800 Subject: [PATCH 1341/2133] initial support of Wannier90-1.2 and 2.0.1 with intel-2016.02-GCC-4.9 --- .../Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 25 ++++++++++++++++++ .../Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 26 +++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..71d744077f --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '1.2' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] + +# ugly hack +prebuildopts = 'rm make.sys; touch make.sys; ' +prebuildopts += 'F90=ifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' + +files_to_copy = [(['wannier90.x'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..e7a229fa5e --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '2.0.1' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] + +# ugly hack +prebuildopts = 'rm make.sys; touch make.sys; ' +prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x'], + 'dirs': [] +} + +moduleclass = 'chem' -- GitLab From 6e96e854e1786abe3f0676ea977c038f95fe4f5f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 12:58:45 +0200 Subject: [PATCH 1342/2133] export path --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 19d6de4aa0..b03011fb99 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -4,8 +4,6 @@ name = 'DB_File' version = '1.835' versionsuffix = '-Perl-%(perlver)s' - - homepage = 'http://perldoc.perl.org/DB_File.html' description = """Perl5 access to Berkeley DB version 1.x.""" @@ -19,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preinstallopts = 'export DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" && ' +preinstallopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], @@ -27,3 +25,4 @@ sanity_check_paths = { } moduleclass = 'data' + -- GitLab From 8a14112aef54d4ff60bfdc915e2ef1c573862fe4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 13:15:33 +0200 Subject: [PATCH 1343/2133] preconfigopts --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index b03011fb99..85e0ba3145 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preinstallopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' +preconfigopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], -- GitLab From e54a2cf119497b7be7322575ab5e5d7bc7efb450 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 13:17:23 +0200 Subject: [PATCH 1344/2133] brackets --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 85e0ba3145..326da3c949 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preconfigopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' +preconfigopts = 'DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], -- GitLab From 281ca1e55eba6725c38c3908d3a9f79d7c294769 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 18 Apr 2016 13:45:40 +0200 Subject: [PATCH 1345/2133] Add easyconfigs for SIONlib (regular and tools) --- .../SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb | 41 +++++++++++++++++++ .../s/SIONlib/SIONlib-1.6.1-foss-2016a.eb | 37 +++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb new file mode 100644 index 0000000000..b8509256ef --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.6.1' +versionsuffix = '-tools' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. This package provides a stripped-down + installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against a tool requiring + a different SIONlib version.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['sionlib-%(version)sl.tar.gz'] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)sl'] + +checksums = [ + '57208e08309cf8892fe3daee90567d21', # sionlib-1.6.1l.tar.gz +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb new file mode 100644 index 0000000000..a093e042cb --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb @@ -0,0 +1,37 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.6.1' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. SIONlib provides different interfaces: + parallel access using MPI, OpenMP, or their combination, and sequential access for post-processing + utilities.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)s'] + +checksums = [ + '47113ebc00ae38c4f0965659427a0242', # sionlib-1.6.1.tar.gz +] + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['sioncom', 'siongen', 'sionser']], + 'dirs': [] +} + +moduleclass = 'lib' -- GitLab From 0b8a1d171cd8ce4edcb8f45412d367407593a480 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 18 Apr 2016 14:28:25 +0200 Subject: [PATCH 1346/2133] Add foss/2016a easyconfig for libunwind 1.1 Enable libunwind support for Score-P --- .../l/libunwind/libunwind-1.1-foss-2016a.eb | 27 +++++++++++++++++++ .../s/Score-P/Score-P-2.0.1-foss-2016a.eb | 1 + 2 files changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb new file mode 100644 index 0000000000..9583401685 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.1' + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index 1657f1511e..66303634bd 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -31,6 +31,7 @@ checksums = [ dependencies = [ # binutils is implicitly available via GCC toolchain # ('binutils', '2.25', '', ('GCCcore', '4.9.3')), + ('libunwind', '1.1'), ('Cube', '4.3.4'), ('OPARI2', '2.0'), ('OTF2', '2.0'), -- GitLab From 7e8ab8b214515ea6b6eaf46ee43d5fcade48778a Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 18 Apr 2016 14:54:42 +0200 Subject: [PATCH 1347/2133] Add SIONlib as a build dependency --- easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb index 42ee5fa840..3b724d990f 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb @@ -28,6 +28,8 @@ checksums = [ '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz ] +builddependencies = [('SIONlib', '1.6.1', '-tools')] + configopts = '--enable-shared' sanity_check_paths = { -- GitLab From aaee1240312cea617f9b801a5f04aaaa4c0cb7e4 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 18 Apr 2016 15:27:53 +0200 Subject: [PATCH 1348/2133] As requested, comment on the tools version --- .../easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb index b8509256ef..e773779617 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb @@ -10,6 +10,8 @@ easyblock = 'ConfigureMake' name = 'SIONlib' version = '1.6.1' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details versionsuffix = '-tools' homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' -- GitLab From 9cca4fb7a7bde5cc26ae1676c8bae8ef71ca0b3f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 18 Apr 2016 13:33:17 -0400 Subject: [PATCH 1349/2133] add IPython 3.2.3 easyconfig for foss 2016a toolchain --- .../IPython-3.2.3-foss-2016a-Python-2.7.11.eb | 85 +++++++++++++++++++ .../l/libsodium/libsodium-1.0.8-foss-2016a.eb | 20 +++++ .../o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb | 27 ++++++ ...MQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb | 29 +++++++ .../util-linux-2.27.1-foss-2016a.eb | 33 +++++++ .../z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb | 35 ++++++++ 6 files changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..02467990c5 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,85 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..ef8bb83cbf --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.8' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb new file mode 100644 index 0000000000..5f92dedd69 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb new file mode 100644 index 0000000000..c279b32410 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.2.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +dependencies = [ + ('Python', '2.7.11'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb new file mode 100644 index 0000000000..6e398ddd1e --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.27.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb new file mode 100644 index 0000000000..c67d70fb3a --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.1.4' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.27.1'), + ('libsodium', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 832b44908ab598ddc706fcd9b75c51e5f3d9103f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 18 Apr 2016 17:04:21 -0400 Subject: [PATCH 1350/2133] add Eigen 3.2.7 for foss 2016a --- .../easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb new file mode 100644 index 0000000000..a45d43c1fa --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.7' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From 2695a9a0755c6dc34e0df8aa241c928479718f44 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 18 Apr 2016 17:53:55 -0400 Subject: [PATCH 1351/2133] include MarkupSafe 0.23 in exts_list --- .../i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb index 02467990c5..f70668f24c 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -48,6 +48,9 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), -- GitLab From 0586ff6d4fcacfd2c8d8b8135c9837d5e2fce4f2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 07:04:59 +0800 Subject: [PATCH 1352/2133] fix prebuildopts --- .../w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 2 +- .../w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index 71d744077f..5359496146 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' +prebuildopts += 'F90=ifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x'], 'bin')] diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index e7a229fa5e..631f9e28bc 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -14,7 +14,8 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' +prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] -- GitLab From b5def49e41686976750ad72b309f87a423364a69 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 19 Apr 2016 13:45:29 +1200 Subject: [PATCH 1353/2133] Removed binutils-2.26 as it is untested and unneeded --- .../b/binutils/binutils-2.26-GCCcore-4.9.2.eb | 42 ------------------- 1 file changed, 42 deletions(-) delete mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb deleted file mode 100644 index 75c194bc7b..0000000000 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'binutils' -version = '2.26' - -homepage = 'http://directory.fsf.org/project/binutils/' -description = "binutils: GNU binary utilities" - -toolchain = {'name': 'GCCcore', 'version': '4.9.2'} - -sources = [SOURCE_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [ - ('M4', '1.4.17'), - ('flex', '2.6.0'), - ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep - ('zlib', '1.2.8'), - # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) -] - -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - -moduleclass = 'tools' -- GitLab From 51f553d9979e251dbf093b75ca12bb52fa5006c3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 15:16:10 +0800 Subject: [PATCH 1354/2133] replace hardcoded ifort with $F90 --- .../w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 2 +- .../w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index 5359496146..73eeb08ff4 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +prebuildopts += 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x'], 'bin')] diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index 631f9e28bc..e4b353566b 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +prebuildopts += 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] -- GitLab From 6a9ae05c1350d30f21dbf43ec17c7d7b2fc378f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 09:34:51 +0200 Subject: [PATCH 1355/2133] clean up Tau easyconfig w.r.t. Tau easyblock --- .../t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb | 110 +++--------------- 1 file changed, 13 insertions(+), 97 deletions(-) diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb index 008012a78d..aef14769f2 100644 --- a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb @@ -6,113 +6,29 @@ # This work is based from experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -import platform - -name = "TAU" -version = "2.22.2" -# --- BM ISSUE --- -# -# Use hardcoded x86_64 here? -machine = platform.machine() +name = 'TAU' +version = '2.22.2' homepage = 'http://tau.uoregon.edu' description = """The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.""" toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} -toolchainopts = {"usempi": True} - -compname = 'GCC' -compver = '4.7.3' - -# compiler toolchain depencies -dependencies = [ - ('OTF', '1.12.4', "", (compname, compver)), - ('PAPI', '5.2.0', "", (compname, compver)), - ('PDT', '3.19', "", (compname, compver)), - #('Scalasca', '1.4.3'), # requires enabling scalasca1 as extra backend - #('Score-P', '1.2.1'), # requires enabling scorep as extra backend - ('VampirTrace', '5.14.4'), # requires enabling vampirtrace as extra backend -] - -extra_backends = [ - #'scalasca1', # deprecated, use scorep backend instead (requires Scalasca v1.x as dependency) - #'vampirtrace', # deprecated, use scorep backend instead (requires VampirTrace as dependency) - 'scorep', # requires Score-P as dependency -] +toolchainopts = {'usempi': True} -# http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.22.2.tar.gz -sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/'] +sources = [SOURCELOWER_TAR_GZ] -# --- BM CONFIGOPTS --- -# -# Compiler should always be specified -- MUCH quicker and SAVER than autodetect -# -c++=[CC|KCC|g++|*xlC*|cxx|pgCC|pgcpp|FCC|guidec++|aCC|c++|ecpc| -# clang++|bgclang++|g++4|icpc|scgcc|scpathCC|pathCC|orCC] -# -cc=[cc|gcc|clang|bgclang|gcc4|scgcc|KCC|pgcc|guidec|*xlc*|ecc|pathcc|orcc] -# -fortran=[gnu|sgi|ibm|ibm64|hp|cray|pgi|absoft|fujitsu|sun|compaq|g95| -# open64|kai|nec|hitachi|intel|absoft|lahey|nagware|pathscale|gfortran|gfortran4] - -# Basic config: compiler, OpenMP, MPI -compcfgopts = ' -cc=gcc -c++=g++ -fortran=gfortran4' -ompcfgopts = ' -opari' -mpicfgopts = ' -mpiinc=${EBROOTOPENMPI}/include -mpilib=${EBROOTOPENMPI}/lib64' - -# Optional extra modes config: -scacfgopts = ' -scalasca=${EBROOTSCALASCA}' -vtcfgopts = ' -vampirtrace=${EBROOTVAMPIRTRACE}' -scocfgopts = ' -scorep=${EBROOTSCOREMINP}' - -# Optional packages config: -pdtcfgopts = ' -pdt=${EBROOTPDT}' -papicfgopts = ' -papi=${EBROOTPAPI}' -optionalcfgs = pdtcfgopts + papicfgopts # + otfcfgopts -# --- BM ISSUE --- -# -# TAU cannot handle name changes yet introduced with OTF-1.12.3 -#otfcfgopts = ' -otf=${EBROOTOTF}' - -# TAU special build procedure -prefix_opt = '-prefix=' -installopts = 'clean' -keeppreviousinstall = True -skipsteps = ['build'] - -# TAU build: Configure + make install for each combination of modes defined above -configopts = [ - # Basic TAU mode + MPI, OMP, OMPI - compcfgopts+mpicfgopts+optionalcfgs, - compcfgopts+ompcfgopts+optionalcfgs, - compcfgopts+mpicfgopts+ompcfgopts+optionalcfgs, - # Scalasca mode + MPI, OMP, OMPI - compcfgopts+mpicfgopts+scacfgopts+optionalcfgs, - compcfgopts+ompcfgopts+scacfgopts+optionalcfgs, - compcfgopts+mpicfgopts+ompcfgopts+scacfgopts+optionalcfgs, - # Vampirtrace mode + MPI, OMP, OMPI - compcfgopts+mpicfgopts+vtcfgopts+optionalcfgs, - compcfgopts+ompcfgopts+vtcfgopts+optionalcfgs, - compcfgopts+mpicfgopts+ompcfgopts+vtcfgopts+optionalcfgs, - # Score-P mode + MPI, OMP, OMPI - compcfgopts+mpicfgopts+scocfgopts+optionalcfgs, - compcfgopts+ompcfgopts+scocfgopts+optionalcfgs, - compcfgopts+mpicfgopts+ompcfgopts+scocfgopts+optionalcfgs, +dependencies = [ + ('OTF', '1.12.4'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), + ('Scalasca', '1.4.3'), + ('Score-P', '1.2.1'), + ('VampirTrace', '5.14.4'), ] -sanity_check_paths = { - 'files': [machine + "/bin/pprof", "include/TAU.h", machine + "/lib/libTAU.so"], - 'dirs': [] -} - - -# default measurement settings -modextravars = { - 'TAU_MAKEFILE': '%(installdir)s/lib/Makefile.tau-papi-mpi-pdt', - 'TAU_PROFILE': '1', - 'TAU_TRACE': '0', - 'TAU_CALLPATH': '1', - 'TAU_CALLPATH_DEPTH': '10', - 'TAU_COMM_MATRIX': '1', -} +# scalasca and vampirtrace backends are deprecated +extra_backends = ['scalasca', 'scorep', 'vampirtrace'] moduleclass = 'perf' -- GitLab From 5ee511dc03e1383691dcf9ce3ce7740a5b091115 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 15:39:45 +0800 Subject: [PATCH 1356/2133] also build and install library --- .../w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 7 +++++-- .../w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 7 +++++-- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index 73eeb08ff4..a1e273882c 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -15,10 +15,13 @@ source_urls = ['http://www.wannier.org/code'] prebuildopts = 'rm make.sys; touch make.sys; ' prebuildopts += 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' -files_to_copy = [(['wannier90.x'], 'bin')] +# build program and library +buildopts = 'all' + +files_to_copy = [(['wannier90.x'], 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x'], + 'files': ['bin/wannier90.x', 'lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index e4b353566b..c85a2e8e7c 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -17,10 +17,13 @@ prebuildopts = 'rm make.sys; touch make.sys; ' prebuildopts += 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] +# build program and library +buildopts = "all" + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x'], + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], 'dirs': [] } -- GitLab From e806c6cde1ebae19b1f2a0083b8f67086b65f01f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 09:42:51 +0200 Subject: [PATCH 1357/2133] clean up VampirTrace easyconfig --- ...VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb | 74 +++++++------------ 1 file changed, 26 insertions(+), 48 deletions(-) diff --git a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb index 304ad188de..7e266eb32f 100644 --- a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb @@ -1,71 +1,49 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD # # This work is based from experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -name = "VampirTrace" -version = "5.14.4" +easyblock = 'ConfigureMake' + +name = 'VampirTrace' +version = '5.14.4' homepage = 'http:/www.tu-dresden.de/zih/vampirtrace/' description = """VampirTrace is an open source library that allows detailed logging of program - execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads). - Besides these typical parallelization paradigms, VampirTrace is capable of tracing GPU accelerated - applications and generates exact time stamps for all GPU related events. - Additional highlights are I/O event and memory allocation tracing as well as recording of counter metrics - like PAPI and external counters. - VampirTrace provides several variants to instrument the application source code, such as manual, automatic - by the compiler, binary (Dyninst) instrumentation and library wrapping. - The log data is written in the Open Trace Format (OTF), which can be analyzed and visualized by the visualization tool Vampir. - VampirTrace has established a wide user base and has become an integral part of Open MPI version 1.3 and higher.""" + execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads).""" toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} -toolchainopts = {"usempi": True} +toolchainopts = {'usempi': True} -compname = 'GCC' -compver = '4.7.3' +sources = [SOURCE_TAR_GZ] +source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get='] -# compiler toolchain depencies dependencies = [ - ('OTF', '1.12.4', "", (compname, compver)), - ('PAPI', '5.2.0', "", (compname, compver)), - ('PDT', '3.19', "", (compname, compver)), + ('OTF', '1.12.4'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), ] -# http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz -sources = [SOURCE_TAR_GZ] -source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get='] +configopts = 'MPIFC="$MPIF90"' -# --- BM CONFIGOPTS --- -# # MPI suite should always be specified -- MUCH quicker and SAVER than autodetect -# --with-hpmpi | --with-pcmpi | --with-intelmpi | --with-intelmpi2 | --with-lam | --with-mpibgl | --with-mpibgp | -# --with-mpibgq | --with-mpich | --with-mpich2 | --with-mvapich | --with-mvapich2 | --with-mpisx | --with-mpisx-ew | -# --with-openmpi | --with-openmpi17 | --with-sgimpt | --with-sunmpi | --with-sunmpi-mt | --with-mpibull2 -# -# --- BM ISSUE --- -# -# MPIxx variable settings and --enable-compinst= options are ToolChain specific!!! -configopts = ' MPIFC=mpif90' -configopts += ' --with-openmpi' # quicker and saver than autodetect -configopts += ' --enable-compinst=gnu' -configopts += ' --with-papi-dir=${EBROOTPAPI}' -configopts += ' --with-extern-otf-dir=${EBROOTOTF}' -configopts += ' --with-tau-instrumentor=${EBROOTPDT}/x86_64/bin/tau_instrumentor' -configopts += ' --with-pdt-cparse=${EBROOTPDT}/x86_64/bin/cparse' -configopts += ' --with-pdt-cxxparse=${EBROOTPDT}/x86_64/bin/cxxparse' -configopts += ' --with-pdt-fparse=${EBROOTPDT}/x86_64/bin/gfparse' -# --- BM EXTENSIONS --- -# -# VamoirTrace does also support CUDA measurements - not yet tested in EasyBuild -# configopts += ' --with-cuda-dir=${CUDADIR}' +# note: these options are toolchain specific! +configopts += " --with-openmpi --enable-compinst=gnu" + +configopts += " --with-papi-dir=${EBROOTPAPI}" +configopts += " --with-extern-otf-dir=${EBROOTOTF}" +configopts += " --with-tau-instrumentor=${EBROOTPDT}/x86_64/bin/tau_instrumentor" +configopts += " --with-pdt-cparse=${EBROOTPDT}/x86_64/bin/cparse" +configopts += " --with-pdt-cxxparse=${EBROOTPDT}/x86_64/bin/cxxparse" +configopts += " --with-pdt-fparse=${EBROOTPDT}/x86_64/bin/gfparse" +# VamoirTrace does also support CUDA measurements - not yet tested +# configopts += " --with-cuda-dir=${CUDADIR}" -# --- BM LIB64 --- -# -# On some systems libraries end up in lib/ sanity_check_paths = { - 'files': ["bin/vtcc", "include/vampirtrace/vt_user.h", "lib64/libvt.a"], + 'files': ['bin/vtcc', 'include/vampirtrace/vt_user.h', ('lib/libvt.a', 'lib64/libvt.a')], 'dirs': [] } -- GitLab From 0332209ac50434cc5c4839baf8e2b627403ba653 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 15:53:41 +0800 Subject: [PATCH 1358/2133] replace ugly hack with patch --- .../Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 6 +++--- .../Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 6 +++--- .../w/Wannier90/Wannier90_1x_ignore_makesys.patch | 11 +++++++++++ .../w/Wannier90/Wannier90_2x_ignore_makesys.patch | 11 +++++++++++ 4 files changed, 28 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index a1e273882c..e92974ac88 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.wannier.org/code'] -# ugly hack -prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +patches = ['Wannier90_1x_ignore_makesys.patch'] + +prebuildopts = 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' # build program and library buildopts = 'all' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index c85a2e8e7c..acef4f4eb1 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -12,9 +12,9 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.wannier.org/code'] -# ugly hack -prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +patches = ['Wannier90_2x_ignore_makesys.patch'] + +prebuildopts = 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' # build program and library diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch new file mode 100644 index 0000000000..66cb495806 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch @@ -0,0 +1,11 @@ +--- src/Makefile.orig 2016-04-19 15:26:27.373047000 +0800 ++++ src/Makefile 2016-04-19 15:26:32.414229150 +0800 +@@ -1,7 +1,7 @@ + # Should be no need to change below this line + # + +-include ../make.sys ++#include ../make.sys + + OBJS = constants.o io.o utility.o parameters.o hamiltonian.o overlap.o \ + kmesh.o disentangle.o wannierise.o plot.o transport.o diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch new file mode 100644 index 0000000000..fa4a6de14a --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch @@ -0,0 +1,11 @@ +--- src/Makefile.2.orig 2016-04-19 15:29:17.248672000 +0800 ++++ src/Makefile.2 2016-04-19 15:29:21.648448096 +0800 +@@ -1,7 +1,7 @@ + # Should be no need to change below this line + # + +-include ../../make.sys ++#include ../../make.sys + + OBJS = constants.o io.o utility.o parameters.o hamiltonian.o overlap.o \ + kmesh.o disentangle.o wannierise.o plot.o transport.o -- GitLab From 00d86c4a4a52e9768716016aa6ab8b2718d6a3c0 Mon Sep 17 00:00:00 2001 From: jgp Date: Tue, 19 Apr 2016 09:58:35 +0200 Subject: [PATCH 1359/2133] PGI: adding Cray's PrgEnv-pgi --- .../easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb diff --git a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb new file mode 100644 index 0000000000..5de532fe82 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb @@ -0,0 +1,21 @@ +easyblock = 'CrayToolchain' + +name = 'CrayPGI' +version = '2016.04' + +homepage = 'http://www.pgroup.com/' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-pgi module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + # ('PrgEnv-pgi/' + version, EXTERNAL_MODULE), + ('PrgEnv-pgi/5.2.82', EXTERNAL_MODULE), + ('pgi/16.3.0' , EXTERNAL_MODULE), + ('cray-mpich/7.3.2', EXTERNAL_MODULE), + # ('cray-libsci/16.03.1', EXTERNAL_MODULE), # Cray does not provide cray-libsci for PrgEnv-pgi +] + +moduleclass = 'toolchain' + -- GitLab From fc2e6ea513107ef4f1dc1e1f88f8757720e52341 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 10:31:14 +0200 Subject: [PATCH 1360/2133] stick to gompi/1.4.12-no-OFED, for which deps are already available --- ...mpi-1.5.12-no-OFED.eb => TAU-2.22.2-gompi-1.4.12-no-OFED.eb} | 2 +- ...12-no-OFED.eb => VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/t/TAU/{TAU-2.22.2-gompi-1.5.12-no-OFED.eb => TAU-2.22.2-gompi-1.4.12-no-OFED.eb} (94%) rename easybuild/easyconfigs/v/VampirTrace/{VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb => VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb} (96%) diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb similarity index 94% rename from easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb index aef14769f2..5632c4ca09 100644 --- a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb @@ -13,7 +13,7 @@ homepage = 'http://tau.uoregon.edu' description = """The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.""" -toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {'usempi': True} source_urls = ['http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/'] diff --git a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb similarity index 96% rename from easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb index 7e266eb32f..02bc1f21cc 100644 --- a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb @@ -15,7 +15,7 @@ homepage = 'http:/www.tu-dresden.de/zih/vampirtrace/' description = """VampirTrace is an open source library that allows detailed logging of program execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads).""" -toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {'usempi': True} sources = [SOURCE_TAR_GZ] -- GitLab From 449cc75fd5e13863595ea0e308c1b36c3d644962 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 17:52:05 +0800 Subject: [PATCH 1361/2133] add explanatory comments to patch files --- .../easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch | 2 ++ .../easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch index 66cb495806..07fb605587 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch @@ -1,3 +1,5 @@ +avoid including make.sys, which contains hardcoding settings we don't need/want +author: Miguel Dias Costa (National University of Singapore) --- src/Makefile.orig 2016-04-19 15:26:27.373047000 +0800 +++ src/Makefile 2016-04-19 15:26:32.414229150 +0800 @@ -1,7 +1,7 @@ diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch index fa4a6de14a..8bf5e9aa01 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch @@ -1,3 +1,5 @@ +avoid including make.sys, which contains hardcoding settings we don't need/want +author: Miguel Dias Costa (National University of Singapore) --- src/Makefile.2.orig 2016-04-19 15:29:17.248672000 +0800 +++ src/Makefile.2 2016-04-19 15:29:21.648448096 +0800 @@ -1,7 +1,7 @@ -- GitLab From 777c8581b0c4d9f63871586b1a28ff6d0f39fc61 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 19 Apr 2016 14:21:08 +0200 Subject: [PATCH 1362/2133] removed newline --- easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb index 4d9f9e29d3..f63a76fa69 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb @@ -26,4 +26,3 @@ sanity_check_paths = { } moduleclass = 'tools' - -- GitLab From 5ae36bfe05d535e1d664cd00d5bb0747a4eb051d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 19 Apr 2016 14:22:53 +0200 Subject: [PATCH 1363/2133] use of env --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 326da3c949..8c069fec94 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preconfigopts = 'DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], -- GitLab From 7010b4032c4c42ea200bdcc329aa738a607c5863 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 15:04:01 +0200 Subject: [PATCH 1364/2133] add easyconfig LLVM-3.8.0-intel-2016a.eb, add easyconfig CMake-3.5.2-intel-2016a.eb --- .../c/CMake/CMake-3.5.2-intel-2016a.eb | 31 +++++++++++++++ .../l/LLVM/LLVM-3.8.0-intel-2016a.eb | 39 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb new file mode 100644 index 0000000000..6d07f31ebd --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb new file mode 100644 index 0000000000..1aa8a611cd --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.5.1'), + ('Python', '2.7.11'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' -- GitLab From 2f12335cd3d739900ac625cc64cee51876236104 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 15:08:40 +0200 Subject: [PATCH 1365/2133] modify easyconfig LLVM-3.8.0-intel-2016a.eb --- easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb index 1aa8a611cd..7a9543d260 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb @@ -28,9 +28,11 @@ dependencies = [ ] configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON" sanity_check_paths = { - 'files': ['bin/llvm-ar'], + 'files': ['bin/llvm-ar', 'bin/FileCheck'], 'dirs': ['include/llvm', 'include/llvm-c'], } -- GitLab From f8842a7e96418b884e6dbdbfa0eb6d8f59dc7981 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 20:12:42 +0200 Subject: [PATCH 1366/2133] add easyconfig Rust-1.8.0-intel-2016a.eb --- .../r/Rust/Rust-1.8.0-intel-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb new file mode 100644 index 0000000000..e2f00427e8 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.8.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] + +builddependencies = [('Python', '2.7.11')] + +dependencies = [ + ('LLVM', '3.8.0'), +] + +configopts = "--llvm-root=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' -- GitLab From eaef4d4ce138181088a256bc62175b61bda94114 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 22:05:31 +0200 Subject: [PATCH 1367/2133] add easyconfig HDF-4.2.11-intel-2016a.eb --- .../h/HDF/HDF-4.2.11-intel-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb new file mode 100644 index 0000000000..1d7ce9b8e5 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.11' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] +dependencies = [ + ('Szip', '2.1'), +] + +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' -- GitLab From b0b683b2d704da4733dd791e2041277c6be48968 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Tue, 19 Apr 2016 23:31:46 -0400 Subject: [PATCH 1368/2133] add libQGLViewer easyconfig for foss 2016a --- .../libQGLViewer-2.6.3-foss-2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb new file mode 100644 index 0000000000..12e821c14c --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'EB_libQGLViewer' + +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Qt', '4.8.7')] + +start_dir = '%(builddir)s/libQGLViewer-2.6.3/QGLViewer' + +moduleclass = 'lib' -- GitLab From 2a6a0dcb8c30c4edc6ac385c528b424601686ee1 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 20 Apr 2016 01:15:13 -0400 Subject: [PATCH 1369/2133] add GDB 7.10.1 easyconfig for foss 2016a --- .../GDB-7.10.1-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..7a28658458 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('Python', '2.7.11'), +] + +configopts = '--with-python' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' -- GitLab From e331243065a34afc93b9af7cc0603fc8faff5b89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Apr 2016 09:30:40 +0200 Subject: [PATCH 1370/2133] modify easyconfig HDF-4.2.11-intel-2016a.eb --- easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb index 1d7ce9b8e5..28e5e6ad36 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ ('Szip', '2.1'), + ('libjpeg-turbo', '1.4.2'), ] configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" -- GitLab From 62cc9b3e75ad621c2b74b36f8d6afe3c373c39d9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:16:16 +0200 Subject: [PATCH 1371/2133] Adjusted MADlib to supported postgresql version --- .../MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb index 35ae5d23c5..074b5142d7 100644 --- a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb @@ -12,18 +12,25 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = ['apache-madlib-%(version)s-incubating-source.tar.gz'] source_urls = ['https://dist.apache.org/repos/dist/release/incubator/madlib/%(version)s-incubating'] -builddependencies = [('CMake', '3.4.3')] +builddependencies = [ + ('CMake', '3.4.3'), + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('M4', '1.4.17'), + ('Boost', '1.60.0', versionsuffix), + ('Eigen', '3.2.7'), + ('PyXB', '1.2.4', versionsuffix), +] dependencies = [ ('Python', '2.7.11'), - ('PostgreSQL', '9.5.2', versionsuffix), + ('PostgreSQL', '9.4.7', versionsuffix), ] separate_build_dir = True sanity_check_paths = { 'files': ['bin/madpack'], - 'dirs': [] } moduleclass = 'data' -- GitLab From 5ad7cefb45a8dc6d5129d7196242ccd18fd01f2c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:47:49 +0200 Subject: [PATCH 1372/2133] Add Postgres-XL --- ...gres-XL-9.5r1-intel-2016a-Python-2.7.11.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..01c5da8a48 --- /dev/null +++ b/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Postgres-XL' +version = '9.5r1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.postgres-xl.org' +description = """Postgres-XL is a horizontally scalable open source SQL database cluster, +flexible enough to handle varying database workloads:""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://files.postgres-xl.org'] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.22.1'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' -- GitLab From ef50f1d4407173b2965c5a94a07d89f9a83fdb40 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:48:32 +0200 Subject: [PATCH 1373/2133] Add PostgreSQL 9.4.7 (needed for compatibility of MADlib) --- ...tgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..20f36a2447 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.4.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.mysql.com/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.22.1'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From fa95df64e5dc0ca93d6df41a3c32f7d125be6d22 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:52:01 +0200 Subject: [PATCH 1374/2133] Drop MADlib in this PR --- .../MADlib-1.9-intel-2016a-Python-2.7.11.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb deleted file mode 100644 index 074b5142d7..0000000000 --- a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'MADlib' -version = '1.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://madlib.incubator.apache.org' -description = """MADlib: Big Data Machine Learning in SQL for Data Scientists""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = ['apache-madlib-%(version)s-incubating-source.tar.gz'] -source_urls = ['https://dist.apache.org/repos/dist/release/incubator/madlib/%(version)s-incubating'] - -builddependencies = [ - ('CMake', '3.4.3'), - ('Bison', '3.0.4'), - ('flex', '2.6.0'), - ('M4', '1.4.17'), - ('Boost', '1.60.0', versionsuffix), - ('Eigen', '3.2.7'), - ('PyXB', '1.2.4', versionsuffix), -] - -dependencies = [ - ('Python', '2.7.11'), - ('PostgreSQL', '9.4.7', versionsuffix), -] - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['bin/madpack'], -} - -moduleclass = 'data' -- GitLab From 677926d3c95857f05067e4b2c6fc06088948ef07 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 11:02:33 +0200 Subject: [PATCH 1375/2133] Extend sanity check postgreSQL --- .../PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 4 ++-- .../PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb index 20f36a2447..9afa456cae 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -37,8 +37,8 @@ builddependencies = [ configopts = '--with-python --with-openssl' sanity_check_paths = { - 'files': ['bin/psql'], - 'dirs': [], + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index a7590c6580..fca7dea11c 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -37,8 +37,8 @@ builddependencies = [ configopts = '--with-python --with-openssl' sanity_check_paths = { - 'files': ['bin/psql'], - 'dirs': [], + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], } moduleclass = 'data' -- GitLab From 40dfcc220736688ada38def26b300fd15ae280ed Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 17:46:24 +0800 Subject: [PATCH 1376/2133] use patch to disable including arck.mk and define everything in prebuildopts --- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 19 +++++++--- ...keleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 35 +++++++++++++++++++ .../BerkeleyGW/BerkeleyGW_ignore_archmk.patch | 12 +++++++ 3 files changed, 62 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 6b0669dd87..7b6ed07c7d 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -4,8 +4,8 @@ name = 'BerkeleyGW' version = "1.0.6" homepage = 'http://www.berkeleygw.org' -description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle - properties and the optical responses of a large variety of materials from bulk +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} @@ -15,10 +15,21 @@ source_urls = ['http://www.berkeleygw.org/releases/'] sources = ['BGW-%(version)s.tar.gz'] checksums = ['8740562da41e87a62eb8d457675e4bfd'] +patches = ['BerkeleyGW_ignore_archmk.patch'] + files_to_copy = ['*'] -prebuildopts = 'touch arch.mk; ' +prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' +prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' +prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' +prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' buildopts = 'all-flavors' -parallel = 1 +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..2001776308 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'BerkeleyGW' +version = "1.1-beta2" + +homepage = 'http://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk + periodic crystals to nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] +sources = ['BGW-%(version)s.tar.gz'] +checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] + +patches = ['BerkeleyGW_ignore_archmk.patch'] + +files_to_copy = ['*'] + +prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' +prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' +prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' +prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' + +buildopts = 'all-flavors' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch new file mode 100644 index 0000000000..47898699a6 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch @@ -0,0 +1,12 @@ +avoid including arch.mk, which contains hardcoding settings we don't need/want +author: Miguel Dias Costa (National University of Singapore) +--- Common/common-rules.mk.orig 2016-04-20 13:44:00.254262000 +0800 ++++ Common/common-rules.mk 2016-04-20 13:44:07.830742486 +0800 +@@ -1,5 +1,5 @@ +-$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) +-include $(PREFIX)/arch.mk ++#$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) ++#include $(PREFIX)/arch.mk + + ifneq ($(wildcard $(PREFIX)/flavor.mk),) + include $(PREFIX)/flavor.mk -- GitLab From cb89189505ade779e2cd9cb9da9bb29f254db6fc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 13:23:46 +0200 Subject: [PATCH 1377/2133] ALPS now builds! --- .../ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb | 8 ++++---- .../a/ALPS/ALPS-2.2.b4-python-embedding.patch | 14 ++++++++++++++ 2 files changed, 18 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb index cf98c0aae4..ce0520f4ab 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://alps.comp-phys.org/static/software/releases'] +patches = ['ALPS-%(version)s-python-embedding.patch'] + builddependencies = [('CMake', '3.4.3')] dependencies = [ @@ -29,11 +31,9 @@ configopts += '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' separate_build_dir = True -maxparallel = 1 - sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['bin/alpspython', 'lib/libalps.%s' % SHLIB_EXT], + 'dirs': ['include/alps', 'lib/python'] } moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch new file mode 100644 index 0000000000..5927e2e784 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch @@ -0,0 +1,14 @@ +# To embed python, it must return a list of needed libraries with `;` instead of whitespace +# Ward Poelmans +diff -ur alps-2.2.b4-src.orig/alps/config/FindPython.cmake alps-2.2.b4-src/alps/config/FindPython.cmake +--- alps-2.2.b4-src.orig/alps/config/FindPython.cmake 2015-09-20 21:21:42.000000000 +0200 ++++ alps-2.2.b4-src/alps/config/FindPython.cmake 2016-04-20 11:28:18.828407677 +0200 +@@ -160,7 +160,7 @@ + # + # libraries which must be linked in when embedding + # +- EXEC_PYTHON_SCRIPT ("from distutils.sysconfig import * ;print (str(get_config_var('LOCALMODLIBS')) + ' ' + str(get_config_var('LIBS'))).strip()" ++ EXEC_PYTHON_SCRIPT ("from distutils.sysconfig import * ;print (str(get_config_var('LOCALMODLIBS')) + ' ' + str(get_config_var('LIBS'))).strip().replace(' ', ';')" + PYTHON_EXTRA_LIBS) + MESSAGE(STATUS "PYTHON_EXTRA_LIBS =${PYTHON_EXTRA_LIBS}" ) + mark_as_advanced(PYTHON_EXTRA_LIBS) -- GitLab From 523b4f05f0dc5b78abb1323e9ddf4cdbab5a86ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Apr 2016 13:26:34 +0200 Subject: [PATCH 1378/2133] add easyconfig Rust-1.8.0-foss-2016a.eb --- .../r/Rust/Rust-1.8.0-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb new file mode 100644 index 0000000000..2254e51fbf --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.8.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] + +builddependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' -- GitLab From 240bbc87f7f4d346cedc3b29e326d7103fc24898 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 13:35:52 +0200 Subject: [PATCH 1379/2133] Let ALPS find Szip --- .../a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb index ce0520f4ab..74ee42be3a 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb @@ -20,14 +20,14 @@ builddependencies = [('CMake', '3.4.3')] dependencies = [ ('zlib', '1.2.8'), + ('Szip', '2.1'), ('Python', '2.7.11'), ('Boost', '1.58.0', versionsuffix), ('HDF5', '1.8.16'), ('matplotlib', '1.5.1', versionsuffix), ] -configopts = '-DSZIP_INCLUDE_DIR=$EBROOTSZIP/include -DSZIP_LIBRARY=$EBROOTSZIP/lib ' -configopts += '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' +configopts = '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' separate_build_dir = True -- GitLab From 11b5379ba4bf016e2b2346f903746b7fd7f76a2f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 13:52:50 +0200 Subject: [PATCH 1380/2133] Fix remarks --- ...ntel-2016a.eb => GDB-7.11-intel-2016a-Python-2.7.11.eb} | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/GDB/{GDB-7.11-intel-2016a.eb => GDB-7.11-intel-2016a-Python-2.7.11.eb} (95%) diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb similarity index 95% rename from easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb rename to easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb index fa5295e98e..7f2305c130 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb @@ -2,14 +2,17 @@ easyblock = 'ConfigureMake' name = 'GDB' version = '7.11' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "The GNU Project Debugger" +toolchain = {'name': 'intel', 'version': '2016a'} + sources = [SOURCELOWER_TAR_XZ] source_urls = [GNU_SOURCE] -toolchain = {'name': 'intel', 'version': '2016a'} +patches = ['GDB-7.9-missing-makeinfo.patch'] dependencies = [ ('zlib', '1.2.8'), @@ -19,8 +22,6 @@ dependencies = [ ('Python', '2.7.11'), ] -patches = ['GDB-7.9-missing-makeinfo.patch'] - configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' configopts += '--with-system-readline --enable-tui --enable-plugins' -- GitLab From 2f64f6c34e127ecd2095843c44409d7690926f31 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 14:52:09 +0200 Subject: [PATCH 1381/2133] Add explicit include for fslsurface --- easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb index 145ff09b91..a26ad87936 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb @@ -14,6 +14,8 @@ patches = [ 'FSL_icc_nan-inf_fix.patch', ] +preconfigopts = 'CFLAGS="-I%(builddir)s/src $CFLAGS"' + dependencies = [ ('freeglut', '3.0.0'), ('expat', '2.1.0'), -- GitLab From 3993ccc5f2970b1a36159c23a3681e14c025a912 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 15:00:08 +0200 Subject: [PATCH 1382/2133] Fix Werror error for MariaDB --- .../m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 8 ++++++-- .../m/MariaDB/MariaDB-10.1.13-remove-Werror.patch | 14 ++++++++++++++ 2 files changed, 20 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index 68f736cb1a..9a05f86ff3 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -11,19 +11,23 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-%(version)s-remove-Werror.patch'] + dependencies = [ ('zlib', '1.2.8'), ('ncurses', '6.0'), ('jemalloc', '4.1.0'), ('PCRE', '8.38'), ('XZ', '5.2.2'), - ('Boost', '1.60.0'), + ('Boost', '1.60.0', '-Python-2.7.11'), ('libxml2', '2.9.3'), ] builddependencies = [('CMake', '3.4.3')] -configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DWITH_INNODB_LZMA=on" +separate_build_dir = True + +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DMYSQL_MAINTAINER_MODE=ON" sanity_check_paths = { 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch new file mode 100644 index 0000000000..c7d04caf71 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch @@ -0,0 +1,14 @@ +diff -ur mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake +--- mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-03-24 10:12:12.000000000 +0100 ++++ mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-04-20 14:29:31.019940551 +0200 +@@ -156,8 +156,8 @@ + endif () + + ## always want these +-set(CMAKE_C_FLAGS "-Wall -Werror ${CMAKE_C_FLAGS}") +-set(CMAKE_CXX_FLAGS "-Wall -Werror ${CMAKE_CXX_FLAGS}") ++set(CMAKE_C_FLAGS "-Wall ${CMAKE_C_FLAGS}") ++set(CMAKE_CXX_FLAGS "-Wall ${CMAKE_CXX_FLAGS}") + + ## need to set -stdlib=libc++ to get real c++11 support on darwin + if (APPLE) -- GitLab From 7cf6555d3c10191f880df6b26dc146d344d44093 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 15:03:08 +0200 Subject: [PATCH 1383/2133] Add doc in patch for Mariadb --- .../easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch index c7d04caf71..eb1812a0ff 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch @@ -1,3 +1,5 @@ +# This -Werror will cause the build to fail because of a warning about using the intel compiler +# Ward Poelmans diff -ur mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake --- mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-03-24 10:12:12.000000000 +0100 +++ mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-04-20 14:29:31.019940551 +0200 -- GitLab From 7329ac036396459a8d987ba66b18919854db545a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 21:51:03 +0800 Subject: [PATCH 1384/2133] use env --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 7b6ed07c7d..573492b3f2 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -19,7 +19,7 @@ patches = ['BerkeleyGW_ignore_archmk.patch'] files_to_copy = ['*'] -prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 2001776308..509645960b 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -19,7 +19,7 @@ patches = ['BerkeleyGW_ignore_archmk.patch'] files_to_copy = ['*'] -prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' -- GitLab From 730ffa4793fdb863db56e34ddd1624b256e014de Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 21:52:12 +0800 Subject: [PATCH 1385/2133] use short indent in description --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 4 ++-- .../BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 573492b3f2..cf8c1e41cf 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -5,8 +5,8 @@ version = "1.0.6" homepage = 'http://www.berkeleygw.org' description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle - properties and the optical responses of a large variety of materials from bulk - periodic crystals to nanostructures such as slabs, wires and molecules.""" + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 509645960b..2b7d7dc5ed 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -5,8 +5,8 @@ version = "1.1-beta2" homepage = 'http://www.berkeleygw.org' description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle - properties and the optical responses of a large variety of materials from bulk - periodic crystals to nanostructures such as slabs, wires and molecules.""" + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} -- GitLab From 57cea100f5dbffb25d4f5eab4e15303622ab55a7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 16:23:37 +0200 Subject: [PATCH 1386/2133] Mariadb: link to -lrt --- .../m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 5 ++++- .../MariaDB-10.1.13-link-rt-for-jemalloc.patch | 14 ++++++++++++++ 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index 9a05f86ff3..ae90e1a3ed 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] sources = [SOURCELOWER_TAR_GZ] -patches = ['MariaDB-%(version)s-remove-Werror.patch'] +patches = [ + 'MariaDB-%(version)s-remove-Werror.patch', + 'MariaDB-%(version)s-link-rt-for-jemalloc.patch', +] dependencies = [ ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch new file mode 100644 index 0000000000..780c41af5b --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch @@ -0,0 +1,14 @@ +# On older systems (like RHEL 6), jemalloc must also link to -lrt for getclock +# On RHEL 7 and greater, this is not needed as it's part of libc there. +# Ward Poelmans +diff -ur mariadb-10.1.13.orig/cmake/jemalloc.cmake mariadb-10.1.13/cmake/jemalloc.cmake +--- mariadb-10.1.13.orig/cmake/jemalloc.cmake 2016-03-24 10:12:10.000000000 +0100 ++++ mariadb-10.1.13/cmake/jemalloc.cmake 2016-04-20 16:21:18.102681504 +0200 +@@ -21,6 +21,7 @@ + SET(what bundled) + ELSE() + SET(libname jemalloc c) ++ SET(CMAKE_REQUIRED_LIBRARIES r) + SET(what system) + ENDIF() + -- GitLab From 6a3bab838e81554fef00f818ee20c01190c71f50 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 22:27:47 +0800 Subject: [PATCH 1387/2133] use ConfigureMake skipping configure instead of MakeCp --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 6 ++++-- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index cf8c1e41cf..570e1b3636 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'BerkeleyGW' version = "1.0.6" @@ -17,7 +17,7 @@ checksums = ['8740562da41e87a62eb8d457675e4bfd'] patches = ['BerkeleyGW_ignore_archmk.patch'] -files_to_copy = ['*'] +skipsteps = ['configure'] prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' @@ -27,6 +27,8 @@ prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLA buildopts = 'all-flavors' +installopts = 'INSTDIR=%(installdir)s' + sanity_check_paths = { 'files': [], 'dirs': ['bin'] diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 2b7d7dc5ed..4c7949cc07 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'BerkeleyGW' version = "1.1-beta2" @@ -17,7 +17,7 @@ checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] patches = ['BerkeleyGW_ignore_archmk.patch'] -files_to_copy = ['*'] +skipsteps = ['configure'] prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' @@ -27,6 +27,8 @@ prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLA buildopts = 'all-flavors' +installopts = 'INSTDIR=%(installdir)s' + sanity_check_paths = { 'files': [], 'dirs': ['bin'] -- GitLab From f3cb8d07b5b4c94abec4f892c8041313ee7f569f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 17:00:41 +0200 Subject: [PATCH 1388/2133] Typo fix --- .../m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch index 780c41af5b..c0a2cfee18 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch @@ -8,7 +8,7 @@ diff -ur mariadb-10.1.13.orig/cmake/jemalloc.cmake mariadb-10.1.13/cmake/jemallo SET(what bundled) ELSE() SET(libname jemalloc c) -+ SET(CMAKE_REQUIRED_LIBRARIES r) ++ SET(CMAKE_REQUIRED_LIBRARIES rt) SET(what system) ENDIF() -- GitLab From 8bce4c48707f8a6e4cc85986c6e013b1085c99a4 Mon Sep 17 00:00:00 2001 From: jgp Date: Wed, 20 Apr 2016 10:05:19 -0500 Subject: [PATCH 1389/2133] PrgEnv-pgi should not be version pinned --- easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb index 5de532fe82..112a9312bc 100644 --- a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb +++ b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb @@ -10,11 +10,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version - # ('PrgEnv-pgi/' + version, EXTERNAL_MODULE), - ('PrgEnv-pgi/5.2.82', EXTERNAL_MODULE), + ('PrgEnv-pgi', EXTERNAL_MODULE), ('pgi/16.3.0' , EXTERNAL_MODULE), ('cray-mpich/7.3.2', EXTERNAL_MODULE), - # ('cray-libsci/16.03.1', EXTERNAL_MODULE), # Cray does not provide cray-libsci for PrgEnv-pgi ] moduleclass = 'toolchain' -- GitLab From ee8043a440abb6accfb24a556ccdb1e391f8c3e9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 23:19:34 +0800 Subject: [PATCH 1390/2133] add most important binaries to sanity_check_path --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 6 ++++-- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 570e1b3636..2b338d6458 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,10 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': [], - 'dirs': ['bin'] + 'files': ['bin/'+name+'.'+flavor+'.x' + for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + for flavor in ['real', 'cplx']], + 'dirs': [] } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 4c7949cc07..42d4b94976 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,10 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': [], - 'dirs': ['bin'] + 'files': ['bin/'+name+'.'+flavor+'.x' + for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + for flavor in ['real', 'cplx']], + 'dirs': [] } moduleclass = 'chem' -- GitLab From 062b8f678410ec70835f69b578bf2778f8f4346a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 21 Apr 2016 00:04:37 +0800 Subject: [PATCH 1391/2133] don't redefine variable 'name' in sanity_check_path --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 4 ++-- .../BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 2b338d6458..452f967939 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,8 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+name+'.'+flavor+'.x' - for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + 'files': ['bin/'+prog+'.'+flavor+'.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] } diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 42d4b94976..04a46cfa50 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,8 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+name+'.'+flavor+'.x' - for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + 'files': ['bin/'+prog+'.'+flavor+'.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] } -- GitLab From 40d739240753148a555a9d0432149f88d93a293d Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 20 Apr 2016 16:47:30 -0400 Subject: [PATCH 1392/2133] including libGLU 9.0.0 as dependency --- .../l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb index 12e821c14c..cd9274f066 100644 --- a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb @@ -11,8 +11,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.libqglviewer.com/src/'] sources = [SOURCE_TAR_GZ] +dependencies = [ + ('libGLU', '9.0.0'), +] + builddependencies = [('Qt', '4.8.7')] -start_dir = '%(builddir)s/libQGLViewer-2.6.3/QGLViewer' +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' moduleclass = 'lib' -- GitLab From d85d97170461ddf8f1b654addca47fc8dfcd2897 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 21 Apr 2016 15:57:05 +0800 Subject: [PATCH 1393/2133] remove patch, copy generic arch.mk instead --- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 14 ++++++-------- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 14 ++++++-------- .../b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch | 12 ------------ 3 files changed, 12 insertions(+), 28 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 452f967939..ef88631251 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -15,17 +15,15 @@ source_urls = ['http://www.berkeleygw.org/releases/'] sources = ['BGW-%(version)s.tar.gz'] checksums = ['8740562da41e87a62eb8d457675e4bfd'] -patches = ['BerkeleyGW_ignore_archmk.patch'] - skipsteps = ['configure'] -prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' -prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' -prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' -prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' -prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' -buildopts = 'all-flavors' +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' +buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' installopts = 'INSTDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 04a46cfa50..07d5635dac 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -15,17 +15,15 @@ source_urls = ['http://www.berkeleygw.org/releases/'] sources = ['BGW-%(version)s.tar.gz'] checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] -patches = ['BerkeleyGW_ignore_archmk.patch'] - skipsteps = ['configure'] -prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' -prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' -prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' -prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' -prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' -buildopts = 'all-flavors' +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' +buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' installopts = 'INSTDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch deleted file mode 100644 index 47898699a6..0000000000 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch +++ /dev/null @@ -1,12 +0,0 @@ -avoid including arch.mk, which contains hardcoding settings we don't need/want -author: Miguel Dias Costa (National University of Singapore) ---- Common/common-rules.mk.orig 2016-04-20 13:44:00.254262000 +0800 -+++ Common/common-rules.mk 2016-04-20 13:44:07.830742486 +0800 -@@ -1,5 +1,5 @@ --$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) --include $(PREFIX)/arch.mk -+#$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) -+#include $(PREFIX)/arch.mk - - ifneq ($(wildcard $(PREFIX)/flavor.mk),) - include $(PREFIX)/flavor.mk -- GitLab From d62ec8db0c825e6d49318e8b7ca39ae771e67717 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 21 Apr 2016 15:58:49 +0800 Subject: [PATCH 1394/2133] edit homepage --- .../a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index ca4b5697db..a8183634de 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'ASE' version = '3.10.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://wiki.fysik.dtu.dk/ase/' +homepage = 'http://wiki.fysik.dtu.dk/ase' description = """ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.""" -- GitLab From 6c33d10734fc28919e332f46e9379110bcd0a316 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 21 Apr 2016 10:50:17 +0200 Subject: [PATCH 1395/2133] Fix remarks --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index e13485c431..7bee41cdcd 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -19,10 +19,10 @@ prebuildopts = "make dist && " sanity_check_paths = { 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, - 'lib/libjemalloc.so.2', 'include/jemalloc/jemalloc.h'], + 'include/jemalloc/jemalloc.h'], 'dirs': ['share'], } -modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.2']} +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} moduleclass = 'lib' -- GitLab From 4cf2eea4df6c8009160944677838d710c796c45d Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 21 Apr 2016 11:26:15 +0200 Subject: [PATCH 1396/2133] Updated easyconfig for Extrae --- .../e/Extrae/Extrae-3.0.1-foss-2015a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb new file mode 100644 index 0000000000..52f70c46db --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "Extrae" +version = "3.0.1" + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools' +description = """Extrae is the core instrumentation package developed by the Performance Tools + group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, + CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered + by Extrae typically includes timestamped events of runtime calls, performance counters and source + code references. Besides, Extrae provides its own API to allow the user to manually instrument his + or her application.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {"usempi": True} + +compname = 'GCC' +compver = '4.8.3' + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.22', "", (compname, compver)), + ('Boost', '1.58.0', '-serial', (compname, compver)), + ('libunwind', '1.1', "", (compname, compver)), + ('libxml2', '2.9.2', "", (compname, compver)), + ('libdwarf', '20150310', "", (compname, compver)), + ('PAPI', '5.4.1'), +] + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = [SOURCELOWER_TAR_BZ2] + +moduleclass = 'perf' -- GitLab From fe659cbc50239dfb0b128bca3a87430c52976f79 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 21 Apr 2016 11:35:43 +0200 Subject: [PATCH 1397/2133] Add easyconfigs for dependencies --- .../b/Boost/Boost-1.58.0-GCC-4.8.3-serial.eb | 25 ++++++++++ .../l/libdwarf/libdwarf-20150310-GCC-4.8.3.eb | 35 ++++++++++++++ .../l/libelf/libelf-0.8.13-GCC-4.8.3.eb | 19 ++++++++ .../l/libunwind/libunwind-1.1-GCC-4.8.3.eb | 23 ++++++++++ .../l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb | 23 ++++++++++ .../p/PAPI/PAPI-5.4.1-foss-2015a.eb | 46 +++++++++++++++++++ 6 files changed, 171 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.8.3-serial.eb create mode 100644 easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.8.3-serial.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.8.3-serial.eb new file mode 100644 index 0000000000..1284a2ff8d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.8.3-serial.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' +versionsuffix = '-serial' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source +libraries.""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +configopts = '--with-libraries=serialization' + +toolset = 'gcc' + +osdependencies = [('zlib-devel','zlib1g-dev')] + +sanity_check_paths = { + 'files': ["lib/libboost_serialization.a"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.8.3.eb new file mode 100644 index 0000000000..251774788a --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.8.3.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'libdwarf' +version = '20140805' + +homepage = 'http://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.prevanders.net'] + +dependencies = [('libelf', '0.8.13')] + +with_configure = True +preconfigopts = 'CFLAGS="-fPIC $CFLAGS" ' +configopts = "--enable-shared " + +# This is dirty but libdwarf cannot find it's own library in the build process... +prebuildopts = ' LD_LIBRARY_PATH="../libdwarf:$LD_LIBRARY_PATH" ' + +files_to_copy = [ + (["dwarfdump2/dwarfdump"], "bin"), + (["libdwarf/libdwarf.a", "libdwarf/libdwarf.so"], "lib"), + (["libdwarf/libdwarf.h", "libdwarf/dwarf.h"], "include"), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["bin", "lib", "include"] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb new file mode 100644 index 0000000000..5a843a2867 --- /dev/null +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libelf' +version = '0.8.13' + +homepage = 'http://www.mr511.de/software/english.html' +description = """libelf is a free ELF object file access library""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.mr511.de/software/'] + +sanity_check_paths = { + 'files': ['lib/libelf.a', 'lib/libelf.so', 'lib/libelf.so.0', 'include/libelf.h'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.8.3.eb new file mode 100644 index 0000000000..fb68bfa6c7 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.8.3.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = "libunwind" +version = "1.1" + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib64/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb new file mode 100644 index 0000000000..36ce015707 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +#dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb new file mode 100644 index 0000000000..b5babf4529 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.4.1' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' +description = """PAPI provides the tool designer and application engineer with a consistent interface and + methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables + software engineers to see, in near real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and software stack.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# Example download URL, for reference: http://icl.cs.utk.edu/projects/papi/downloads/papi-5.0.0.tar.gz +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +# parallel build doesn't always work +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", "version", + "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 4afabab6c7531707ac95380064ee8104f82f970c Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 21 Apr 2016 11:43:09 +0200 Subject: [PATCH 1398/2133] Updated easyconfigs for Paraver and dependencies --- .../p/Paraver/Paraver-4.5.6-foss-2015a.eb | 33 +++++++++++++++++++ .../wxPropertyGrid-1.4.15-GCC-4.8.3.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb create mode 100644 easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.8.3.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb new file mode 100644 index 0000000000..03007f6aa9 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "Paraver" +version = "4.5.6" + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +compname = 'GCC' +compver = '4.8.3' + +dependencies = [ + ('wxPropertyGrid', '1.4.15', "", (compname, compver)), + ('Boost', '1.58.0', '-serial', (compname, compver)), +] + +osdependencies = ['wxWidgets-ansi-devel'] + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.gz'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.8.3.eb b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.8.3.eb new file mode 100644 index 0000000000..3c8c6c406c --- /dev/null +++ b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.8.3.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' + +name = "wxPropertyGrid" +version = "1.4.15" + +homepage = 'http://wxpropgrid.sourceforge.net/' +description = """wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is + a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +osdependencies = ['wxWidgets-ansi-devel'] + +# http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz?download +sources = ['wxpropgrid' + '-%(version)s-src.tar.gz'] +source_urls = ['http://prdownloads.sourceforge.net/wxpropgrid/'] + +sanity_check_paths = { + 'files': ["include/wx/propgrid/propgrid.h", "lib64/libwxcode_gtk2_propgrid-2.8.so"], + 'dirs': [] +} + +parallel = 1 + +moduleclass = 'devel' -- GitLab From 6a4d11c588f7e31daf36f0f34262d769f3c1f92f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 08:41:23 +0800 Subject: [PATCH 1399/2133] generated with 'eb netCDF-Fortran-4.4.2-intel-2015b.eb --try-toolchain=intel,2016.02-GCC-4.9 -r' --- .../Bison-3.0.4-intel-2016.02-GCC-4.9.eb | 22 ++++++++++++ .../CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 31 +++++++++++++++++ .../cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb | 31 +++++++++++++++++ .../Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb | 19 +++++++++++ .../flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb | 14 ++++++++ ...DF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb | 26 ++++++++++++++ .../ncurses-5.9-intel-2016.02-GCC-4.9.eb | 18 ++++++++++ ...CDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb | 20 +++++++++++ .../netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb | 34 +++++++++++++++++++ .../s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb | 23 +++++++++++++ 10 files changed, 238 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..64d95d529f --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..c09f6ccec0 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..7135e0d493 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.45.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..6c27df0850 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.10' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.1'), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..154963c1c8 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..42dda90335 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.15-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..5385893f9b --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,18 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +# see https://bbs.archlinux.org/viewtopic.php?id=194029&p=3 +buildopts = 'CPP="$CC -E -P"' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..80d70623d7 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +version = '4.4.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.3.3.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..a58bf39670 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.3.3.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.15-patch1'), + ('cURL', '7.45.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.10'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..d8f05c9dd2 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c87e72f236cf524b40675127c28af5e3e637a479 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 22 Apr 2016 02:14:39 -0400 Subject: [PATCH 1400/2133] include Loki as dependency of Yade --- .../l/Loki/Loki-0.1.7-foss-2016a.eb | 23 +++++++++++++++++++ .../l/Loki/Loki-0.1.7_change_prefix.patch | 9 ++++++++ 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb new file mode 100644 index 0000000000..dcb7370cfb --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Loki' +version = '0.1.7' + +homepage = 'http://loki-lib.sourceforge.net/' +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +preinstallopts = "export EB_INSTALL_DIR=%(installdir)s &&" + +source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +sanity_check_paths={ + 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], + 'dirs': ['include/loki'], +} + +patches = [('Loki-0.1.7_change_prefix.patch')] diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch b/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch new file mode 100644 index 0000000000..8a0666c803 --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch @@ -0,0 +1,9 @@ +diff -ru loki-0.1.7.orig/Makefile.common loki-0.1.7/Makefile.common +--- loki-0.1.7.orig/Makefile.common 2007-05-28 22:26:26.000000000 -0400 ++++ loki-0.1.7/Makefile.common 2016-04-21 18:20:54.280476472 -0400 +@@ -4,4 +4,4 @@ + CXXWARNFLAGS := -Wall -Wold-style-cast -Wundef -Wsign-compare -Wconversion -Wpointer-arith -pedantic + CXXFLAGS := $(CXXWARNFLAGS) -g -O2 + +-prefix := /usr ++prefix := $(EB_INSTALL_DIR) -- GitLab From b19ad0a671fe667e1e66833ee29de83515a95e62 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 22 Apr 2016 02:28:24 -0400 Subject: [PATCH 1401/2133] add minieigen easyconfig --- .../Boost-1.60.0-foss-2016a-Python-2.7.11.eb | 23 +++++++++++++++ .../m/minieigen/minieigen-0.5.3-foss-2016a.eb | 28 +++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a913c20849 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.60.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb new file mode 100644 index 0000000000..9012d7f022 --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'minieigen' +version = '0.5.3' + +homepage = 'https://launchpad.net/minieigen/' +description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +versionsuffix = '-Python-%(pyver)s' + +dependencies = [ + ('Boost', '1.60.0', versionsuffix), + ('Eigen', '3.2.7'), + ('Python', '2.7.11'), +] + +#incomplete +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'lib' -- GitLab From f14b5d592e7c8f9f679adc07e1acd3946fff8c27 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 22 Apr 2016 02:31:24 -0400 Subject: [PATCH 1402/2133] improve Yade easyconfig but still not finished --- .../y/Yade/Yade-1.20.0-foss-2016a.eb | 66 ++++++++----------- 1 file changed, 28 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb index 3711be5fc1..83be6ba55d 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'Yade' version = '1.20.0' -homepage = 'www.yade-dem.org' +homepage = 'https://yade-dem.org/doc/' description = """ Yade is an extensible open-source framework for discrete numerical models, focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, allowing independent implementation of new alogrithms and interfaces. @@ -14,50 +14,38 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] sources = [SOURCELOWER_TAR_GZ] -pyver = '2.7.11' -versionsuffix = '-Python-%s' % pyver +versionsuffix = '-Python-%(pyver)s' dependencies = [ - ('git', '2.8.0'), - ('freeglut', '3.0.0'), - ('loki', '-------'), - ('Boost', '1.60.0'), - ('fakeroot', '-------'), - ('dpkg', '-------'), - ('IPython', '3.2.3', versionsuffix), - ('matplotlib', '1.5.1'), - ('SQLite', '3.9.2'), - ('numpy', '1.10.4', versionsuffix) - ('TK', '8.6.4', 'no-X11'), - ('gnuplot', '5.0.3'), - ('gts', '0.7.6'), - ('Graphviz', '2.38'), - ('ScientificPython', '2.9.4', versionsuffix), + ('Loki', '0.1.7'), + ('Boost', '1.60.0', versionsuffix), +# ('IPython', '3.2.3', versionsuffix), +# ('matplotlib', '1.5.1'), +# ('SQLite', '3.9.2'), + ('numpy', '1.8.2', versionsuffix), ('Eigen', '3.2.7'), - ('Qt', '4.8.7'), - ('gtk+', '2.24.28'), - ('libqglviewer-dev', '-------'), - ('libjs-jquery', '---------'), - ('Sphinx', '1.3.3'), - ('bibtexparser', '0.6.0'), - ('libXmu', '1.1.2'), - ('libXi', '1.7.6'), - ('help2man', '--------'), - ('bzip2', '1.0.6'), - ('ziblg-dev', '---------------'), - ('GDB', '7.10.1',versionsuffix), + ('minieigen', '0.5.3') + ('Qt', '4.8.7'), + ('Python', '2.7.11'), +# ('libQGLViewer', '2.6.3'), +# ('GDB', '7.10.1',versionsuffix), # optional - ('VTK', '6.3.0'), - ('CGAL', '4.7'), - ('SuiteSparse', '4.5.1'), - ('OpenBLAS', '0.2.15'), - ('METIS', '5.1.0'), +# ('VTK', '6.3.0'), +# ('CGAL', '4.7'), +# ('SuiteSparse', '4.5.1'), +# ('OpenBLAS', '0.2.15'), +# ('METIS', '5.1.0'), ] -builddependencies = [('CMake', '3.2.3')] +builddependencies = [('CMake', '3.4.3')] separate_build_dir = True +configopts = '-DENABLE_GUI=OFF' +configopts += '-DENABLE_VTK=OFF' +configopts += '-DENABLE_CGAL=OFF' +configopts += '-DENABLE_PFVFLOW=OFF' + # In case you want disable some Yade features # configopts = '-OPTION_1 = OFF -OPTION_2 = OFF ...' @@ -80,9 +68,11 @@ separate_build_dir = True # VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) # USE_QT5: use QT5 for GUI, experimental (OFF by default) + +#incomplete sanity_check_paths = { - 'files': ['bin/%s-%s' %(namelower, version), 'bin/%s-%s-batch' %(namelower, version)], - 'dirs': ['lib/x86_64-linux-gnu'] + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch'], + 'dirs': ["."] } moduleclass = 'devel' -- GitLab From af63af4269d95dc953f708bbaf55655f30273915 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 15:17:53 +0800 Subject: [PATCH 1403/2133] [phys]{intel/2016.02-GCC-4.9} Yambo 3.4.2 --- .../Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..aaa16d016b --- /dev/null +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Yambo' +version = '3.4.2' + +homepage = 'http://www.yambo-code.org' +description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. + Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +dependencies = [('netCDF-Fortran', '4.4.2')] + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/yambo-3.4.2.tgz'] +checksums = ['f0820a0f42dfc81ce3811af647bed777'] + +configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' +configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' +configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff -L$EBROOTNETCDF/lib64 -lnetcdf"' + +buildopts = 'all' + +# no make install +buildininstalldir = 'True' +skipsteps = ['install'] +modextrapaths = {'PATH': '%(namelower)s-%(version)s/bin'} + +sanity_check_paths = { + 'files': ['%(namelower)s-%(version)s/bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', + 'yambo_kerr', 'yambo_ph', 'yambo_surf', 'ypp', 'ypp_ph', 'ypp_surf']], + 'dirs': [] +} + +moduleclass = 'phys' + +parallel = 1 -- GitLab From 2eca14f6b542eb457c27f4aebe36d6fb4496f7ee Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 15:30:48 +0800 Subject: [PATCH 1404/2133] bump ncurses to 6.0 --- .../easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb index c09f6ccec0..df5823de42 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' dependencies = [ - ('ncurses', '5.9'), + ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons #('OpenSSL', '1.0.1p'), -- GitLab From b76df745227c017890c908f28810ae55c805ae1b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 15:42:27 +0800 Subject: [PATCH 1405/2133] change module class --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index ef88631251..c0d639cc89 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -34,4 +34,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'chem' +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 07d5635dac..4700de27c4 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -34,4 +34,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'chem' +moduleclass = 'phys' -- GitLab From 22fc709acd211c30baf89829b9cafdaa0709e873 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 16:54:42 +0800 Subject: [PATCH 1406/2133] remove ncurses-5.9-intel-2016.02-GCC-4.9.eb --- .../ncurses-5.9-intel-2016.02-GCC-4.9.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb deleted file mode 100644 index 5385893f9b..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -# see https://bbs.archlinux.org/viewtopic.php?id=194029&p=3 -buildopts = 'CPP="$CC -E -P"' - -moduleclass = 'devel' -- GitLab From e20edb315e0af6f790c4efa27e69eb4f887bd960 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 17:29:16 +0800 Subject: [PATCH 1407/2133] bump HDF5 to 1.8.16 and cURL to 7.47.0 --- ...016.02-GCC-4.9.eb => cURL-7.47.0-intel-2016.02-GCC-4.9.eb} | 4 ++-- ...016.02-GCC-4.9.eb => HDF5-1.8.16-intel-2016.02-GCC-4.9.eb} | 2 +- .../n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/c/cURL/{cURL-7.45.0-intel-2016.02-GCC-4.9.eb => cURL-7.47.0-intel-2016.02-GCC-4.9.eb} (94%) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb => HDF5-1.8.16-intel-2016.02-GCC-4.9.eb} (96%) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb similarity index 94% rename from easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb rename to easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb index 7135e0d493..45e6650292 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'cURL' -version = '7.45.0' +version = '7.47.0' homepage = 'http://curl.haxx.se' description = """libcurl is a free and easy-to-use client-side URL transfer library, @@ -18,7 +18,7 @@ source_urls = ['http://curl.haxx.se/download/'] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -# dependencies = [('OpenSSL', '1.0.1p')] +# dependencies = [('OpenSSL', '1.0.1s')] # configopts = "--with-ssl=$EBROOTOPENSSL" modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb similarity index 96% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb index 42dda90335..d1c17ce30e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb @@ -1,5 +1,5 @@ name = 'HDF5' -version = '1.8.15-patch1' +version = '1.8.16' homepage = 'http://www.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb index a58bf39670..cff46757ad 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb @@ -16,8 +16,8 @@ source_urls = [ ] dependencies = [ - ('HDF5', '1.8.15-patch1'), - ('cURL', '7.45.0'), + ('HDF5', '1.8.16'), + ('cURL', '7.47.0'), ] builddependencies = [ -- GitLab From bc66427075d6045dce28ff41b2364668b5b56436 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 17:37:27 +0800 Subject: [PATCH 1408/2133] fix source_urls --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index aaa16d016b..f1e84f6a06 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ toolchainopts = {'usempi': True} dependencies = [('netCDF-Fortran', '4.4.2')] sources = [SOURCELOWER_TGZ] -source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/yambo-3.4.2.tgz'] +source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/'] checksums = ['f0820a0f42dfc81ce3811af647bed777'] configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' -- GitLab From 6eca75d940ee822d1eab2eb2c88e973f3b4d596a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 17:38:22 +0800 Subject: [PATCH 1409/2133] move dependencies below checksums --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index f1e84f6a06..bcb6f56739 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -10,12 +10,12 @@ description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid s toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} -dependencies = [('netCDF-Fortran', '4.4.2')] - sources = [SOURCELOWER_TGZ] source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/'] checksums = ['f0820a0f42dfc81ce3811af647bed777'] +dependencies = [('netCDF-Fortran', '4.4.2')] + configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' -- GitLab From 595721d4fb95078144d99129ff0a28a394b79ed2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 11:48:07 +0200 Subject: [PATCH 1410/2133] Biopython sanity check fix --- .../Biopython-1.65-foss-2016a-2.7.11.eb | 45 ------------------- ...Biopython-1.65-foss-2016a-Python-2.7.11.eb | 13 +++--- 2 files changed, 5 insertions(+), 53 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb deleted file mode 100644 index fc337c6c52..0000000000 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas -# License:: MIT/GPL -# -## -easyblock = "PythonPackage" - -name = 'Biopython' -version = '1.65' - -homepage = 'http://www.biopython.org' -description = """Biopython is a set of freely available tools for biological computation written -in Python by an international team of developers. It is a distributed collaborative effort to -develop Python libraries and applications which address the needs of current and future work in -bioinformatics. """ - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['http://biopython.org/DIST'] -sources = ['%(namelower)s-%(version)s.tar.gz'] - -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = "-%s-%s" % (python, pyver) - -dependencies = [ - (python, pyver), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, - 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ - pyshortver), - 'lib/python%s/site-packages/BioSQL' % pyshortver] -} - -options = {'modulename': 'Bio'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index 8730db898f..822334825f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -29,18 +29,15 @@ pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pyver), - ('numpy', '1.10.1', versionsuffix) + (python, pyver) ] sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, - 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ - pyshortver), - 'lib/python%s/site-packages/BioSQL' % pyshortver] + 'files': ['lib/python%(pyshortver)s/site-packages/biopython-%(version)s-py%(pyshortver)s.egg-info'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] } options = {'modulename': 'Bio'} -moduleclass = 'bio' +moduleclass = 'bio' \ No newline at end of file -- GitLab From 9bca295d623e5a844af78e774d8d2e8752b28006 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 11:49:20 +0200 Subject: [PATCH 1411/2133] String fix --- .../b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index 822334825f..f4b92dace0 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -26,7 +26,7 @@ python = 'Python' pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = "-%s-%s" % (python, pyver) +versionsuffix = "-%(python)s-%(pyver)s" dependencies = [ (python, pyver) -- GitLab From 5e94418f4931181e31c47d3be9882d0e6f232dc8 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 18:18:51 +0800 Subject: [PATCH 1412/2133] remove library paths, not needed --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index bcb6f56739..e98b1483ff 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -19,7 +19,7 @@ dependencies = [('netCDF-Fortran', '4.4.2')] configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' -configopts += '--with-netcdf-libs="-L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff -L$EBROOTNETCDF/lib64 -lnetcdf"' +configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' -- GitLab From 37731eef8b1705bc86ad2224890ed318bc6e4329 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 18:33:13 +0800 Subject: [PATCH 1413/2133] use $LIBFFT --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index e98b1483ff..4f192a0588 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -18,7 +18,7 @@ dependencies = [('netCDF-Fortran', '4.4.2')] configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' -configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' +configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="$LIBFFT" ' configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' -- GitLab From 98b99c783631409424f36993ac8b6a14de0f74ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 12:43:11 +0200 Subject: [PATCH 1414/2133] add easyconfig numexpr-2.5.2-intel-2016a-Python-2.7.11.eb --- ...numexpr-2.5.2-intel-2016a-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f3e0914bd5 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'numexpr' +version = '2.5.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From 4046ca8caf31526416dc2842edef61a8b2eb32b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 12:43:29 +0200 Subject: [PATCH 1415/2133] add easyconfig gdist-1.0.3-intel-2016a-Python-2.7.11.eb --- .../gdist-1.0.3-intel-2016a-Python-2.7.11.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f6f38f5d9f --- /dev/null +++ b/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'gdist' +version = '1.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/gdist' +description = """The gdist module is a Cython interface to a C++ library (http://code.google.com/p/geodesic/) for + computing geodesic distance which is the length of shortest line between two vertices on a triangulated mesh in three + dimensions, such that the line lies on the surface.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From 86b9fbf96e643400c35e6ce3eefa37323fe758a5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 12:43:44 +0200 Subject: [PATCH 1416/2133] ext list ? --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index c3ca739024..1e9c0c19f5 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -18,6 +18,12 @@ dependencies = [ ('DB_File', '1.835', versionsuffix), ] +exts_list = [ + ('CGI', '4.28', { + 'source_tmpl': 'CGI-4.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + }), +] options = {'modulename': 'Bio::Perl'} moduleclass = 'bio' -- GitLab From 5307a71e915dea2e5c22e0a634ffd5129298aac2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 12:43:52 +0200 Subject: [PATCH 1417/2133] add easyconfig NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb, add easyconfig PIL-1.1.7-intel-2016a-Python-2.7.11.eb, add easyconfig pydicom-0.9.9-intel-2016a-Python-2.7.11.eb --- ...NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb | 29 +++++++++++++++ .../PIL-1.1.7-intel-2016a-Python-2.7.11.eb | 36 +++++++++++++++++++ ...pydicom-0.9.9-intel-2016a-Python-2.7.11.eb | 26 ++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..77bcd52bff --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'NiBabel' +version = '2.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('PIL', '1.1.7', versionsuffix), + ('pydicom', '0.9.9', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f996585e10 --- /dev/null +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'PIL' +version = '1.1.7' +versionsuffix = '-Python-%(ppyver)s' + +homepage = 'http://www.pythonware.com/products/pil' +description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. + This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://effbot.org/downloads/'] +sources = ['Imaging-%(version)s.tar.gz'] + +patches = ['PIL-%(version)s-find-deps.patch'] + +pyver = '2.7.11' +versionsuffix = '-Python-%s' % pyver +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pyver), + ('libjpeg-turbo', '1.4.2'), + # currently not used because of dependency hell + # ('freetype', '2.6.1'), +] + +options = {'modulename': 'PIL'} + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%s/site-packages/%%(name)s' % pyshortver], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..ab11ff4c9f --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '0.9.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/darcymason/pydicom' +description = """Read, modify and write DICOM files with python code""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/darcymason/pydicom/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('Python', '2.7.11')] + +start_dir = 'source' + +options = {'modulename': 'dicom'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pydicom-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'data' -- GitLab From e2d71772432a501aed37e770db3eec9ea1ddcf08 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 18:58:14 +0800 Subject: [PATCH 1418/2133] switch to MakeCp with configure --- .../y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index 4f192a0588..23778bb6d6 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'Yambo' version = '3.4.2' @@ -16,6 +16,8 @@ checksums = ['f0820a0f42dfc81ce3811af647bed777'] dependencies = [('netCDF-Fortran', '4.4.2')] +with_configure = 'True' + configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="$LIBFFT" ' @@ -23,10 +25,7 @@ configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' -# no make install -buildininstalldir = 'True' -skipsteps = ['install'] -modextrapaths = {'PATH': '%(namelower)s-%(version)s/bin'} +files_to_copy = [(['bin/*'], 'bin')] sanity_check_paths = { 'files': ['%(namelower)s-%(version)s/bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', -- GitLab From d05d19be93bde3c4e31429ccaed73c50213b3406 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 13:43:38 +0200 Subject: [PATCH 1419/2133] modify easyconfig numexpr-2.5.2-intel-2016a-Python-2.7.11.eb --- .../n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb index f3e0914bd5..c352743328 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb @@ -11,7 +11,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'usempi': True} source_urls = ['https://github.com/pydata/numexpr/archive/'] sources = ['v%(version)s.tar.gz'] -- GitLab From 88ddd7a1b72945cb902ef2526ef8b8861b835be1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 13:51:17 +0200 Subject: [PATCH 1420/2133] modify easyconfig PIL-1.1.7-intel-2016a-Python-2.7.11.eb --- .../easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb index f996585e10..dabb8b2f35 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb @@ -27,10 +27,9 @@ dependencies = [ options = {'modulename': 'PIL'} -pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], - 'dirs': ['bin', 'lib/python%s/site-packages/%%(name)s' % pyshortver], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], } moduleclass = 'vis' -- GitLab From 47f5dbe7cec4797ad7745b808c06525bbb6c5c14 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 19:55:50 +0800 Subject: [PATCH 1421/2133] fix path in sanity checks --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index 23778bb6d6..d06eb6d47f 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -28,7 +28,7 @@ buildopts = 'all' files_to_copy = [(['bin/*'], 'bin')] sanity_check_paths = { - 'files': ['%(namelower)s-%(version)s/bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', + 'files': ['bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', 'yambo_kerr', 'yambo_ph', 'yambo_surf', 'ypp', 'ypp_ph', 'ypp_surf']], 'dirs': [] } -- GitLab From aa313b0431ca16e479e1be7c4795aa7befe6ad18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 14:34:28 +0200 Subject: [PATCH 1422/2133] usempi is not required for numexpr --- .../n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb | 1 - .../n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 1 - .../n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb | 1 - .../n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb index b59dd7b4f3..12e8271d88 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'usempi': True} source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 0f25285835..986566870c 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'usempi': True} source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb index 585a1680b7..7b2e107b82 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'usempi': True} source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb index a1e1df7d77..0012640a1c 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'usempi': True} source_urls = ['https://github.com/pydata/numexpr/archive/'] sources = ['v%(version)s.tar.gz'] -- GitLab From fbb287eb014e34d2f02e1f96ed017af399d46e51 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 14:44:11 +0200 Subject: [PATCH 1423/2133] add easyconfig PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb --- ...PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb new file mode 100644 index 0000000000..93ba3d3868 --- /dev/null +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'PIL' +version = '1.1.7' +versionsuffix = '-Python-%(ppyver)s' + +homepage = 'http://www.pythonware.com/products/pil' +description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. + This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://effbot.org/downloads/'] +sources = ['Imaging-%(version)s.tar.gz'] + +patches = ['PIL-%(version)s-find-deps.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + ('libjpeg-turbo', '1.4.2'), + ('freetype', '2.6.3'), +] + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' -- GitLab From e2ced009d6dec638e457588563d90907b8a2f26f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 14:52:58 +0200 Subject: [PATCH 1424/2133] Commet with foss2016a --- ...ommet-20160422-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..037900565c --- /dev/null +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'Commet' +version = '20160422' + +homepage = 'https://colibread.inria.fr/software/commet/' +description = """ COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# there is no tarball provided, only git checkout through: +# https://github.com/pierrepeterlongo/commet/archive/master.zip +sources = [SOURCE_ZIP] +files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] + +pythonversion = '2.7.11' +versionsuffix = '-Python-%(pythonversion)s' + +dependencies = [ + ('Python', pythonversion), +] + +checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["Commet.py","bvop","compare_reads","extract_reads","filter_reads","index_and_search"]], + 'dirs' : ['doc','include'] +} + +moduleclass = 'bio' -- GitLab From 7ac6d46d9d2b1bf23b8bd44dd02adcd717c0b08f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 15:14:36 +0200 Subject: [PATCH 1425/2133] stick to freetype 2.6.2 for compatibility with matplotlib 1.5.1 --- .../p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb index dabb8b2f35..0fd64f3fd2 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'PIL' version = '1.1.7' -versionsuffix = '-Python-%(ppyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.pythonware.com/products/pil' description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. @@ -15,14 +15,11 @@ sources = ['Imaging-%(version)s.tar.gz'] patches = ['PIL-%(version)s-find-deps.patch'] -pyver = '2.7.11' -versionsuffix = '-Python-%s' % pyver dependencies = [ ('zlib', '1.2.8'), - ('Python', pyver), + ('Python', '2.7.11'), ('libjpeg-turbo', '1.4.2'), - # currently not used because of dependency hell - # ('freetype', '2.6.1'), + ('freetype', '2.6.2'), ] options = {'modulename': 'PIL'} -- GitLab From ab90ad2507bc8890a2aaa665e307cebe60f057d3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 15:29:11 +0200 Subject: [PATCH 1426/2133] fixed pyver --- .../c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb index 037900565c..abd2d674a6 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -3,6 +3,9 @@ easyblock = 'MakeCp' name = 'Commet' version = '20160422' +pyver = '2.7.11' +versionsuffix = '-Python-%(pyver)s' + homepage = 'https://colibread.inria.fr/software/commet/' description = """ COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. """ @@ -14,11 +17,9 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_ZIP] files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] -pythonversion = '2.7.11' -versionsuffix = '-Python-%(pythonversion)s' dependencies = [ - ('Python', pythonversion), + ('Python', pyver), ] checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] @@ -28,4 +29,4 @@ sanity_check_paths = { 'dirs' : ['doc','include'] } -moduleclass = 'bio' +moduleclass = 'bio' \ No newline at end of file -- GitLab From 3966bc3e025065c771252bae4528eee8d3c653e2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 15:52:23 +0200 Subject: [PATCH 1427/2133] CrossTalkZ with foss 2016a --- .../c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb new file mode 100644 index 0000000000..f798c72eb5 --- /dev/null +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CrossTalkZ' +version = '1.4' + +homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +description = """ +CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +] +sources = ['%(name)s_%(version)s.tgz'] + +dependencies = [('Boost', '1.60.0')] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" + +builddependencies = [('CMake', '3.4.3', '', ('foss','2016a'))] + +sanity_check_paths = { + 'files': ['bin/CrossTalkZ'], + 'dirs': [''], +} + +moduleclass = 'bio' \ No newline at end of file -- GitLab From a9a96a44eecdb03cc1396f86fd35ad79e5a8c2db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 16:02:37 +0200 Subject: [PATCH 1428/2133] add test configuration for Travis --- .travis.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000000..07d8498dcd --- /dev/null +++ b/.travis.yml @@ -0,0 +1,18 @@ +language: python +python: + - 2.6 + - 2.7 +addons: + apt: + packages: + - tcl8.5 +install: + # install easybuild-framework/easybuild-easyblocks (and dependencies) + # use 'develop' branch of framework/easyblocks, except when testing 'master' + if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz + - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz + # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework + - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT +script: + - python -O -m test.easyconfigs.suite -- GitLab From e23363ce6f9b632096702d193242e5221c5f7cc4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 22 Apr 2016 16:06:42 +0200 Subject: [PATCH 1429/2133] Fix failing FSL on RHEL 7 --- .../easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb | 4 ++-- .../easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch | 14 ++++++++++++++ 2 files changed, 16 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb index a26ad87936..5b9dfba11b 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb @@ -11,15 +11,15 @@ sources = ['%(namelower)s-%(version)s-sources.tar.gz'] patches = [ 'FSL-%(version)s_makefile_fixes.patch', + 'FSL-%(version)s_missing_lib.patch', 'FSL_icc_nan-inf_fix.patch', ] -preconfigopts = 'CFLAGS="-I%(builddir)s/src $CFLAGS"' - dependencies = [ ('freeglut', '3.0.0'), ('expat', '2.1.0'), ('libX11', '1.6.3'), + ('zlib', '1.2.8'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch new file mode 100644 index 0000000000..40e5baff2f --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch @@ -0,0 +1,14 @@ +# On RHEL 7 and friends, you need to link to libglapi too +# Ward Poelmans +diff -ur fsl.oirg/src/fslsurface/Makefile fsl/src/fslsurface/Makefile +--- fsl.oirg/src/fslsurface/Makefile 2014-02-24 12:09:05.000000000 +0100 ++++ fsl/src/fslsurface/Makefile 2016-04-21 18:03:50.246117983 +0200 +@@ -37,7 +37,7 @@ + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} + + +-LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass ++LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass -lglapi + + APPLY_ZLIB = -DHAVE_ZLIB + -- GitLab From 54f93414557afa15e4d1234300f5a0ca53ff46d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 17:37:00 +0200 Subject: [PATCH 1431/2133] add easyconfig i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb --- ...-1.0-20160213-intel-2016a-Python-2.7.11.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a0ac2c0885 --- /dev/null +++ b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name ='i-PI' +version = '1.0-20160213' +commit = '2a09a6d' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/i-pi/i-pi' +description = """A Python wrapper for (ab initio) (path integrals) molecular dynamics""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/i-pi/i-pi/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('Python', '2.7.11'), +] + +options = {'modulename': 'ipi'} + +sanity_check_paths = { + 'files': ['bin/i-pi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' -- GitLab From 48744e84a92f73b252f175f9925e0af41fc8f35a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 17:46:56 +0200 Subject: [PATCH 1432/2133] make dev version PEP440 compliant --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 72cf85df21..cf1d254d29 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.8.0dev0' +VERSION = '2.8.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 40f5979f3457df08f8f40f1afa54a122f9ad2ece Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 18:20:43 +0200 Subject: [PATCH 1433/2133] remove faulty PIL easyconfig --- ...PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb deleted file mode 100644 index 93ba3d3868..0000000000 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PIL' -version = '1.1.7' -versionsuffix = '-Python-%(ppyver)s' - -homepage = 'http://www.pythonware.com/products/pil' -description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. - This library supports many file formats, and provides powerful image processing and graphics capabilities.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://effbot.org/downloads/'] -sources = ['Imaging-%(version)s.tar.gz'] - -patches = ['PIL-%(version)s-find-deps.patch'] - -dependencies = [ - ('zlib', '1.2.8'), - ('Python', '2.7.11'), - ('libjpeg-turbo', '1.4.2'), - ('freetype', '2.6.3'), -] - -options = {'modulename': 'PIL'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], -} - -moduleclass = 'vis' -- GitLab From 3209fcc10eff09c48149a435a4d568b3a8e7a94d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:06:07 +0200 Subject: [PATCH 1434/2133] query GitHub for commit ID of framework/easyblocks branch being used --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 07d8498dcd..de7edac95e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,7 +10,9 @@ install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - curl -si https://api.github.com/repos/hpcugent/easybuild-framework/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz + - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT -- GitLab From e2387d1953bd9797547e5da2016e2ec1bf333897 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:12:42 +0200 Subject: [PATCH 1435/2133] fix typo --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index de7edac95e..9e395b922a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,7 +9,7 @@ addons: install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi - curl -si https://api.github.com/repos/hpcugent/easybuild-framework/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha -- GitLab From 643d94631fe876912443b51ad8eb7483da39c284 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:14:33 +0200 Subject: [PATCH 1436/2133] set $PYTHONPATH --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 9e395b922a..74257fabfb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,4 +17,5 @@ install: # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT script: + - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -- GitLab From 9a7580590297de695981ebf84c327abb39fff3b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:48:22 +0200 Subject: [PATCH 1437/2133] install python-graph-core library required by easyconfig tests --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 74257fabfb..47842a3535 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,6 +7,8 @@ addons: packages: - tcl8.5 install: + # required for test_dep_graph + - pip install python-graph-core # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi -- GitLab From d65154ee61c23a8fdc6583d5a66920fb9aae445b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 20:03:14 +0200 Subject: [PATCH 1438/2133] also install python-graph-dot --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 47842a3535..a67e42aebf 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,7 +8,7 @@ addons: - tcl8.5 install: # required for test_dep_graph - - pip install python-graph-core + - pip install python-graph-core python-graph-dot # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi -- GitLab From 7bce8c9d5f52d8d7a1588db7100f65e75adc16d5 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 22 Apr 2016 15:43:48 -0400 Subject: [PATCH 1439/2133] add patch to include Egien --- .../m/minieigen/minieigen-0.5.3-foss-2016a.eb | 2 ++ .../m/minieigen/minieigen-0.5.3_Eigen.patch | 24 +++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb index 9012d7f022..4a8f2d9f28 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] +patches = ['minieigen-0.5.3_Eigen.patch'] + versionsuffix = '-Python-%(pyver)s' dependencies = [ diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch new file mode 100644 index 0000000000..2d683420ff --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch @@ -0,0 +1,24 @@ +diff -ru minieigen-0.5.3.orig/setup.py minieigen-0.5.3/setup.py +--- minieigen-0.5.3.orig/setup.py 2015-09-18 12:15:40.000000000 -0400 ++++ minieigen-0.5.3/setup.py 2016-04-22 15:34:16.527587398 -0400 +@@ -1,6 +1,6 @@ + # encoding: utf-8 + from distutils.core import setup,Extension +-import sys, glob ++import os, sys, glob + + # vectorization is currently broken and experimental ONLY + vectorize=False +@@ -19,10 +19,11 @@ + # * https://bugs.launchpad.net/panda3d/+bug/919237 + define_macros+=[('EIGEN_DONT_VECTORIZE',None)] + else: ++ eigen_prefix = os.environ["EBROOTEIGEN"] + py3k=(sys.version_info[0]==3) + libraries=['boost_python-py3%d'%sys.version_info[1] if py3k else 'boost_python'] + library_dirs=[] +- include_dirs=['/usr/include/eigen3','/usr/local/include/eigen3','minieigen'] ++ include_dirs=['%s/include/eigen3' % eigen_prefix, 'minieigen'] + + setup(name='minieigen', + version='0.5.3', -- GitLab From e2b1e2bf1eea6eeee0813e05dd8a0e6d004c76f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 22:29:53 +0200 Subject: [PATCH 1440/2133] remove Rust easyconfig using intel toolchain, rustc doesn't work --- .../r/Rust/Rust-1.8.0-intel-2016a.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb deleted file mode 100644 index e2f00427e8..0000000000 --- a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Rust' -version = '1.8.0' - -homepage = 'https://www.rust-lang.org' -description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, - and guarantees thread safety.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['https://static.rust-lang.org/dist/'] -sources = ['rustc-%(version)s-src.tar.gz'] - -builddependencies = [('Python', '2.7.11')] - -dependencies = [ - ('LLVM', '3.8.0'), -] - -configopts = "--llvm-root=$EBROOTLLVM" - -sanity_check_paths = { - 'files': ['bin/rustc', 'bin/rustdoc'], - 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], -} - -moduleclass = 'lang' -- GitLab From dea89b699b0c8bb51fd847f807d32b2285885326 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 23 Apr 2016 08:18:33 +0800 Subject: [PATCH 1441/2133] fix style --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index d06eb6d47f..d3ce57aec0 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -25,6 +25,8 @@ configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' +parallel = 1 + files_to_copy = [(['bin/*'], 'bin')] sanity_check_paths = { @@ -34,5 +36,3 @@ sanity_check_paths = { } moduleclass = 'phys' - -parallel = 1 -- GitLab From cf3fc8237183fa5f3bae7eb7e67089f11f3a4162 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 23 Apr 2016 10:29:18 +0200 Subject: [PATCH 1442/2133] also test with Lmod as modules tool on Travis --- .travis.yml | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index a67e42aebf..82661648a7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,7 +1,17 @@ language: python -python: - - 2.6 - - 2.7 +python: 2.6 +env: + matrix: + - ENV_MOD_VERSION=3.2.10 + - LMOD_VERSION=5.6.3 EASYBUILD_MODULES_TOOL=Lmod + - LMOD_VERSION=6.3.1 EASYBUILD_MODULES_TOOL=Lmod EASYBUILD_MODULE_SYNTAX=Lua +matrix: + # mark build as finished as soon as job has failed + fast_finish: true + include: + # also test default configuration with Python 2.7 + - python: 2.7 + env: ENV_MOD_VERSION=3.2.10 addons: apt: packages: @@ -17,7 +27,9 @@ install: - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT + - if [ ! -z $ENV_MOD_VERSION ]; then source $(which install_eb_dep.sh) modules-${ENV_MOD_VERSION} $HOME; fi + - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi + - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) Lmod-${LMOD_VERSION} $HOME; fi script: - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -- GitLab From 25e957fafed3d7db1f16375949d364e499a37747 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 13:09:49 +0200 Subject: [PATCH 1443/2133] long line fix --- .../c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb index abd2d674a6..0ddc0b62f9 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -25,8 +25,9 @@ dependencies = [ checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["Commet.py","bvop","compare_reads","extract_reads","filter_reads","index_and_search"]], - 'dirs' : ['doc','include'] + 'files': ["bin/%s" % binfile for binfile in ["Commet.py", "bvop", + "compare_reads", "extract_reads", "filter_reads", "index_and_search"]], + 'dirs' : ['doc', 'include'] } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From 92df775e7f99a7067490b356bcf00af058e51f60 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 13:14:34 +0200 Subject: [PATCH 1444/2133] style fixes --- .../Commet-20160422-foss-2016a-Python-2.7.11.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb index 0ddc0b62f9..2c16bccce7 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -7,7 +7,8 @@ pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' homepage = 'https://colibread.inria.fr/software/commet/' -description = """ COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. +description = """ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of +a large metagenomic project. """ toolchain = {'name': 'foss', 'version': '2016a'} @@ -15,15 +16,15 @@ toolchain = {'name': 'foss', 'version': '2016a'} # there is no tarball provided, only git checkout through: # https://github.com/pierrepeterlongo/commet/archive/master.zip sources = [SOURCE_ZIP] -files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] +checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] + +files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ] -checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] - sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["Commet.py", "bvop", "compare_reads", "extract_reads", "filter_reads", "index_and_search"]], -- GitLab From 5576182d21a0dfacf0aa8a1a9b990c254c7cf111 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 19:08:36 +0200 Subject: [PATCH 1445/2133] quickfixes --- .../Biopython-1.65-foss-2016a-Python-2.7.11.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index f4b92dace0..2abd2af08c 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -10,6 +10,8 @@ easyblock = "PythonPackage" name = 'Biopython' version = '1.65' +versionsuffix = "-Python-%(pyver)s" + homepage = 'http://www.biopython.org' description = """Biopython is a set of freely available tools for biological computation written @@ -22,20 +24,13 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://biopython.org/DIST'] sources = ['%(namelower)s-%(version)s.tar.gz'] -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = "-%(python)s-%(pyver)s" - dependencies = [ - (python, pyver) + ('Python', '2.7.11') ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/biopython-%(version)s-py%(pyshortver)s.egg-info'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', - 'lib/python%(pyshortver)s/site-packages/BioSQL'] + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] } options = {'modulename': 'Bio'} -- GitLab From 2c0e1b6d8ab6bc2727421dc4a8d214a886c2f516 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 19:31:05 +0200 Subject: [PATCH 1446/2133] quickfixes --- .../c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb index f798c72eb5..59c924d670 100644 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb @@ -5,11 +5,12 @@ version = '1.4' homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' description = """ -CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. +CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of +gene or protein groups in large biological networks. """ toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} +toolchainopts = {'usempi': True, 'pic': True} source_urls = [ 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' @@ -22,11 +23,11 @@ start_dir = 'src' configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" -builddependencies = [('CMake', '3.4.3', '', ('foss','2016a'))] +builddependencies = [('CMake', '3.4.3',)] sanity_check_paths = { 'files': ['bin/CrossTalkZ'], 'dirs': [''], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From 086c0dbb972a7084122b4b5eaf39da87a6bcaacb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 23 Apr 2016 23:56:48 +0100 Subject: [PATCH 1447/2133] Update SAMtools to 1.3.1 --- .../s/SAMtools/SAMtools-1.3.1-foss-2015b.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3.1-foss-2016a.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3.1-intel-2016a.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3.1_Makefile.patch | 24 ++++++++++++++ 4 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb new file mode 100644 index 0000000000..4ee9352c3d --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb new file mode 100644 index 0000000000..fea05c529c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb new file mode 100644 index 0000000000..d88f5e50e8 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch new file mode 100644 index 0000000000..c5b04c6958 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch @@ -0,0 +1,24 @@ +Common subdirectories: samtools-1.3.1/examples and samtools-1.3.1.new/examples +Common subdirectories: samtools-1.3.1/htslib-1.3.1 and samtools-1.3.1.new/htslib-1.3.1 +diff -u samtools-1.3.1/Makefile samtools-1.3.1.new/Makefile +--- samtools-1.3.1/Makefile 2016-04-22 10:51:16.000000000 +0100 ++++ samtools-1.3.1.new/Makefile 2016-04-23 23:53:26.266962157 +0100 +@@ -82,13 +82,13 @@ + # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally + ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz -ldl $(LIBS) ++ALL_LIBS = -L$(EBROOTZLIB)/lib -lz -ldl $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. + + config.mk: +- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3.1#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ ++ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3.1#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-L$$(EBROOTNCURSES)\/lib -lcurses/g' config.mk.in > $@ + + config.h: + echo '/* Basic config.h generated by Makefile */' > $@ +Common subdirectories: samtools-1.3.1/misc and samtools-1.3.1.new/misc +Common subdirectories: samtools-1.3.1/test and samtools-1.3.1.new/test +Common subdirectories: samtools-1.3.1/win32 and samtools-1.3.1.new/win32 -- GitLab From 2ab4d6d539228f0e637f1e5817cd9b983da10d7b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 24 Apr 2016 19:44:15 +0200 Subject: [PATCH 1448/2133] cutadapt with foss 2016a --- ...cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0a504a247d --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.9.1' +pyver = '2.7.11' +versionsuffix = '-Python-%(pyver)s' +pyshortver = '.'.join(pyver.split('.')[:2]) + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cutadapt/'], +} + +moduleclass = 'bio' -- GitLab From efb8760eacfd270bfefb526017504bc11f0bc3e7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 25 Apr 2016 11:57:53 +0200 Subject: [PATCH 1449/2133] libgtextutils with foss 2016a --- .../libgtextutils-0.7-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb new file mode 100644 index 0000000000..c1b5b27e46 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'libgtextutils' +version = '0.7' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/libgtextutils/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'lib' -- GitLab From 7fd4c7a674c4b93466fb96abf122f53e4dc3dbd5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 25 Apr 2016 11:59:57 +0200 Subject: [PATCH 1450/2133] FASTX-Toolket-0.0.14 with foss 2016a --- .../FASTX-Toolkit-0.0.14-foss-2016a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb new file mode 100644 index 0000000000..a69a7b9e2f --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['fastx_toolkit-%(version)s.tar.bz2'] + +builddependencies = [('libgtextutils', '0.7')] + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']], + 'dirs': ['.'] +} + +moduleclass = 'bio' -- GitLab From ee61831b0499b51bbb5684d61ec1772ffa0c1021 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 25 Apr 2016 12:00:17 +0200 Subject: [PATCH 1451/2133] Add Clang 3.8 --- .../c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb | 31 ++++++++++++ .../c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb | 50 +++++++++++++++++++ .../i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb | 21 ++++++++ .../l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb | 28 +++++++++++ .../n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb | 34 +++++++++++++ .../Python-2.7.11-GCC-4.9.3-2.25-bare.eb | 32 ++++++++++++ .../s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb | 41 +++++++++++++++ 7 files changed, 237 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..7c4301fdfe --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..23fe1ddcc9 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.8.0" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", + "openmp-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.0'), + ('ISL', '0.16'), +] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Python', '2.7.11', '-bare'), + ('libxml2', '2.9.3'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..6b38a91f39 --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.16' + +homepage = 'http://isl.gforge.inria.fr/' +description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GMP', '6.1.0')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..ba6d0a4c3f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..02e4aae6ca --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb new file mode 100644 index 0000000000..895d73b128 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb @@ -0,0 +1,32 @@ +name = 'Python' +version = '2.7.11' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3', '', ('GCCcore', '4.9.3')), + ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..5c86155323 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3', '', ('GCCcore', '4.9.3')), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' -- GitLab From bfca7b250a70b412b02b70921c158c85923ab215 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 25 Apr 2016 12:57:08 +0200 Subject: [PATCH 1452/2133] Fix conflict --- easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb index 7c4301fdfe..619aaa3ab8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' dependencies = [ - ('ncurses', '6.0'), + ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons #('OpenSSL', '1.0.1s'), -- GitLab From fa805fce3c0dc0dafb44c6c99351fe1d415ace8b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 26 Apr 2016 11:11:25 +0800 Subject: [PATCH 1453/2133] [phys]{intel/2016.02-GCC-4.9} VASP 5.4.1 --- .../VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..f631c4aebb --- /dev/null +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'VASP' +version = '5.4.1' + +homepage = 'http://www.vasp.at' +description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale +materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, +from first principles.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include; ' +prebuildopts += 'env LIBS="" ' + +buildopts = 'all BLACS="$LIBBLACS" ' +buildopts += 'OBJECTS="fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o $FFTW_LIB_DIR/libfftw3xf_intel.a"' + +parallel = 1 + +files_to_copy = [(['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'], + 'dirs': [] +} + +moduleclass = 'phys' -- GitLab From ebc6dc8fdd062abf4da5cbc1b71570b46f4cc211 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 26 Apr 2016 16:33:46 +0800 Subject: [PATCH 1454/2133] {chem}[intel/2016.02-GCC-4.9] pymatgen 3.5.10 and spglib 1.9.2 --- ...5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 33 +++++++++++++++++++ .../spglib-1.9.2-intel-2016.02-GCC-4.9.eb | 21 ++++++++++++ .../spglib-1.9.2_remove_duplicate.patch | 11 +++++++ 3 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb new file mode 100644 index 0000000000..cacf27ebc3 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '3.5.0' + +homepage = 'https://pypi.python.org/pypi/pymatgen' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +# source not in url PYPI_SOURCE ? +#source_urls = [PYPI_SOURCE] +source_urls = ['http://pypi.python.org/packages/7a/ae/c1bbe01227514bec203934d608c7319fec173791b3c58afa8e169affb976/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.11' + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('spglib', '1.9.2'), +] + +py_short_ver = '.'.join(pythonversion.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % py_short_ver], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..99c05961d7 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.9.2' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['spglib-1.9.2_remove_duplicate.patch'] + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch new file mode 100644 index 0000000000..c228aceb25 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch @@ -0,0 +1,11 @@ +--- src/Makefile.in.orig 2016-04-26 16:21:29.900203000 +0800 ++++ src/Makefile.in 2016-04-26 16:21:43.531192514 +0800 +@@ -562,7 +562,7 @@ + version.h + + libsymspg_la_SOURCES = $(spglib_c) $(spglib_h) +-pkginclude_HEADERS = $(spglib_h) debug.h ++pkginclude_HEADERS = $(spglib_h) + # libsymspg_la_LDFLAGS = -version-info 0:1:0 + libsymspg_la_LIBADD = -lm + spglib_test_SOURCES = test.c $(spglib_c) $(spglib_h) -- GitLab From 38ac1422594760bc4281382bd4f22bea36297de7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 17:33:32 +0200 Subject: [PATCH 1455/2133] fix use of resolve_dependencies in tests --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f3b329c872..db5060f0b6 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -113,7 +113,7 @@ class EasyConfigTest(TestCase): if dep.get('external_module', False): ec['dependencies'].remove(dep) - self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, retain_all_deps=True) + self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, modules_tool(), retain_all_deps=True) def test_dep_graph(self): """Unit test that builds a full dependency graph.""" -- GitLab From 4df336393a0094535ed365c30f094d682a2a9bd2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 17:37:38 +0200 Subject: [PATCH 1456/2133] add easyconfig travis-1.8.2-Ruby-2.3.1.eb, add easyconfig Ruby-2.3.1.eb --- easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb | 63 +++++++++++++++++++ .../t/travis/travis-1.8.2-Ruby-2.3.1.eb | 24 +++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb create mode 100644 easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb new file mode 100644 index 0000000000..873541fd42 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb @@ -0,0 +1,63 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.3.1' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +ext_options = { + 'source_urls': ['http://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_list = [ + ('ffi', '1.9.10', ext_options), + ('childprocess', '0.5.9', ext_options), + ('json', '1.8.3', ext_options), + ('cabin', '0.8.1', ext_options), + ('backports', '3.6.8', ext_options), + ('arr-pm', '0.0.10', ext_options), + ('clamp', '1.0.0', ext_options), + ('multipart-post', '2.0.0', ext_options), + ('faraday', '0.9.2', ext_options), + ('faraday_middleware', '0.10.0', ext_options), + ('highline', '1.7.8', ext_options), + ('net-http-pipeline', '1.0.1', ext_options), + ('net-http-persistent', '2.9.4', ext_options), + ('multi_json', '1.11.3', ext_options), + ('addressable', '2.4.0', ext_options), + ('gh', '0.14.0', ext_options), + ('launchy', '2.4.3', ext_options), + ('ethon', '0.8.1', ext_options), + ('typhoeus', '0.8.0', ext_options), + ('websocket', '1.2.3', ext_options), + ('pusher-client', '0.6.2', ext_options), + ('diff-lcs', '1.2.5', ext_options), + ('rspec-support', '3.4.1', ext_options), + ('rspec-mocks', '3.4.1', ext_options), + ('rspec-expectations', '3.4.0', ext_options), + ('rspec-core', '3.4.4', ext_options), + ('rspec', '3.4.0', ext_options), + ('rack', '1.6.4', ext_options), + ('rack-protection', '1.5.3', ext_options), + ('tilt', '2.0.2', ext_options), + ('sinatra', '1.4.7', ext_options), + ('rack-test', '0.6.3', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb b/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb new file mode 100644 index 0000000000..ebac3ec2d3 --- /dev/null +++ b/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb @@ -0,0 +1,24 @@ +easyblock = 'RubyGem' + +name = 'travis' +version = '1.8.2' + +rubyver = '2.3.1' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://github.com/travis-ci/travis.rb' +description = """Travis CI Client (CLI and Ruby library)""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://rubygems.org/downloads/'] +sources = ['%(namelower)s-%(version)s.gem'] + +dependencies = [('Ruby', rubyver)] + +sanity_check_paths = { + 'files': ['bin/travis'], + 'dirs': ['gems/travis-%(version)s/lib/travis'], +} + +moduleclass = 'tools' -- GitLab From 0e7e6ad93bed78ec974e24ad4e697a16f4e6a90c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 19:37:42 +0200 Subject: [PATCH 1457/2133] install easybuild-framework & easybuild-easyblocks via git clone && easy_install --- .travis.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 82661648a7..00f7860f26 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,10 +22,12 @@ install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi - - curl -si https://api.github.com/repos/hpcugent/easybuild-framework/git/refs/heads/${BRANCH} | grep sha - - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz - - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha - - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz + - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-framework.git + - cd easybuild-framework; git log -n 1; cd - + - easy_install $PWD/easybuild-framework + - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-easyblocks.git + - cd easybuild-easyblocks; git log -n 1; cd - + - easy_install $PWD/easybuild-easyblocks # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - if [ ! -z $ENV_MOD_VERSION ]; then source $(which install_eb_dep.sh) modules-${ENV_MOD_VERSION} $HOME; fi - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi -- GitLab From 40a6f5d08a0399cc544dd39ba8145a345e4a3414 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 19:55:13 +0200 Subject: [PATCH 1458/2133] fix cwd when cloning --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 00f7860f26..127edacd18 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,6 +22,7 @@ install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - cd $HOME - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-framework.git - cd easybuild-framework; git log -n 1; cd - - easy_install $PWD/easybuild-framework -- GitLab From fe83740c235f48de4924f02e3a463cce5adc1d68 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 26 Apr 2016 21:39:01 +0100 Subject: [PATCH 1459/2133] Add patch information and apply more macros --- .../easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb | 4 +++- .../easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb | 4 +++- .../easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb | 4 +++- .../easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch | 8 +++----- 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb index 4ee9352c3d..a7026c36d0 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb @@ -6,6 +6,8 @@ # License:: MIT/GPL # $Id$ # +# Modified by: Adam Huffman +# The Francis Crick Institute ## name = 'SAMtools' version = '1.3.1' @@ -21,7 +23,7 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve sources = [SOURCELOWER_TAR_BZ2] # Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-1.3.1_Makefile.patch'] +patches = ['SAMtools-%(version)s_Makefile.patch'] dependencies = [ ('ncurses', '5.9'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb index fea05c529c..7fa65122da 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb @@ -6,6 +6,8 @@ # License:: MIT/GPL # $Id$ # +# Modified by: Adam Huffman +# The Francis Crick Institute ## name = 'SAMtools' version = '1.3.1' @@ -21,7 +23,7 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve sources = [SOURCELOWER_TAR_BZ2] # Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-1.3.1_Makefile.patch'] +patches = ['SAMtools-%(version)s_Makefile.patch'] dependencies = [ ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb index d88f5e50e8..91ca187c34 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb @@ -6,6 +6,8 @@ # License:: MIT/GPL # $Id$ # +# Modified by: Adam Huffman +# The Francis Crick Institute ## name = 'SAMtools' version = '1.3.1' @@ -21,7 +23,7 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve sources = [SOURCELOWER_TAR_BZ2] # Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-1.3.1_Makefile.patch'] +patches = ['SAMtools-%(version)s_Makefile.patch'] dependencies = [ ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch index c5b04c6958..4d74b2e9b1 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch @@ -1,5 +1,6 @@ -Common subdirectories: samtools-1.3.1/examples and samtools-1.3.1.new/examples -Common subdirectories: samtools-1.3.1/htslib-1.3.1 and samtools-1.3.1.new/htslib-1.3.1 +# Use EB modules for zlib and ncurses +# Author: Adam Huffman +# The Francis Crick Institute diff -u samtools-1.3.1/Makefile samtools-1.3.1.new/Makefile --- samtools-1.3.1/Makefile 2016-04-22 10:51:16.000000000 +0100 +++ samtools-1.3.1.new/Makefile 2016-04-23 23:53:26.266962157 +0100 @@ -19,6 +20,3 @@ diff -u samtools-1.3.1/Makefile samtools-1.3.1.new/Makefile config.h: echo '/* Basic config.h generated by Makefile */' > $@ -Common subdirectories: samtools-1.3.1/misc and samtools-1.3.1.new/misc -Common subdirectories: samtools-1.3.1/test and samtools-1.3.1.new/test -Common subdirectories: samtools-1.3.1/win32 and samtools-1.3.1.new/win32 -- GitLab From 5145c090f795ab0ef73ae3c6d5b6fe91dc6ab847 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 26 Apr 2016 21:42:56 +0100 Subject: [PATCH 1460/2133] Second attempt at MuTect update to 1.1.7 --- .../m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb new file mode 100644 index 0000000000..fb72a09f73 --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Version 1.1.7 modified by +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'MuTect' +version = '1.1.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +# Need to be logged in to download, at this URL +# source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +sources = ['muTect-%(version)s-bin.zip'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ["muTect-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +""" + +moduleclass = 'bio' -- GitLab From 41ccd5905b4c848474c5c1744cf05d0b97e607c5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 26 Apr 2016 21:52:42 +0100 Subject: [PATCH 1461/2133] Cleanup macros and provide legacy version --- .../v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 30 +++++++++++++++++++ .../v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb | 11 +++---- 2 files changed, 36 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb new file mode 100644 index 0000000000..db71fa9969 --- /dev/null +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = 'JAR' + +name = 'VarScan' +version = '2.3.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://varscan.sourceforge.net/' +description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [('%(name)s.v%(version)s.jar', 'download')] +source_urls = ['https://sourceforge.net/projects/varscan/files/'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +modloadmsg = """ +to execute: java -jar \\$EBROOTVARSCAN/VarScan.v%(version)s.jar +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb index 36d97df090..186dfc58cc 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb @@ -6,6 +6,7 @@ easyblock = 'JAR' name = 'VarScan' version = '2.4.1' +versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/dkoboldt/varscan' description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" @@ -15,15 +16,15 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['%(name)s.v%(version)s.jar'] source_urls = ['https://github.com/dkoboldt/varscan/releases/download/v%(version)s'] -java = 'Java' -javaver = '1.7.0_80' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] +dependencies = [('Java', '1.7.0_80')] sanity_check_paths = { 'files': sources, 'dirs': [], } +modloadmsg = """ +to execute: java -jar \\$EBROOTVARSCAN/VarScan.v%(version)s.jar +""" + moduleclass = 'bio' -- GitLab From 3ccaa14607ffcae465f2e5e94926886fae26a10e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 11:32:39 +0800 Subject: [PATCH 1462/2133] add comments --- .../v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index f631c4aebb..1647ef39db 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -11,12 +11,14 @@ from first principles.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} +# Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code sources = [SOURCELOWER_TAR_GZ] -prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include; ' -prebuildopts += 'env LIBS="" ' +prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' -buildopts = 'all BLACS="$LIBBLACS" ' +buildopts = 'all LIBS="lib" BLACS="$LIBBLACS" ' + +# override path to libfftw3xf_intel.a buildopts += 'OBJECTS="fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o $FFTW_LIB_DIR/libfftw3xf_intel.a"' parallel = 1 -- GitLab From bede2f51f66ffd99701e4b03c1b94b94a51aaa60 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 11:39:01 +0800 Subject: [PATCH 1463/2133] add comment to patch --- .../easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch index c228aceb25..8382a4ebe3 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch @@ -1,3 +1,5 @@ +debug.h is already in $(spglib_h), which causes make install to fail +author: Miguel Dias Costa (National University of Singapore) --- src/Makefile.in.orig 2016-04-26 16:21:29.900203000 +0800 +++ src/Makefile.in 2016-04-26 16:21:43.531192514 +0800 @@ -562,7 +562,7 @@ -- GitLab From c0b8bf724521669e0d3d03746c38ab85d9e3e02d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 12:05:19 +0800 Subject: [PATCH 1464/2133] use pyshortver template --- .../pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index cacf27ebc3..786e233e0c 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -9,7 +9,7 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -# source not in url PYPI_SOURCE ? +# source package not (yet?) in url PYPI_SOURCE #source_urls = [PYPI_SOURCE] source_urls = ['http://pypi.python.org/packages/7a/ae/c1bbe01227514bec203934d608c7319fec173791b3c58afa8e169affb976/'] sources = [SOURCE_TAR_GZ] @@ -24,10 +24,9 @@ dependencies = [ ('spglib', '1.9.2'), ] -py_short_ver = '.'.join(pythonversion.split('.')[:2]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages' % py_short_ver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] } moduleclass = 'chem' -- GitLab From f716f392e6b4b4c6b613e468d5bf07ab021cbbc2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 12:20:13 +0800 Subject: [PATCH 1465/2133] use && instead of ; between commands --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index c0d639cc89..5afb842c80 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -17,7 +17,7 @@ checksums = ['8740562da41e87a62eb8d457675e4bfd'] skipsteps = ['configure'] -prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 4700de27c4..9d064dae20 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -17,7 +17,7 @@ checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] skipsteps = ['configure'] -prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' -- GitLab From 4134e68be75d60ac1889c06af12238baa54fe69b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 27 Apr 2016 09:20:12 +0200 Subject: [PATCH 1466/2133] Remove redundant easyconfig --- .../n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb deleted file mode 100644 index 02e4aae6ca..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '6.0' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' -- GitLab From f1a4154428e398d2c45117c91b6cd62af1806829 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 16:31:43 +0800 Subject: [PATCH 1467/2133] fix style --- ...tgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 12 +++--------- .../s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 786e233e0c..f6c2197ee2 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = "PythonPackage" name = 'pymatgen' version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/pymatgen' description = """Python Materials Genomics is a robust materials analysis code that defines core object @@ -9,18 +10,11 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -# source package not (yet?) in url PYPI_SOURCE -#source_urls = [PYPI_SOURCE] -source_urls = ['http://pypi.python.org/packages/7a/ae/c1bbe01227514bec203934d608c7319fec173791b3c58afa8e169affb976/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = 'Python' -pythonversion = '2.7.11' - -versionsuffix = '-%s-%s' % (python, pythonversion) - dependencies = [ - (python, pythonversion), + ('Python', '2.7.11'), ('spglib', '1.9.2'), ] diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb index 99c05961d7..8451bf0c50 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['spglib-1.9.2_remove_duplicate.patch'] +patches = ['spglib-%(version)s_remove_duplicate.patch'] sanity_check_paths = { 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], -- GitLab From ea2c7c13c4a117b2983cbc8d09bc220672cca07c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 16:56:44 +0800 Subject: [PATCH 1468/2133] explain and cleanup --- .../v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index 1647ef39db..5a21fc97d7 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -16,10 +16,13 @@ sources = [SOURCELOWER_TAR_GZ] prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' -buildopts = 'all LIBS="lib" BLACS="$LIBBLACS" ' +# path to libfftw3xf_intel.a is hardcoded in makefile.include +prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$FFTW_LIB_DIR|" makefile.include && ' -# override path to libfftw3xf_intel.a -buildopts += 'OBJECTS="fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o $FFTW_LIB_DIR/libfftw3xf_intel.a"' +# VASP uses LIBS as a list of folders +prebuildopts += 'unset LIBS && ' + +buildopts = 'all BLACS="$LIBBLACS" ' parallel = 1 -- GitLab From 435eab2e07d7f781915cb672792e3ed0506dfa96 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 10:04:20 +0100 Subject: [PATCH 1469/2133] Don't specify version for dummy toolchain --- easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb index db71fa9969..ba30d5877f 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -11,7 +11,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://varscan.sourceforge.net/' description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [('%(name)s.v%(version)s.jar', 'download')] source_urls = ['https://sourceforge.net/projects/varscan/files/'] -- GitLab From a9193aaca3032ffc844843556cba05e5957a3382 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 11:38:17 +0200 Subject: [PATCH 1470/2133] add easyconfig netCDF-Fortran-4.4.3-intel-2016a.eb --- .../netCDF-Fortran-4.4.3-intel-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb new file mode 100644 index 0000000000..4b898dd0fe --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb @@ -0,0 +1,19 @@ +name = 'netCDF-Fortran' +version = '4.4.3' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-fortran/archive/' +] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' -- GitLab From 0ff3e40f352c19ec30bc19fac917588e318ba4fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 11:38:47 +0200 Subject: [PATCH 1471/2133] add easyconfig tcsh-6.19.00-intel-2016a.eb --- .../t/tcsh/tcsh-6.19.00-intel-2016a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb new file mode 100644 index 0000000000..4a02bab4b4 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.19.00' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 45e20dbc351d80c93701dfc2fa9231d99019607f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 11:39:16 +0200 Subject: [PATCH 1472/2133] add easyconfig JasPer-1.900.1-intel-2016a.eb --- .../j/JasPer/JasPer-1.900.1-intel-2016a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb new file mode 100644 index 0000000000..ea3c592427 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' -- GitLab From 7f79c14c4dcfd9d7aa02352f8bdc537325276a25 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 17:51:09 +0800 Subject: [PATCH 1473/2133] fix variable --- .../easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index 5a21fc97d7..2a6923ac23 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' # path to libfftw3xf_intel.a is hardcoded in makefile.include -prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$FFTW_LIB_DIR|" makefile.include && ' +prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$(FFTW_LIB_DIR)|" makefile.include && ' # VASP uses LIBS as a list of folders prebuildopts += 'unset LIBS && ' -- GitLab From 7f749b704350f3618123f17349c3b2599408bbbd Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 11:56:43 +0100 Subject: [PATCH 1474/2133] Use new download URL and apply new Java macros to existing 1.1.4 easyconfig --- .../m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb | 15 ++++---- .../m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 37 ------------------- 2 files changed, 8 insertions(+), 44 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index 1434f1c176..b7e4fa9091 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -2,11 +2,15 @@ # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +# Modified by +# Adam Huffman +# The Francis Crick Institute easyblock = 'Tarball' name = 'MuTect' version = '1.1.4' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' description = """ MuTect is a method developed at the Broad Institute for the reliable @@ -15,14 +19,11 @@ description = """ MuTect is a method developed at the Broad Institute for the re toolchain = {'name': 'dummy', 'version': ''} -source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +# Need to be logged in to download, at this URL +# source_urls = ['http://www.broadinstitute.org/cancer/cga/mutect_download'] sources = ['muTect-%(version)s-bin.zip'] -java = 'Java' -javaver = '1.7.0_80' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] +dependencies = [('Java', '1.7.0_80')] sanity_check_paths = { 'files': ["muTect-%(version)s.jar"], @@ -30,7 +31,7 @@ sanity_check_paths = { } modloadmsg = """ -to execute: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar """ moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb deleted file mode 100644 index fb72a09f73..0000000000 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb +++ /dev/null @@ -1,37 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# Version 1.1.7 modified by -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'Tarball' - -name = 'MuTect' -version = '1.1.7' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' -description = """ MuTect is a method developed at the Broad Institute for the reliable - and accurate identification of somatic point mutations in next generation sequencing - data of cancer genomes. """ - -toolchain = {'name': 'dummy', 'version': ''} - -# Need to be logged in to download, at this URL -# source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] -sources = ['muTect-%(version)s-bin.zip'] - -dependencies = [('Java', '1.7.0_80')] - -sanity_check_paths = { - 'files': ["muTect-%(version)s.jar"], - 'dirs': [], -} - -modloadmsg = """ -To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar -""" - -moduleclass = 'bio' -- GitLab From 836bced923277203a737f146a839a8fd491ea0cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 13:39:28 +0200 Subject: [PATCH 1475/2133] add easyconfig ParMETIS-4.0.3-intel-2016a.eb, add easyconfig METIS-5.1.0-intel-2016a-32bitIDX.eb, add easyconfig SCOTCH-6.0.4-intel-2016a.eb, add easyconfig ParMGridGen-1.0-intel-2016a.eb, add easyconfig OpenFOAM-Extend-3.2-intel-2016a.eb, add easyconfig numactl-2.0.11-intel-2016a.eb, add easyconfig hwloc-1.11.3-intel-2016a.eb --- .../h/hwloc/hwloc-1.11.3-intel-2016a.eb | 23 +++++++++ .../METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb | 24 ++++++++++ .../n/numactl/numactl-2.0.11-intel-2016a.eb | 23 +++++++++ .../OpenFOAM-Extend-3.2-intel-2016a.eb | 48 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb | 22 +++++++++ .../ParMGridGen-1.0-intel-2016a.eb | 27 +++++++++++ .../s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb | 14 ++++++ 7 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb new file mode 100644 index 0000000000..aad28dd23b --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb new file mode 100644 index 0000000000..a9aa0626e9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb @@ -0,0 +1,24 @@ +name = 'METIS' +version = '5.1.0' +# default 32-bit IDTYPEWIDTH, no patch used +versionsuffix = '-32bitIDX' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.5.2')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb new file mode 100644 index 0000000000..6379096747 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb new file mode 100644 index 0000000000..00e9eaf007 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'EB_OpenFOAM' + +name = 'OpenFOAM-Extend' +version = '3.2' + +homepage = 'http://www.extend-project.de/' +description = """OpenFOAM is a free, open source CFD software package. +OpenFOAM has an extensive range of features to solve anything from complex fluid flows +involving chemical reactions, turbulence and heat transfer, +to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-%(version)s/archive'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'OpenFOAM-Extend-%(version)s-ParMGridGen.patch', + 'OpenFOAM-Extend-3.1_build-qa.patch', + 'OpenFOAM-Extend-3.1_comp-mpi.patch', + 'OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch', +] + +dependencies = [ + ('hwloc', '1.11.3'), + ('ParMETIS', '4.0.3'), + ('METIS', '5.1.0', '-32bitIDX'), # order matters, METIS need to be listed after ParMETIS to get $CPATH right + ('SCOTCH', '6.0.4'), + ('Mesquite', '2.3.0'), + ('ParMGridGen', '1.0'), + ('Python', '2.7.11'), + # Libccmio v2.6.1, zoltan v3.5 +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('M4', '1.4.17'), + ('CMake', '3.5.2'), +] + +prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) + +# too many builds in parallel actually slows down the build +maxparallel = 4 + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb new file mode 100644 index 0000000000..d1d34fb057 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, + meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes + routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in + ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning + schemes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.5.2')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb new file mode 100644 index 0000000000..081f188ad5 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'ParMGridGen' +version = '1.0' + +homepage = 'http://www-users.cs.umn.edu/~moulitsa/software.html' +description = """ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, + that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited + for geometric multigrid methods.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://www-users.cs.umn.edu/~moulitsa/download/'] +sources = [SOURCE_TAR_GZ] + +patches = ['ParMGridGen-1.0_malloc_include.patch'] + +buildopts = 'parallel CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' + +files_to_copy = [ + (['MGridGen/Programs/mgridgen', 'ParMGridGen/Programs/parmgridgen'], 'bin'), + (['mgridgen.h', 'parmgridgen.h'], 'include'), + (['libmgrid.a', 'libparmgrid.a'], 'lib'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb new file mode 100644 index 0000000000..a90bb75fa5 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb @@ -0,0 +1,14 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' -- GitLab From 34b5d5abfa255f3464ce6dabefc279d14b2b67e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 13:44:11 +0200 Subject: [PATCH 1476/2133] add easyconfig JAGS-4.2.0-intel-2016a.eb --- .../j/JAGS/JAGS-4.2.0-intel-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb new file mode 100644 index 0000000000..1474dde18b --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.2.0' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [('http://sourceforge.net/projects/mcmc-jags/files/JAGS/%(version_major)s.x/Source/', 'download')] +sources = [SOURCE_TAR_GZ] + +configopts = ' --with-blas="-lmkl" --with-lapack="-lmkl" ' + +sanity_check_paths = { + 'files': ["bin/jags", "libexec/jags-terminal", "lib/libjags.%s" % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/JAGS', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' -- GitLab From cb092140059005c5fc0468dfb57ad2b5b4f04726 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 14:03:24 +0200 Subject: [PATCH 1477/2133] add easyconfig Mesquite-2.3.0-intel-2016a.eb --- .../m/Mesquite/Mesquite-2.3.0-intel-2016a.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb new file mode 100644 index 0000000000..fd518b2227 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'Mesquite' +version = '2.3.0' + +homepage = 'https://software.sandia.gov/mesquite/' +description = """Mesh-Quality Improvement Library""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://software.sandia.gov/mesquite/'] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'math' -- GitLab From 7bb25d33b0db30e01c8e995fdc0c3c4df76a5769 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 14:13:13 +0100 Subject: [PATCH 1478/2133] Clean up download URL --- easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index b7e4fa9091..0d2d28d47b 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -20,7 +20,7 @@ description = """ MuTect is a method developed at the Broad Institute for the re toolchain = {'name': 'dummy', 'version': ''} # Need to be logged in to download, at this URL -# source_urls = ['http://www.broadinstitute.org/cancer/cga/mutect_download'] +# http://www.broadinstitute.org/cancer/cga/mutect_download sources = ['muTect-%(version)s-bin.zip'] dependencies = [('Java', '1.7.0_80')] -- GitLab From 7706f3436e6b061846889c767616bfb3dbce8478 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 15:53:30 +0200 Subject: [PATCH 1479/2133] {geo}[intel/2016a] WRF 3.8 --- .../w/WRF/WRF-3.8-intel-2016a-dmpar.eb | 39 +++ ...F-3.8.0_netCDF-Fortran_separate_path.patch | 225 ++++++++++++++++++ 2 files changed, 264 insertions(+) create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb new file mode 100644 index 0000000000..8afc4ff822 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb @@ -0,0 +1,39 @@ +name = 'WRF' +version = '3.8.0' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version_major_minor)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.19.00')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.3'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF_tests_limit-runtimes.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch new file mode 100644 index 0000000000..f46ae78e87 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch @@ -0,0 +1,225 @@ +add support for using netCDF and netCDF-Fortran installations in separate paths +author: Kenneth Hoste (HPC-UGent) +diff -ru WRFV3.orig/arch/Config_new.pl WRFV3/arch/Config_new.pl +--- WRFV3.orig/arch/Config_new.pl 2015-12-11 19:38:11.000000000 +0100 ++++ WRFV3/arch/Config_new.pl 2016-04-27 12:07:59.419553000 +0200 +@@ -8,6 +8,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib may be in a different path + $sw_pnetcdf_path = "" ; + $sw_hdf5_path=""; + $sw_phdf5_path=""; +@@ -87,6 +88,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -114,6 +119,7 @@ + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { + $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -417,6 +423,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; + $_ =~ s/CONFIGURE_PHDF5_PATH/$sw_phdf5_path/g ; +Only in WRFV3/arch: Config_new.pl.orig +diff -ru WRFV3.orig/arch/configure_new.defaults WRFV3/arch/configure_new.defaults +--- WRFV3.orig/arch/configure_new.defaults 2016-02-29 07:22:29.000000000 +0100 ++++ WRFV3/arch/configure_new.defaults 2016-04-27 12:07:59.429182000 +0200 +@@ -1626,6 +1626,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +Only in WRFV3/arch: configure_new.defaults.orig +diff -ru WRFV3.orig/arch/conf_tokens WRFV3/arch/conf_tokens +--- WRFV3.orig/arch/conf_tokens 2008-02-26 16:39:38.000000000 +0100 ++++ WRFV3/arch/conf_tokens 2016-04-27 12:07:59.435906000 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -ru WRFV3.orig/arch/postamble_new WRFV3/arch/postamble_new +--- WRFV3.orig/arch/postamble_new 2016-02-05 22:22:09.000000000 +0100 ++++ WRFV3/arch/postamble_new 2016-04-27 12:08:58.368686000 +0200 +@@ -45,6 +45,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ + -I$(NETCDFPATH)/include \ ++ -I$(NETCDFFPATH)/include \ + CONFIGURE_RTTOV_INC + REGISTRY = Registry + CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE +@@ -67,6 +68,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH +++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + PNETCDFPATH = CONFIGURE_PNETCDF_PATH +@@ -97,7 +99,7 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + +Only in WRFV3/arch: postamble_new.orig +Only in WRFV3/arch: postamble_new.rej +diff -ru WRFV3.orig/configure WRFV3/configure +--- WRFV3.orig/configure 2015-12-11 19:38:11.000000000 +0100 ++++ WRFV3/configure 2016-04-27 12:58:24.475136000 +0200 +@@ -287,16 +287,28 @@ + USENETCDFF="" # see below + if [ -n "$NETCDF" ] ; then + echo "Will use NETCDF in dir: $NETCDF" ++ # for netCDF 4.2 and greater, the Fortran library is a separate install ++ if [ -z "$NETCDFF" ]; then ++ NETCDFF="$NETCDFF" ++ fi + # Oh UNIDATA, why make it so hard ... + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" ] ; then + USENETCDFF="-lnetcdff" + else +- USENETCDFF=" " ++ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++ else ++ USENETCDFF=" " ++ fi + fi + if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else +- USENETCDF=" " ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then ++ USENETCDF="-L$NETCDF/lib!-L$NETCDF/lib64!-lnetcdf" # ! will be replaced with space ++ else ++ USENETCDF=" " ++ fi + fi + else + echo "Will configure for use without NetCDF" +@@ -595,7 +607,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure_new.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config_new.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -707,10 +719,10 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure_new.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + echo + if test -n "$NETCDF4" ; then +@@ -719,7 +731,7 @@ + fi + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +Only in WRFV3: configure.orig +Only in WRFV3: configure.rej +diff -ru WRFV3.orig/external/io_netcdf/makefile WRFV3/external/io_netcdf/makefile +--- WRFV3.orig/external/io_netcdf/makefile 2014-07-13 01:39:10.000000000 +0200 ++++ WRFV3/external/io_netcdf/makefile 2016-04-27 12:07:59.490731000 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -ru WRFV3.orig/Makefile WRFV3/Makefile +--- WRFV3.orig/Makefile 2016-03-11 18:47:37.000000000 +0100 ++++ WRFV3/Makefile 2016-04-27 12:09:30.391608000 +0200 +@@ -867,7 +867,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) framework; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" FC="$(FC) $(FCBASEOPTS)" RANLIB="$(RANLIB)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" FC="$(SFC) $(FCBASEOPTS)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ + ESMF_MOD_DEPENDENCE="$(ESMF_MOD_DEPENDENCE)" AR="INTERNAL_BUILD_ERROR_SHOULD_NOT_NEED_AR" diffwrf; \ +Only in WRFV3: Makefile.orig +Only in WRFV3: Makefile.rej -- GitLab From 4734e785722c5b78cd0fe7420776439273e22727 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 16:14:00 +0200 Subject: [PATCH 1480/2133] fix easyconfig filename --- ...RF-3.8-intel-2016a-dmpar.eb => WRF-3.8.0-intel-2016a-dmpar.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/w/WRF/{WRF-3.8-intel-2016a-dmpar.eb => WRF-3.8.0-intel-2016a-dmpar.eb} (100%) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb rename to easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb -- GitLab From 39ddf5a97d55a5b9248c9bf3916d1b9fb41f8513 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 15:14:27 +0100 Subject: [PATCH 1481/2133] Update MuTect for 1.1.7 from new download site --- .../m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb new file mode 100644 index 0000000000..86bd5019e2 --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'MuTect' +version = '1.1.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +# Need to be logged in to download, at this URL +# and to click the checkbox to agree to the licence +# https://www.broadinstitute.org/gatk/download/auth?package=MuTect +sources = ['%(namelower)s-%(version)s.jar.zip'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ["%(namelower)s-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +To start MuTect: java -jar \\$EBROOTMUTECT/%(namelower)s-%(version)s.jar +""" + +moduleclass = 'bio' -- GitLab From bc263b4af815e026b5f205a443e4acb83d39e66b Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 27 Apr 2016 23:56:45 -0400 Subject: [PATCH 1482/2133] changing minieigen easyconfig --- ...-2016a.eb => minieigen-0.5.3-foss-2016a-Python-2.7.11.eb} | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/m/minieigen/{minieigen-0.5.3-foss-2016a.eb => minieigen-0.5.3-foss-2016a-Python-2.7.11.eb} (86%) diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb similarity index 86% rename from easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb rename to easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb index 4a8f2d9f28..bc907e8f48 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb @@ -21,10 +21,9 @@ dependencies = [ ('Python', '2.7.11'), ] -#incomplete sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['lib/python2.7/site-packages/minieigen.%s' % SHLIB_EXT], + 'dirs': [] } moduleclass = 'lib' -- GitLab From 6731122a46e0039315726eb9b9b25c089ae83c62 Mon Sep 17 00:00:00 2001 From: jrbosch Date: Thu, 28 Apr 2016 00:10:40 -0400 Subject: [PATCH 1483/2133] Update minieigen-0.5.3-foss-2016a-Python-2.7.11.eb --- .../m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb index bc907e8f48..bcc3a6db18 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ dependencies = [ sanity_check_paths = { 'files': ['lib/python2.7/site-packages/minieigen.%s' % SHLIB_EXT], - 'dirs': [] + 'dirs': [], } moduleclass = 'lib' -- GitLab From 0034a297d2af91edbdc0eb9d83903219ec07c612 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 28 Apr 2016 02:41:08 -0400 Subject: [PATCH 1484/2133] add GTS easyconfig dependency and improve yade easyconfig --- .../easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb | 25 +++++++++++++++++++ .../y/Yade/Yade-1.20.0-foss-2016a.eb | 22 ++++++++-------- 2 files changed, 36 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb new file mode 100644 index 0000000000..6e89234d6b --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.47.5'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb index 83be6ba55d..11f2219023 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb @@ -14,21 +14,23 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] sources = [SOURCELOWER_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' +suffix = '-Python-%(pyver)s' dependencies = [ ('Loki', '0.1.7'), - ('Boost', '1.60.0', versionsuffix), -# ('IPython', '3.2.3', versionsuffix), + ('Boost', '1.60.0', suffix), + ('GL2PS', '1.3.9'), + ('IPython', '3.2.3', suffix), # ('matplotlib', '1.5.1'), # ('SQLite', '3.9.2'), - ('numpy', '1.8.2', versionsuffix), + ('numpy', '1.8.2', suffix), ('Eigen', '3.2.7'), - ('minieigen', '0.5.3') + ('minieigen', '0.5.3', suffix), ('Qt', '4.8.7'), + ('GTS', '0.7.6'), ('Python', '2.7.11'), -# ('libQGLViewer', '2.6.3'), -# ('GDB', '7.10.1',versionsuffix), + ('libQGLViewer', '2.6.3'), +# ('GDB', '7.10.1',suffix), # optional # ('VTK', '6.3.0'), # ('CGAL', '4.7'), @@ -68,11 +70,9 @@ configopts += '-DENABLE_PFVFLOW=OFF' # VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) # USE_QT5: use QT5 for GUI, experimental (OFF by default) - -#incomplete sanity_check_paths = { - 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch'], - 'dirs': ["."] + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], + 'dirs': ['lib/x86_64-linux-gnu/yade-%(versio)s/py/yade'], } moduleclass = 'devel' -- GitLab From 16218db65d867ab958db13dcbe99fcbf93724337 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2016 11:32:51 +0200 Subject: [PATCH 1485/2133] add dependency extensions for MarkupSafe and jsonscheme in IPython 3.2.3 easyconfigs --- .../i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb | 9 +++++++++ .../i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb index 693b2889a6..440fcbb412 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb @@ -52,9 +52,18 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb index e3341fcf31..7cf61546f1 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb @@ -52,9 +52,18 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), -- GitLab From d5d14e4f772188d6772c1dd9f3453ccc2725845c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2016 11:28:48 +0200 Subject: [PATCH 1486/2133] add vcversioner and functiools32 dependencies for jsonscheme in IPython easyconfig --- .../i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb index f70668f24c..5a7a6fc6ee 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -50,10 +50,16 @@ exts_list = [ }), ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], - }), + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), -- GitLab From 364ccf36a72ed191b8641e62239e7f924f228a1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2016 11:35:26 +0200 Subject: [PATCH 1487/2133] use %(pyver)s and %(pyshortver)s in IPython 3.2.3 easyconfigs --- .../IPython-3.2.3-foss-2015a-Python-2.7.11.eb | 12 ++++-------- .../IPython-3.2.3-intel-2015b-Python-2.7.10.eb | 12 ++++-------- 2 files changed, 8 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb index 440fcbb412..59f875819a 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'IPython' version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -13,13 +14,8 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'foss', 'version': '2015a'} -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.11'), ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), ] @@ -82,11 +78,11 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb index 7cf61546f1..4c8be19f1d 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'IPython' version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -13,13 +14,8 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015b'} -python = 'Python' -pyver = '2.7.10' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.10'), ('PyZMQ', '15.1.0', '%s-zmq4' % versionsuffix), ] @@ -82,11 +78,11 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ -- GitLab From 699e52ba961e329166861b28967659ef5284534b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 28 Apr 2016 14:51:54 +0200 Subject: [PATCH 1488/2133] dropped (new)lines --- .../c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb index 0a504a247d..5c57e5846c 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -9,9 +9,7 @@ easyblock = "PythonPackage" name = 'cutadapt' version = '1.9.1' -pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' -pyshortver = '.'.join(pyver.split('.')[:2]) homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and @@ -22,7 +20,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] - dependencies = [ ('Python', '2.7.11'), ] -- GitLab From 4b3f26cdb67eae384e941d5a9358502f27376475 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 28 Apr 2016 14:55:11 +0200 Subject: [PATCH 1489/2133] Version fix --- .../c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb new file mode 100644 index 0000000000..444de341bf --- /dev/null +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'CrossTalkZ' +version = '1.4' + +homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +description = """ +CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment +between pairs of gene or protein groups in large biological networks. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +] +sources = ['%(name)s_%(version)s.tgz'] + +dependencies = [('Boost', '1.60.0')] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" + +builddependencies = [('CMake', '3.4.3',)] + +sanity_check_paths = { + 'files': ['bin/CrossTalkZ'], + 'dirs': [''], +} + +moduleclass = 'bio' -- GitLab From 1f5400281627eb85afc587878f025e95fe58e9d5 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 28 Apr 2016 10:37:28 -0400 Subject: [PATCH 1490/2133] remove easyblock specification. it's not necessary --- .../easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb index cd9274f066..7bcbf378aa 100644 --- a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_libQGLViewer' - name = 'libQGLViewer' version = '2.6.3' -- GitLab From 4b632a70fb083454a252435f93947990715fce77 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 28 Apr 2016 16:42:26 +0200 Subject: [PATCH 1491/2133] remove 1.0 version --- .../c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb deleted file mode 100644 index 59c924d670..0000000000 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'CrossTalkZ' -version = '1.4' - -homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' -description = """ -CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of -gene or protein groups in large biological networks. -""" - -toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = [ - 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' -] -sources = ['%(name)s_%(version)s.tgz'] - -dependencies = [('Boost', '1.60.0')] - -start_dir = 'src' - -configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" - -builddependencies = [('CMake', '3.4.3',)] - -sanity_check_paths = { - 'files': ['bin/CrossTalkZ'], - 'dirs': [''], -} - -moduleclass = 'bio' -- GitLab From 191c0834d484b49927c15006879a7a6266d9253e Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 28 Apr 2016 15:01:15 -0400 Subject: [PATCH 1492/2133] improve Loki and minieigen easyconfig files --- easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb | 4 ++-- .../easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch | 9 --------- .../easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch | 4 ++-- 3 files changed, 4 insertions(+), 13 deletions(-) delete mode 100644 easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb index dcb7370cfb..990683c5b7 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb @@ -8,7 +8,7 @@ description = """ Loki is a C++ library of designs, containing flexible implemen toolchain = {'name': 'foss', 'version': '2016a'} -preinstallopts = "export EB_INSTALL_DIR=%(installdir)s &&" +installopts = "prefix=%(installdir)s" source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] sources = [SOURCELOWER_TAR_GZ] @@ -20,4 +20,4 @@ sanity_check_paths={ 'dirs': ['include/loki'], } -patches = [('Loki-0.1.7_change_prefix.patch')] +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch b/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch deleted file mode 100644 index 8a0666c803..0000000000 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch +++ /dev/null @@ -1,9 +0,0 @@ -diff -ru loki-0.1.7.orig/Makefile.common loki-0.1.7/Makefile.common ---- loki-0.1.7.orig/Makefile.common 2007-05-28 22:26:26.000000000 -0400 -+++ loki-0.1.7/Makefile.common 2016-04-21 18:20:54.280476472 -0400 -@@ -4,4 +4,4 @@ - CXXWARNFLAGS := -Wall -Wold-style-cast -Wundef -Wsign-compare -Wconversion -Wpointer-arith -pedantic - CXXFLAGS := $(CXXWARNFLAGS) -g -O2 - --prefix := /usr -+prefix := $(EB_INSTALL_DIR) diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch index 2d683420ff..95775909f2 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch @@ -1,6 +1,6 @@ diff -ru minieigen-0.5.3.orig/setup.py minieigen-0.5.3/setup.py --- minieigen-0.5.3.orig/setup.py 2015-09-18 12:15:40.000000000 -0400 -+++ minieigen-0.5.3/setup.py 2016-04-22 15:34:16.527587398 -0400 ++++ minieigen-0.5.3/setup.py 2016-04-28 14:12:46.507198765 -0400 @@ -1,6 +1,6 @@ # encoding: utf-8 from distutils.core import setup,Extension @@ -13,7 +13,7 @@ diff -ru minieigen-0.5.3.orig/setup.py minieigen-0.5.3/setup.py # * https://bugs.launchpad.net/panda3d/+bug/919237 define_macros+=[('EIGEN_DONT_VECTORIZE',None)] else: -+ eigen_prefix = os.environ["EBROOTEIGEN"] ++ eigen_prefix = os.environ.get('EBROOTEIGEN', 'EBROOTEIGEN_NOT_DEFINED') py3k=(sys.version_info[0]==3) libraries=['boost_python-py3%d'%sys.version_info[1] if py3k else 'boost_python'] library_dirs=[] -- GitLab From 34c2d2a3f23f82a1584528664c4efd174ffd5c04 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 28 Apr 2016 23:22:11 +0100 Subject: [PATCH 1493/2133] add easyconfig cramtools-3.0-Java-1.7.0_80.eb --- .../cramtools/cramtools-3.0-Java-1.7.0_80.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb new file mode 100644 index 0000000000..d00a912e71 --- /dev/null +++ b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'cramtools' +version = '3.0' +versionsuffix = "-Java-%(javaver)s" + +homepage = 'https://github.com/enasequence/cramtools/' +description = """CRAMTools is a set of Java tools and APIs for efficient compression of sequence +read data. Although this is intended as a stable version the code is released as +early access. Parts of the CRAMTools are experimental and may not be supported +in the future.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/enasequence/%(name)s/archive/'] + +dependencies = [('Java', '1.7.0_80')] + +modloadmsg = "To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" + +sanity_check_paths = { + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': ["lib"] +} + +moduleclass = 'bio' -- GitLab From 942f96a8f5f8a5b8b2586aa101d78ab815598490 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 28 Apr 2016 22:18:01 -0400 Subject: [PATCH 1494/2133] add PyGTS easyconfig with foss 2016a toolchain --- .../PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..d74951a2d3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyGTS' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourceforge.net/projects/pygts/' +description = """ PyGTS is a python package used to construct, manipulate, + and perform computations on triangulated surfaces. + It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('GLib', '2.47.5'), + ('GTS' ,'0.7.6'), + ('numpy', '1.8.2', versionsuffix), +] + +options = {'modulename': 'gts'} + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], + 'dirs':[], +} + +moduleclass = 'vis' -- GitLab From 38eb196e7de2b754a1c0205e11df8a50d9b2075b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 15:30:02 +0200 Subject: [PATCH 1495/2133] add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being used --- ...tplotlib-1.5.1-foss-2015b-Python-2.7.10.eb | 1 + ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 1 + ...plotlib-1.5.1-intel-2015b-Python-2.7.11.eb | 1 + ...plotlib-1.5.1-intel-2016a-Python-2.7.11.eb | 1 + ...tplotlib-1.5.1-intel-2016a-Python-3.5.1.eb | 1 + .../matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch | 26 +++++++++++++++++++ 6 files changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb index 712519a60c..96e332c757 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb index 182905c4bb..a29279c43f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb index 8b047bb737..790acc6037 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb index 551c06ecef..0e7eed5918 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb index 2c2c674d2c..8f02974208 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb @@ -29,6 +29,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch new file mode 100644 index 0000000000..39e34a937a --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch @@ -0,0 +1,26 @@ +ensure that Tcl/Tk library paths are correct, to fix segmentation fault that occurs when plotting because system +libraries are picked up; +the problem is that the query_tcktl method guesses the Tk library path based on the Tcl library path by simply +replacing 'Tcl'/'tcl' with 'Tk'/'tk', which doesn't work if the Tk install prefix is different (e.g. due to a +versionsuffix) +author: Kenneth Hoste (HPC-UGent) +-- matplotlib-1.5.1.orig/setupext.py 2016-01-11 04:06:08.000000000 +0100 ++++ matplotlib-1.5.1/setupext.py 2016-04-29 15:43:21.280170000 +0200 +@@ -1560,7 +1560,16 @@ + + # Query Tcl/Tk system for library paths and version string + try: +- tcl_lib_dir, tk_lib_dir, tk_ver = self.query_tcltk() ++ tcl_lib_dir, tk_lib_dir, tk_ver = None, None, None ++ if 'EBROOTTCL' in os.environ and 'EBVERSIONTCL' in os.environ: ++ tcl_ver = '.'.join(os.environ['EBVERSIONTCL'].split('.')[:2]) ++ tcl_lib_dir = os.path.join(os.environ['EBROOTTCL'], 'lib', 'tcl%s' % tcl_ver) ++ if 'EBROOTTK' in os.environ and 'EBVERSIONTK' in os.environ: ++ tk_ver = '.'.join(os.environ['EBVERSIONTK'].split('.')[:2]) ++ tk_lib_dir = os.path.join(os.environ['EBROOTTK'], 'lib', 'tk%s' % tk_ver) ++ ++ if tcl_lib_dir is None or tk_lib_dir is None or tk_ver is None: ++ tcl_lib_dir, tk_lib_dir, tk_ver = self.query_tcltk() + except: + tk_ver = '' + result = self.hardcoded_tcl_config() -- GitLab From a2850e36d1656a502b69931419974015537c8ab3 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 29 Apr 2016 10:08:49 -0400 Subject: [PATCH 1496/2133] add GTS easyconfig and improve PyGTS easyconfig --- .../easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb | 25 +++++++++++++++++++ .../PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 1 - 2 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb new file mode 100644 index 0000000000..6e89234d6b --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.47.5'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb index d74951a2d3..9d7551949d 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -18,7 +18,6 @@ dependencies = [ ('Python', '2.7.11'), ('GLib', '2.47.5'), ('GTS' ,'0.7.6'), - ('numpy', '1.8.2', versionsuffix), ] options = {'modulename': 'gts'} -- GitLab From 6a2282637a078b69ace9f82d62765e22779c1241 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 29 Apr 2016 11:02:01 -0400 Subject: [PATCH 1497/2133] improve Yade easyconfig --- .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..5e5fa25372 --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,74 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '1.20.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://yade-dem.org/doc/' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Loki', '0.1.7'), + ('Boost', '1.60.0', versionsuffix), + ('GL2PS', '1.3.9'), + ('Python', '2.7.11'), + ('IPython', '3.2.3', versionsuffix), + ('PyGTS', '0.3.1', versionsuffix), + ('Eigen', '3.2.7'), + ('minieigen', '0.5.3', versionsuffix), + ('Qt', '4.8.7'), + ('GTS', '0.7.6'), + ('libQGLViewer', '2.6.3'), + ('GDB', '7.10.1', versionsuffix), + ('zlib', '1.2.8'), + # optional +# ('CGAL', '4.7'), +] + +builddependencies = [('CMake', '3.4.3')] + +separate_build_dir = True + +configopts = '-DENABLE_GUI=OFF ' +configopts += '-DENABLE_VTK=OFF ' +configopts += '-DENABLE_CGAL=OFF' +configopts += '-DENABLE_LINSOLV=OFF ' +configopts += '-DENABLE_PFVFLOW=OFF ' +configopts += '-DQGLVIEWER_INCLUDE_DIR=$EBROOTLIBQGLVIEWER/include ' + +# In case you want disable some Yade features +# configopts = '-OPTION_1 = OFF -OPTION_2 = OFF ...' + +# options available, +# ENABLE_GUI: enable GUI option (ON by default) +# ENABLE_CGAL: enable CGAL option (ON by default) +# ENABLE_VTK: enable VTK-export option (ON by default) +# ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default) +# ENABLE_GTS: enable GTS-option (ON by default) +# ENABLE_GL2PS: enable GL2PS-option (ON by default) +# ENABLE_LINSOLV: enable LINSOLV-option (ON by default) +# ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default) +# ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default) +# ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default) +# ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013] for details (OFF by default) +# ENABLE_MASK_ARBITRARY: enable MASK_ARBITRARY option (OFF by default) +# ENABLE_PROFILING: enable profiling, e.g., shows some more metrics, which can define bottlenecks of the code (OFF by default) +# runtimePREFIX: used for packaging, when install directory is not the same as runtime directory (/usr/local by default) +# CHUNKSIZE: specifiy the chunk size if you want several sources to be compiled at once. Increases compilation speed but RAM-consumption during compilation as well (1 by default) +# VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) +# USE_QT5: use QT5 for GUI, experimental (OFF by default) + +sanity_check_paths = { + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], + 'dirs': ['lib/x86_64-linux-gnu/yade-%(version)s/py/yade'], +} + +moduleclass = 'devel' -- GitLab From be83e907e89d1d3ac81cc14416412fb4ee9f9c58 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:23:05 +0200 Subject: [PATCH 1498/2133] add easyconfig MPFR-3.1.4-intel-2016a.eb --- .../m/MPFR/MPFR-3.1.4-intel-2016a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb new file mode 100644 index 0000000000..6101f2969d --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.0')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 3cd38ae9e6ddbf1c0541b9aab0c608dc4976e654 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:23:26 +0200 Subject: [PATCH 1499/2133] add easyconfig GLib-2.48.0-intel-2016a.eb, add easyconfig gettext-0.19.7-intel-2016a.eb --- .../g/GLib/GLib-2.48.0-intel-2016a.eb | 33 +++++++++++++++++++ .../g/gettext/gettext-0.19.7-intel-2016a.eb | 22 +++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb new file mode 100644 index 0000000000..6f5acf6419 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.48.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb new file mode 100644 index 0000000000..d256bae534 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' -- GitLab From b9b61a1d3edfbc23b79c5c001ee8a03bf8e584cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:26:30 +0200 Subject: [PATCH 1500/2133] add easyconfig Mesa-11.2.1-intel-2016a.eb, modify easyconfig freetype-2.6.3-intel-2016a.eb, add easyconfig pkg-config-0.29.1-intel-2016a.eb, add easyconfig libdrm-2.4.68-intel-2016a.eb, add easyconfig libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb --- ...bXfont-1.5.1-intel-2016a-freetype-2.6.3.eb | 34 ++++++++++ .../l/libdrm/libdrm-2.4.68-intel-2016a.eb | 28 ++++++++ .../m/Mesa/Mesa-11.2.1-intel-2016a.eb | 68 +++++++++++++++++++ .../pkg-config-0.29.1-intel-2016a.eb | 27 ++++++++ 4 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb new file mode 100644 index 0000000000..45a31bc1bd --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +freetype_ver = '2.6.3' +versionsuffix = '-freetype-%s' % freetype_ver + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', freetype_ver), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb new file mode 100644 index 0000000000..e64ac66c51 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.68' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb new file mode 100644 index 0000000000..54f7d8a513 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.2.1' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.68'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1', '-freetype-2.6.3'), + ('LLVM', '3.8.0'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb new file mode 100644 index 0000000000..eeb50eabb1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From eadd15710a076003297e0f6a504471fb0352c211 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:37:23 +0200 Subject: [PATCH 1501/2133] add easyconfig xcb-util-0.4.0-intel-2016a.eb, add easyconfig xcb-util-image-0.4.0-intel-2016a.eb, add easyconfig xcb-util-keysyms-0.4.0-intel-2016a.eb, add easyconfig xcb-util-renderutil-0.3.9-intel-2016a.eb, add easyconfig xcb-util-wm-0.4.1-intel-2016a.eb --- .../xcb-util-image-0.4.0-intel-2016a.eb | 23 ++++++++++++++++++ .../xcb-util-keysyms-0.4.0-intel-2016a.eb | 24 +++++++++++++++++++ .../xcb-util-renderutil-0.3.9-intel-2016a.eb | 23 ++++++++++++++++++ .../xcb-util-wm-0.4.1-intel-2016a.eb | 23 ++++++++++++++++++ .../x/xcb-util/xcb-util-0.4.0-intel-2016a.eb | 24 +++++++++++++++++++ 5 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb new file mode 100644 index 0000000000..a0cf9f13dd --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-image' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-image package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('xcb-util', '0.4.0'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-image.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb new file mode 100644 index 0000000000..ab965a9d36 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-keysyms' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-keysyms package contains a library for + handling standard X key constants and conversion to/from keycodes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-keysyms.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb new file mode 100644 index 0000000000..c926c17dd1 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-renderutil' +version = '0.3.9' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-renderutil package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-render-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb new file mode 100644 index 0000000000..5d58f2a9b2 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-wm' +version = '0.4.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-%s.so' % x for x in ['ewmh', 'icccm']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb new file mode 100644 index 0000000000..18a587a56e --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util package provides additional extensions to the XCB library, + many that were previously found in Xlib, but are not part of core X protocol""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 5a09c330918abdab2e6129d2c9767a6a29b3b704 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:37:45 +0200 Subject: [PATCH 1502/2133] add easyconfig fontconfig-2.11.95-intel-2016a.eb, add easyconfig expat-2.1.1-intel-2016a.eb, modify easyconfig freetype-2.6.3-intel-2016a.eb --- .../e/expat/expat-2.1.1-intel-2016a.eb | 16 ++++++++++++++ .../fontconfig-2.11.95-intel-2016a.eb | 22 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb new file mode 100644 index 0000000000..a442e3de7f --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.1' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb new file mode 100644 index 0000000000..09b5a49088 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.95' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.1'), + ('freetype', '2.6.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' -- GitLab From 88739b6f181046a73e49da989652c1cd433c6d9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:42:32 +0200 Subject: [PATCH 1503/2133] add easyconfig Qt5-5.6.0-intel-2016a.eb, add easyconfig libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb, add easyconfig libxkbcommon-0.6.1-intel-2016a.eb, add easyconfig XKeyboardConfig-2.17-intel-2016a.eb, add easyconfig libxslt-1.1.28-intel-2016a.eb --- .../libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb | 27 +++++++++++++ .../libxkbcommon-0.6.1-intel-2016a.eb | 32 +++++++++++++++ .../l/libxslt/libxslt-1.1.28-intel-2016a.eb | 24 ++++++++++++ .../q/Qt5/Qt5-5.6.0-intel-2016a.eb | 39 +++++++++++++++++++ .../XKeyboardConfig-2.17-intel-2016a.eb | 36 +++++++++++++++++ 5 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..fe3cfb14d6 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesaver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesaver + +dependencies = [ + ('Mesa', mesaver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb new file mode 100644 index 0000000000..8611f0332b --- /dev/null +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxkbcommon' +version = '0.6.1' + +homepage = 'http://xkbcommon.org/' +description = """xkbcommon is a library to handle keyboard descriptions, + including loading them from disk, parsing them and handling their state. + It's mainly meant for client toolkits, window systems, + and other system applications.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xkbcommon.org/download/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libxcb', '1.11.1'), + ('XKeyboardConfig', '2.17'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': ['lib/libxkbcommon%s.so' % x for x in ['', '-x11']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb new file mode 100644 index 0000000000..b3d064b443 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb new file mode 100644 index 0000000000..f4f0ab35bd --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.6.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +dependencies = [ + ('GLib', '2.48.0'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXi', '1.7.6'), + ('xcb-util', '0.4.0'), + ('xcb-util-image', '0.4.0'), + ('xcb-util-keysyms', '0.4.0'), + ('xcb-util-renderutil', '0.3.9'), + ('xcb-util-wm', '0.4.1'), + ('libxkbcommon', '0.6.1'), + ('libXrender', '0.9.9'), + ('fontconfig', '2.11.95'), + ('freetype', '2.6.3'), + ('libXfixes', '5.0.1'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('libXrandr', '1.5.0'), + ('libpng', '1.6.21'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb new file mode 100644 index 0000000000..e72178d939 --- /dev/null +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'XKeyboardConfig' +version = '2.17' + +homepage = 'http://www.freedesktop.org/wiki/Software/XKeyboardConfig/' +description = """The non-arch keyboard configuration database for X Window. + The goal is to provide the consistent, well-structured, + frequently released open source of X keyboard configuration data + for X Window System implementations (free, open source and commercial). + The project is targeted to XKB-based systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.x.org/pub/individual/data/xkeyboard-config/'] +sources = ['xkeyboard-config-%(version)s.tar.bz2'] + +builddependencies = [ + ('libxslt', '1.1.28'), + ('gettext', '0.19.7'), + ('intltool', '0.51.0', '-Perl-5.22.1'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +# see http://www.linuxfromscratch.org/blfs/view/svn/x/xkeyboard-config.html +configopts = '--with-xkb-rules-symlink=xorg ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/X11/xkb'] +} + +moduleclass = 'devel' -- GitLab From d6ed5a22d8156e7fec24f3a3865afa0cb59ba4c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:44:07 +0200 Subject: [PATCH 1504/2133] bump to CGAL 4.8 using Mesa 11.2.1 as dependency --- ...1.eb => CGAL-4.8-intel-2016a-Python-2.7.11.eb} | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/c/CGAL/{CGAL-4.7-intel-2016a-Python-2.7.11.eb => CGAL-4.8-intel-2016a-Python-2.7.11.eb} (76%) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb similarity index 76% rename from easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb index 1e7bf4a653..fd4219e206 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb @@ -1,5 +1,5 @@ name = 'CGAL' -version = '4.7' +version = '4.8' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.cgal.org/' @@ -12,17 +12,14 @@ toolchainopts = {'strict': True} # note: source URL needs to be updated for a new version (checksums too)! source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] sources = [SOURCE_TAR_XZ] -checksums = ['623d91fb2ab0a35049dc6098a0f235cc'] +checksums = ['e31e7039b5cdc74ac7b106db8ba644f3'] - -mesaver = '11.1.2' dependencies = [ ('Python', '2.7.11'), ('Boost', '1.60.0', versionsuffix), - ('MPFR', '3.1.3', '-GMP-6.1.0'), - ('Qt5', '5.5.1', '-Mesa-%s' % mesaver), - ('Mesa', mesaver, versionsuffix), - ('libGLU', '9.0.0', '-Mesa-%s' % mesaver), + ('MPFR', '3.1.4'), + ('Qt5', '5.6.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " @@ -30,7 +27,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT builddependencies = [ - ('CMake', '3.4.1'), + ('CMake', '3.5.2'), ] moduleclass = 'numlib' -- GitLab From 73c8947bf09632f27010a1a8cd8ea77afa5e73d9 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 29 Apr 2016 16:07:15 -0400 Subject: [PATCH 1505/2133] I forgot to remove the old easyconfig file --- .../y/Yade/Yade-1.20.0-foss-2016a.eb | 78 ------------------- 1 file changed, 78 deletions(-) delete mode 100644 easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb deleted file mode 100644 index 11f2219023..0000000000 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb +++ /dev/null @@ -1,78 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Yade' -version = '1.20.0' - -homepage = 'https://yade-dem.org/doc/' -description = """ Yade is an extensible open-source framework for discrete numerical models, - focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, - allowing independent implementation of new alogrithms and interfaces. - Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] -sources = [SOURCELOWER_TAR_GZ] - -suffix = '-Python-%(pyver)s' - -dependencies = [ - ('Loki', '0.1.7'), - ('Boost', '1.60.0', suffix), - ('GL2PS', '1.3.9'), - ('IPython', '3.2.3', suffix), -# ('matplotlib', '1.5.1'), -# ('SQLite', '3.9.2'), - ('numpy', '1.8.2', suffix), - ('Eigen', '3.2.7'), - ('minieigen', '0.5.3', suffix), - ('Qt', '4.8.7'), - ('GTS', '0.7.6'), - ('Python', '2.7.11'), - ('libQGLViewer', '2.6.3'), -# ('GDB', '7.10.1',suffix), - # optional -# ('VTK', '6.3.0'), -# ('CGAL', '4.7'), -# ('SuiteSparse', '4.5.1'), -# ('OpenBLAS', '0.2.15'), -# ('METIS', '5.1.0'), -] - -builddependencies = [('CMake', '3.4.3')] - -separate_build_dir = True - -configopts = '-DENABLE_GUI=OFF' -configopts += '-DENABLE_VTK=OFF' -configopts += '-DENABLE_CGAL=OFF' -configopts += '-DENABLE_PFVFLOW=OFF' - -# In case you want disable some Yade features -# configopts = '-OPTION_1 = OFF -OPTION_2 = OFF ...' - -# options available, -# ENABLE_GUI: enable GUI option (ON by default) -# ENABLE_CGAL: enable CGAL option (ON by default) -# ENABLE_VTK: enable VTK-export option (ON by default) -# ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default) -# ENABLE_GTS: enable GTS-option (ON by default) -# ENABLE_GL2PS: enable GL2PS-option (ON by default) -# ENABLE_LINSOLV: enable LINSOLV-option (ON by default) -# ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default) -# ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default) -# ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default) -# ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013] for details (OFF by default) -# ENABLE_MASK_ARBITRARY: enable MASK_ARBITRARY option (OFF by default) -# ENABLE_PROFILING: enable profiling, e.g., shows some more metrics, which can define bottlenecks of the code (OFF by default) -# runtimePREFIX: used for packaging, when install directory is not the same as runtime directory (/usr/local by default) -# CHUNKSIZE: specifiy the chunk size if you want several sources to be compiled at once. Increases compilation speed but RAM-consumption during compilation as well (1 by default) -# VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) -# USE_QT5: use QT5 for GUI, experimental (OFF by default) - -sanity_check_paths = { - 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], - 'dirs': ['lib/x86_64-linux-gnu/yade-%(versio)s/py/yade'], -} - -moduleclass = 'devel' -- GitLab From 7c81af64d32804f56413cc5416b97fb2677def34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 23:49:31 +0200 Subject: [PATCH 1506/2133] modify easyconfig expat-2.1.1-intel-2016a.eb --- easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb index a442e3de7f..6e5b60c35f 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb @@ -10,7 +10,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCELOWER_TAR_BZ2] source_urls = [SOURCEFORGE_SOURCE] moduleclass = 'tools' -- GitLab From 122f7ad45fc9a1a435d6d64345cc2b05dbbf397e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 00:00:08 +0200 Subject: [PATCH 1507/2133] add missing ncurses dep + --with-libxml2-prefix to gettext easyconfigs --- easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb index d256bae534..4f86721ed0 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb @@ -15,6 +15,7 @@ source_urls = [GNU_SOURCE] dependencies = [ ('libxml2', '2.9.3'), + ('ncurses', '6.0'), ] configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' -- GitLab From 58f5d1437754085e98623da578ab3b58ad86bb29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 00:01:41 +0200 Subject: [PATCH 1508/2133] add missing ncurses dep + --with-libxml2-prefix to gettext easyconfigs --- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb index b35aee8501..690872c686 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb @@ -18,6 +18,6 @@ dependencies = [ ('ncurses', '5.9'), ] -configopts = '--without-emacs' +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb index 168b2490e6..4580e48c6a 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -18,6 +18,6 @@ dependencies = [ ('ncurses', '6.0'), ] -configopts = '--without-emacs' +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' moduleclass = 'vis' -- GitLab From e069726a05c66e508bbf5651d5a5f935e2856f8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 00:45:06 +0200 Subject: [PATCH 1509/2133] modify easyconfig GLib-2.48.0-intel-2016a.eb --- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index 6f5acf6419..d241317450 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -21,7 +21,9 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" + +parallel = 1 postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] -- GitLab From 98217a3d259ea96af0512a3970fac83d2d6621d7 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 29 Apr 2016 21:11:40 -0400 Subject: [PATCH 1510/2133] add GL2PS-1.3.9_foss2016a-mesa11.2.1 --- .../c/CMake/CMake-3.5.2-foss-2016a.eb | 31 +++++++++ .../freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb | 40 +++++++++++ .../f/freetype/freetype-2.6.3-foss-2016a.eb | 22 ++++++ .../GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb | 37 ++++++++++ .../l/LLVM/LLVM-3.8.0-foss-2016a.eb | 41 +++++++++++ .../libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb | 27 ++++++++ ...ibXfont-1.5.1-foss-2016a-freetype-2.6.3.eb | 34 ++++++++++ .../l/libdrm/libdrm-2.4.68-foss-2016a.eb | 28 ++++++++ .../m/Mesa/Mesa-11.2.1-foss-2016a.eb | 68 +++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb | 21 ++++++ .../pkg-config-0.29.1-foss-2016a.eb | 27 ++++++++ 11 files changed, 376 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb new file mode 100644 index 0000000000..9075c094fb --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..1965349120 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', mesa_ver), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb new file mode 100644 index 0000000000..bc610c637e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.3' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..726a6db2a2 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', mesa_ver), + ('libGLU', '9.0.0', versionsuffix), + ('freeglut', '3.0.0', versionsuffix), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb new file mode 100644 index 0000000000..fc0af540c1 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Python', '2.7.11'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..38c8310594 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('Mesa', mesa_ver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb new file mode 100644 index 0000000000..63d5bbf444 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +freetype_ver = '2.6.3' +versionsuffix = '-freetype-%s' % freetype_ver + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', freetype_ver), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb new file mode 100644 index 0000000000..68f8a6be89 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.68' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb new file mode 100644 index 0000000000..a919f2eab9 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.2.1' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.68'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1', '-freetype-2.6.3'), + ('LLVM', '3.8.0'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb new file mode 100644 index 0000000000..a5aab91ad9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1s' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-1.0.1q_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb new file mode 100644 index 0000000000..bb2fea6cae --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 8763ec11daf42708cb05942de98f37dc6f1547fb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 30 Apr 2016 08:51:13 +0100 Subject: [PATCH 1511/2133] add easyconfig kallisto-0.42.5-foss-2016a.eb --- .../k/kallisto/kallisto-0.42.5-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb new file mode 100644 index 0000000000..2287c59cc6 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.42.5' + +homepage = 'http://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/pachterlab/kallisto/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.4.3')] +dependencies = [('HDF5', '1.8.16', '-serial')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e9a1f252c40bda55d59d7f28cf83b4bbefed3088 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 10:19:47 +0200 Subject: [PATCH 1512/2133] no need to disable parallel building of GLib --- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index d241317450..918c5aec06 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -23,8 +23,6 @@ builddependencies = [('Python', '2.7.11')] configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" -parallel = 1 - postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] sanity_check_paths = { -- GitLab From ac03452b0d0306e26a04f301fa06be66aae5c288 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 10:28:00 +0200 Subject: [PATCH 1513/2133] use check_conflicts function in easyconfigs tests --- test/easyconfigs/easyconfigs.py | 54 ++------------------------------- 1 file changed, 2 insertions(+), 52 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index db5060f0b6..a3f79cddc5 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -54,7 +54,7 @@ from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool -from easybuild.tools.robot import resolve_dependencies +from easybuild.tools.robot import check_conflicts, resolve_dependencies from easybuild.tools.options import set_tmpdir @@ -145,57 +145,7 @@ class EasyConfigTest(TestCase): if self.ordered_specs is None: self.process_all_easyconfigs() - def mk_dep_mod_name(spec): - return tuple(EasyBuildMNS().det_full_module_name(spec).split(os.path.sep)) - - # construct a dictionary: (name, installver) tuple to (build) dependencies - depmap = {} - for spec in self.ordered_specs: - # exclude external modules, since we can't check conflicts on them (we don't even know the software name) - build_deps = [mk_dep_mod_name(d) for d in spec['builddependencies'] if not d.get('external_module', False)] - deps = [mk_dep_mod_name(d) for d in spec['ec'].all_dependencies if not d.get('external_module', False)] - - # separate runtime deps from build deps - runtime_deps = [d for d in deps if d not in build_deps] - key = tuple(spec['full_mod_name'].split(os.path.sep)) - depmap.update({key: [build_deps, runtime_deps]}) - - # iteratively expand list of dependencies - depmap_last = None - while depmap != depmap_last: - depmap_last = copy.deepcopy(depmap) - for (spec, (build_deps, runtime_deps)) in depmap_last.items(): - # extend runtime dependencies with non-build dependencies of own runtime dependencies - for dep in runtime_deps: - depmap[spec][1].extend([d for d in depmap[dep][1] if d not in depmap[dep][0]]) - depmap[spec][1] = sorted(nub(depmap[spec][1])) - # extend build dependencies with non-build dependencies of own build dependencies - for dep in build_deps: - depmap[spec][0].extend([d for d in depmap[dep][1] if d not in depmap[dep][0]]) - depmap[spec][0] = sorted(nub(depmap[spec][0])) - - def check_conflict((name, installver), (name1, installver1), (name2, installver2)): - """Check whether dependencies with given name/(install) version conflict with each other.""" - # dependencies with the same name should have the exact same install version - # if not => CONFLICT! - if name1 == name2 and installver1 != installver2: - specname = '%s-%s' % (name, installver) - vs_msg = "%s-%s vs %s-%s" % (name1, installver1, name2, installver2) - print "Conflict found for dependencies of %s: %s" % (specname, vs_msg) - return True - else: - return False - - # for each of the easyconfigs, check whether the dependencies (incl. build deps) contain any conflicts - conflicts = False - for ((name, installver), (build_deps, runtime_deps)) in depmap.items(): - # also check whether module itself clashes with any of its dependencies - for i, dep1 in enumerate(build_deps + runtime_deps + [(name, installver)]): - for dep2 in (build_deps + runtime_deps)[i+1:]: - # don't worry about conflicts between module itself and any of its build deps - if dep1 != (name, installver) or dep2 not in build_deps: - conflicts |= check_conflict((name, installver), dep1, dep2) - self.assertFalse(conflicts, "No conflicts detected") + self.assertFalse(check_conflicts(self.ordered_specs, modules_tool()), "No conflicts detected") def test_sanity_check_paths(self): """Make sure specified sanity check paths adher to the requirements.""" -- GitLab From a953b7c3339cf33506e33cdbaa31854adcc17ecc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 30 Apr 2016 15:25:19 +0200 Subject: [PATCH 1514/2133] modify easyconfig makedepend-1.0.5-foss-2016a.eb --- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index 863911703e..3ab1f8aa60 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = [XORG_UTIL_SOURCE] +source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] + +builddependencies = [ + ('xproto', '7.0.28'), +] sanity_check_paths = { 'files': ['bin/makedepend'], -- GitLab From e169054960d7fe14c56efbe8ab31848b0834a460 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 1 May 2016 00:15:18 +0100 Subject: [PATCH 1515/2133] add easyconfig SCons-2.4.1-foss-2016a-Python-2.7.11.eb --- .../SCons-2.4.1-foss-2016a-Python-2.7.11.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..35083b9098 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' -- GitLab From aa31d54e3c255b37ae53239a86b93ae09956e6ec Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 1 May 2016 00:17:18 +0100 Subject: [PATCH 1516/2133] add easyconfig Rosetta-2016.13.58602-foss-2016a.eb --- .../Rosetta-2016.13.58602-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb new file mode 100644 index 0000000000..86250d9275 --- /dev/null +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb @@ -0,0 +1,20 @@ +name = 'Rosetta' +version = '2016.13.58602' + +homepage = 'https://www.rosettacommons.org' +description = """Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, +multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and +nucleic acids.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] + +builddependencies = [('SCons', '2.4.1', '-Python-2.7.11')] + +modextravars = { + 'ROSETTA3_DB': '$root/database', +} + +moduleclass = 'bio' -- GitLab From 6c0806d4dee7561c9a7465275e9be2dfdee26d7a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:37:57 +0200 Subject: [PATCH 1517/2133] modify easyconfig makedepend-1.0.5-foss-2016a.eb --- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index 3ab1f8aa60..c9e59044e7 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +#source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] builddependencies = [ ('xproto', '7.0.28'), -- GitLab From f50236ed9bf05c28dfe03514332307491b0550a9 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:39:37 +0200 Subject: [PATCH 1518/2133] modify easyconfig makedepend-1.0.5-foss-2016a.eb --- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index c9e59044e7..c4a3658b9f 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -#source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] source_urls = [XORG_UTIL_SOURCE] builddependencies = [ -- GitLab From 1ceb9f59820d3cce159fb76b4c12175c99c2169b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:43:30 +0200 Subject: [PATCH 1519/2133] modify easyconfig Doxygen-1.8.11-foss-2016a.eb --- easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb index fea350b755..45e774b0e3 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' -- GitLab From f05b80bccdb74af88f109105f8f5423d0f50f6c1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:47:00 +0200 Subject: [PATCH 1520/2133] modify easyconfig Perl-5.22.1-foss-2016a.eb --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb index 404b98df7e..f1ad7853f0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -137,7 +137,7 @@ exts_list = [ }), ('FreezeThaw', '0.5001', { 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], }), ('DBI', '1.634', { 'source_tmpl': 'DBI-1.634.tar.gz', @@ -221,7 +221,7 @@ exts_list = [ }), ('Tie::Function', '0.02', { 'source_tmpl': 'Tie-Function-0.02.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], }), ('Template::Plugin::Number::Format', '1.06', { 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', -- GitLab From 53c9b1c80a460c6543bbef815d616a396917d8fe Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:57:16 +0200 Subject: [PATCH 1521/2133] add easyconfig PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- ...-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb new file mode 100644 index 0000000000..0d3d65891c --- /dev/null +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'PLplot' +version = '5.11.1' + +homepage = 'http://plplot.sourceforge.net' +description = """PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols + and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +pyver = '2.7.11' +javaver = '1.7.0_79' +pyshortver = '.'.join(pyver.split('.')[0:2]) +versionsuffix = '-Java-%s-Python-%s' % (javaver, pyver) + +glibver = '2.47.5' + +builddependencies = [ + ('CMake', '3.4.3'), + ('SWIG', '3.0.8', '-foss-2016a-Python-%s' % pyver, True), + ('xproto', '7.0.28'), +] + +dependencies = [ + ('Java', javaver, '', True), + ('Python', pyver), + ('Perl', '5.22.1'), + ('Tcl', '8.6.4'), + ('Tk', '8.6.4', '-no-X11'), + ('cairo', '1.14.6'), + ('expat', '2.1.0'), + ('fontconfig', '2.11.94'), + ('freetype', '2.6.2'), + ('GLib', glibver), + ('libICE', '1.0.9'), + ('libtool', '2.4.6'), + ('libX11', '1.6.3'), + ('libXau', '1.0.8'), + ('libxcb', '1.11.1'), + ('libXdmcp', '1.1.2'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), + ('Pango', '1.39.0'), + ('pixman', '0.34.0'), + ('zlib', '1.2.8') +] + +separate_build_dir = True + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': ['lib/libplplot.so', 'lib/pkgconfig/plplot-f95.pc'], + 'dirs': ['bin', 'include/plplot', 'lib/fortran/modules/plplot', 'lib/pkgconfig', 'share/man/man1'], +} + +moduleclass = 'vis' -- GitLab From 44b6590f2ca4b0683e2a2b922ebec71d555f0e25 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 15:50:56 +0200 Subject: [PATCH 1522/2133] builddep up --- .../easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb index 444de341bf..2facea57d9 100644 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb @@ -19,12 +19,13 @@ sources = ['%(name)s_%(version)s.tgz'] dependencies = [('Boost', '1.60.0')] +builddependencies = [('CMake', '3.4.3',)] + + start_dir = 'src' configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" -builddependencies = [('CMake', '3.4.3',)] - sanity_check_paths = { 'files': ['bin/CrossTalkZ'], 'dirs': [''], -- GitLab From d5f98a30a0c96ca87d29c8b47200cb2c4d6450a5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 16:08:28 +0200 Subject: [PATCH 1523/2133] version fix, commit version provided --- ....eb => Commet-20150415-foss-2016a-Python-2.7.11.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/c/Commet/{Commet-20160422-foss-2016a-Python-2.7.11.eb => Commet-20150415-foss-2016a-Python-2.7.11.eb} (76%) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb similarity index 76% rename from easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 2c16bccce7..88a548fab4 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -1,7 +1,8 @@ easyblock = 'MakeCp' name = 'Commet' -version = '20160422' +version = '20150415' +commit = '4ef0705' pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' @@ -13,11 +14,10 @@ a large metagenomic project. toolchain = {'name': 'foss', 'version': '2016a'} -# there is no tarball provided, only git checkout through: -# https://github.com/pierrepeterlongo/commet/archive/master.zip -sources = [SOURCE_ZIP] +source_urls = ['https://github.com/pierrepeterlongo/commet/archive'] +sources = ['%s.tar.gz' % commit] -checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] +checksums = ['19cba09ca7a92eaed75ed6af820d9451'] files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] -- GitLab From 540113e091905d193da3fcdc0c803424c34acd4a Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 17:24:15 +0200 Subject: [PATCH 1524/2133] Exonerate with foss2016a --- .../e/Exonerate/Exonerate-2.4.0-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb new file mode 100644 index 0000000000..0cfe11f239 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'http://www.ebi.ac.uk/~guy/exonerate/' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/nathanweeks/exonerate/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GLib', '2.47.5')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' -- GitLab From 01bc3c39e0364364ea288d9e64c6adacf4533d63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 1 May 2016 18:54:55 +0200 Subject: [PATCH 1525/2133] also add xproto as build dep in other makedepend 1.0.5 easyconfigs --- .../makedepend-1.0.5-gimkl-2.11.5.eb | 4 ++++ .../makedepend-1.0.5-intel-2015a.eb | 4 ++++ .../makedepend-1.0.5-intel-2015b.eb | 4 ++++ .../makedepend-1.0.5-intel-2016a.eb | 4 ++++ .../x/xproto/xproto-7.0.28-intel-2015a.eb | 24 +++++++++++++++++++ 5 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb index 38d76d37d2..29139d3313 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb index 282179280a..2a137852f4 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb index ca6025105b..32cc5814c9 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb index e38d07d26e..943da96f82 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb new file mode 100644 index 0000000000..532a92d315 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 4a496d0696387804d39ae0782243921dcc9a5006 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 21:45:01 +0200 Subject: [PATCH 1526/2133] Style fixes --- .../Commet-20150415-foss-2016a-Python-2.7.11.eb | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 88a548fab4..6c4d59ab68 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -3,13 +3,11 @@ easyblock = 'MakeCp' name = 'Commet' version = '20150415' commit = '4ef0705' - -pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' homepage = 'https://colibread.inria.fr/software/commet/' description = """ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of -a large metagenomic project. + a large metagenomic project. """ toolchain = {'name': 'foss', 'version': '2016a'} @@ -19,15 +17,15 @@ sources = ['%s.tar.gz' % commit] checksums = ['19cba09ca7a92eaed75ed6af820d9451'] -files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] - dependencies = [ ('Python', '2.7.11'), ] +files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] + sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["Commet.py", "bvop", - "compare_reads", "extract_reads", "filter_reads", "index_and_search"]], + 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', + 'extract_reads', 'filter_reads', 'index_and_search']], 'dirs' : ['doc', 'include'] } -- GitLab From 9e74175aa5e6096dcc34ad1f3a502b9a84dcfecc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 08:42:42 +0200 Subject: [PATCH 1527/2133] Add SWIG-3.0.8-foss-2016a-Python-2.7.11.eb --- .../SWIG-3.0.8-foss-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..2ffde034da --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '3.0.8' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.11' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' -- GitLab From 7c7e981088c0df6a663f3ad8626980db936c01b3 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 08:49:05 +0200 Subject: [PATCH 1528/2133] Modify Perl-5.22.1-intel-2016a.eb to update source_urls --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index aed8a467d0..b58ce50af4 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -137,7 +137,7 @@ exts_list = [ }), ('FreezeThaw', '0.5001', { 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], }), ('DBI', '1.634', { 'source_tmpl': 'DBI-1.634.tar.gz', @@ -221,7 +221,7 @@ exts_list = [ }), ('Tie::Function', '0.02', { 'source_tmpl': 'Tie-Function-0.02.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], }), ('Template::Plugin::Number::Format', '1.06', { 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', -- GitLab From 1d32aabaede918e266733560e3c7e573cd63b066 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 09:00:15 +0200 Subject: [PATCH 1529/2133] Modify Doxygen-1.8.11-* files to only build in serial --- easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb | 2 ++ easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb | 2 ++ easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb index 5adccf48d7..9af65e4593 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb index 1db648e43d..5b5d5f06cd 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb index 2d5dc8597f..a63ff80fea 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' -- GitLab From 752eeed94e82927ba6a1e12b2966bd95cd1a0342 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 10:07:56 +0200 Subject: [PATCH 1530/2133] bump Java to 1.7.0_80, use %(pyver)s, %(javaver)s templates --- ...-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb} | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/p/PLplot/{PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb => PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb} (77%) diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb similarity index 77% rename from easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb rename to easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb index 0d3d65891c..a77bf58f49 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'CMakeMake' name = 'PLplot' version = '5.11.1' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' homepage = 'http://plplot.sourceforge.net' description = """PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols @@ -13,22 +14,15 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -pyver = '2.7.11' -javaver = '1.7.0_79' -pyshortver = '.'.join(pyver.split('.')[0:2]) -versionsuffix = '-Java-%s-Python-%s' % (javaver, pyver) - -glibver = '2.47.5' - builddependencies = [ ('CMake', '3.4.3'), - ('SWIG', '3.0.8', '-foss-2016a-Python-%s' % pyver, True), + ('SWIG', '3.0.8', '-Python-%(pyver)s'), ('xproto', '7.0.28'), ] dependencies = [ - ('Java', javaver, '', True), - ('Python', pyver), + ('Java', '1.7.0_80', '', True), + ('Python', '2.7.11'), ('Perl', '5.22.1'), ('Tcl', '8.6.4'), ('Tk', '8.6.4', '-no-X11'), @@ -36,7 +30,7 @@ dependencies = [ ('expat', '2.1.0'), ('fontconfig', '2.11.94'), ('freetype', '2.6.2'), - ('GLib', glibver), + ('GLib', '2.47.5'), ('libICE', '1.0.9'), ('libtool', '2.4.6'), ('libX11', '1.6.3'), @@ -52,7 +46,7 @@ dependencies = [ separate_build_dir = True -modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_paths = { 'files': ['lib/libplplot.so', 'lib/pkgconfig/plplot-f95.pc'], -- GitLab From 68da87ecb25dc92b328c3c313eaeb8192e6269d2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 10:59:03 +0200 Subject: [PATCH 1531/2133] add easyconfig SPRNG-2.0b-foss-2016a.eb --- .../s/SPRNG/SPRNG-2.0b-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb new file mode 100644 index 0000000000..59be5269fa --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'SPRNG' +version = '2.0b' + +homepage = 'http://www.sprng.org/' +description = "Scalable Parallel Pseudo Random Number Generators Library" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.sprng.org/Version2.0/'] +sources = ['%(namelower)s%(version)s.tar.gz'] + +patches = ['SPRNG-2.0_fix-metropolis-test.patch'] + +dependencies = [('GMP', '6.1.0')] + +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' + +# does not support parallel build +parallel = 1 + +files_to_copy = [ + (['lib/libsprng.a'], 'lib'), + (['include/interface.h', 'include/sprng.h', 'include/sprng_f.h'], 'include'), +] + +sanity_check_paths = { + 'files': ["lib/libsprng.a"], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From f12417d1caa6603e778b58af79d1235ad42d74db Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 2 May 2016 11:53:18 +0200 Subject: [PATCH 1532/2133] removed tab --- .../c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 6c4d59ab68..549296f08e 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -25,7 +25,7 @@ files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', - 'extract_reads', 'filter_reads', 'index_and_search']], + 'extract_reads', 'filter_reads', 'index_and_search']], 'dirs' : ['doc', 'include'] } -- GitLab From d9ccb6471e949227ec1acd518aa95cf819737b81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 11:56:40 +0200 Subject: [PATCH 1533/2133] add easyconfig TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb, add easyconfig molmod-1.1-intel-2016a-Python-2.7.11.eb --- .../molmod-1.1-intel-2016a-Python-2.7.11.eb | 31 ++++++++++++++++++ .../TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb | 32 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1673c64e60 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), +] + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" + +# fix permissions issue on files in share/molmod subdir +postinstallcmds = ['chmod -R o+r %(installdir)s/share/molmod'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/molmod'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..34a9b5e9f5 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'TAMkin' +version = '1.0.9' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), + ('molmod', '1.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'chem' -- GitLab From 7e1df6e4e780696abbb408d269a01c77f473ee82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 12:10:49 +0200 Subject: [PATCH 1534/2133] add easyconfig FFmpeg-2.8.7-intel-2016a.eb --- .../f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb new file mode 100644 index 0000000000..05478ccada --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.7' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('x264', '20160430'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From 56d851d169447389e2ee3cdfd4b04ef3e6f12a8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 12:55:35 +0200 Subject: [PATCH 1535/2133] add easyconfig GTK+-2.24.30-intel-2016a.eb, add easyconfig Pango-1.40.1-intel-2016a.eb, add easyconfig cairo-1.14.6-intel-2016a-GLib-2.48.0.eb, add easyconfig HarfBuzz-1.2.7-intel-2016a.eb, add easyconfig ATK-2.20.0-intel-2016a.eb, add easyconfig Gdk-Pixbuf-2.35.1-intel-2016a.eb, add easyconfig GObject-Introspection-1.48.0-intel-2016a.eb --- .../a/ATK/ATK-2.20.0-intel-2016a.eb | 34 +++++++++++ .../cairo-1.14.6-intel-2016a-GLib-2.48.0.eb | 56 +++++++++++++++++++ ...Object-Introspection-1.48.0-intel-2016a.eb | 48 ++++++++++++++++ .../g/GTK+/GTK+-2.24.30-intel-2016a.eb | 25 +++++++++ .../Gdk-Pixbuf-2.35.1-intel-2016a.eb | 34 +++++++++++ .../h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb | 34 +++++++++++ .../p/Pango/Pango-1.40.1-intel-2016a.eb | 31 ++++++++++ 7 files changed, 262 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb new file mode 100644 index 0000000000..2c8911864b --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.20.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000..ecd56f9166 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' +glibver = '2.48.0' +versionsuffix = '-GLib-%s' % glibver + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.3'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.95'), + ('expat', '2.1.1'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] +builddependencies = [ + ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb new file mode 100644 index 0000000000..3d59c6fe7c --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.48.0' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('Python', '2.7.11'), + ('GLib', glibver), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6', '-GLib-%s' % glibver), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb new file mode 100644 index 0000000000..6dfeab0526 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.30' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.20.0'), + ('Gdk-Pixbuf', '2.35.1'), + ('Pango', '1.40.1'), + ('GObject-Introspection', '1.48.0'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb new file mode 100644 index 0000000000..f06da781d8 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.35.1' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb new file mode 100644 index 0000000000..23c2924fab --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.2.7' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('freetype', '2.6.3'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb new file mode 100644 index 0000000000..b251f8ef22 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.1' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('HarfBuzz', '1.2.7'), + ('GObject-Introspection', '1.48.0'), + ('fontconfig', '2.11.95') +] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From b430a93dab623ccdbb1cbab087ef880ceac1942c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 13:12:56 +0200 Subject: [PATCH 1536/2133] add easyconfig NASM-2.12.01-intel-2016a.eb, add easyconfig x264-20160430-intel-2016a.eb --- .../n/NASM/NASM-2.12.01-intel-2016a.eb | 31 +++++++++++++++++++ .../x/x264/x264-20160430-intel-2016a.eb | 24 ++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb new file mode 100644 index 0000000000..dc884fc260 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.01' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb new file mode 100644 index 0000000000..2525aff2b3 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160430' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://ftp.videolan.org/pub/videolan/x264/snapshots/'] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From a4e13eba05271a1af27d9e133bab189308dfe211 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 13:48:06 +0200 Subject: [PATCH 1537/2133] modify easyconfig x264-20160430-intel-2016a.eb --- easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb index 2525aff2b3..5f7b69a6bc 100644 --- a/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb +++ b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb @@ -9,7 +9,10 @@ description = """x264 is a free software library and application for encoding vi toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['ftp://ftp.videolan.org/pub/videolan/x264/snapshots/'] +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] dependencies = [('Yasm', '1.3.0')] -- GitLab From e98a77f0534b917a23df6f63b4f7975391815725 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 15:09:25 +0200 Subject: [PATCH 1538/2133] add easyconfig OpenCV-2.4.12-intel-2016a.eb --- .../o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb new file mode 100644 index 0000000000..5cbe53aac8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -0,0 +1,69 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '2.4.12' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_ZIP] +source_urls = [('http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/%(version)s', 'download')] + +patches = ['OpenCV-%(version)s_with_IPP.patch'] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +javaver = '1.7.0_80' +dependencies = [ + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('FFmpeg', '2.8.7'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('JasPer', '1.900.1'), + ('Java', javaver, '', True), + ('ant', '1.9.6', '-Java-%s' % javaver, True), + ('GLib', '2.48.0'), + ('GTK+', '2.24.30'), +] + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.so ' +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.so ' +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.so ' +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' -- GitLab From 01c5819ff4a7441070afba2a3d05fc512b2e3e1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 16:37:32 +0200 Subject: [PATCH 1539/2133] use existing patch file, fix conflict on NASM version --- ...eg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb | 33 +++++++++++++++++++ .../o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 8 ++--- 2 files changed, 37 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb new file mode 100644 index 0000000000..c1f7d100e0 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +nasmver = '2.12.01' +versionsuffix = '-NASM-%s' % nasmver + +dependencies = [ + ('NASM', nasmver), +] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb index 5cbe53aac8..89e2746bd8 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -11,10 +11,10 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCELOWER_ZIP] -source_urls = [('http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/%(version)s', 'download')] +source_urls = ['https://github.com/Itseez/opencv/archive/'] +sources = ['%(version)s.zip'] -patches = ['OpenCV-%(version)s_with_IPP.patch'] +patches = ['OpenCV-2.4.9_with_IPP.patch'] builddependencies = [ ('CMake', '3.5.2'), @@ -25,7 +25,7 @@ dependencies = [ ('Python', '2.7.11'), ('zlib', '1.2.8'), ('FFmpeg', '2.8.7'), - ('libjpeg-turbo', '1.4.2'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), -- GitLab From 1dc2cb9ea6258091ac20deafdd03dc35dfd23bcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 17:05:52 +0200 Subject: [PATCH 1540/2133] add sed command to worker easyconfig files to fix module_path in conf/worker.conf --- .../easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 9 +++++---- .../easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index cdf0174497..66e66633d0 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -21,11 +21,12 @@ dependencies = [ # adjust worker configuration file # note: tweak this to your local setup postinstallcmds = [ - 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', - 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', # tweak this - 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', # tweak this (maybe) - 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2015a@g" %(installdir)s/conf/worker.conf', # tweak this (maybe) + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb index 3c373e597a..f840fe2253 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb @@ -21,11 +21,12 @@ dependencies = [ # adjust worker configuration file # note: tweak this to your local setup postinstallcmds = [ - 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', - 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', # tweak this - 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', # tweak this (maybe) - 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', # tweak this (maybe) + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' -- GitLab From 674a21915757f47ee9b7847046f3342ea1c5f39a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 17:26:36 +0200 Subject: [PATCH 1541/2133] add easyconfig FFTW-3.3.4-intel-2016a.eb --- .../f/FFTW/FFTW-3.3.4-intel-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb new file mode 100644 index 0000000000..09d52dd755 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +# no quad precision, requires GCC v4.6 or higher +# see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' -- GitLab From 9c81999977bfae80711d38da02ebd8912caa5468 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 17:32:59 +0200 Subject: [PATCH 1542/2133] make Gdk-Pixbug 2.35.1 compatible with NASM 2.12.01 --- .../easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb index f06da781d8..ec51681b28 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('GLib', '2.48.0'), - ('libjpeg-turbo', '1.4.2'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('GObject-Introspection', '1.48.0') -- GitLab From 0933f2c4ce3c791af9049d58a213777de638df6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 19:13:57 +0200 Subject: [PATCH 1543/2133] correct sed command in worker easyconfig files to fix module_path in conf/worker.conf --- easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index 66e66633d0..1bd2831171 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -26,7 +26,7 @@ postinstallcmds = [ 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', - 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb index f840fe2253..1882b094dc 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb @@ -26,7 +26,7 @@ postinstallcmds = [ 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', - 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' -- GitLab From dcd16bf4a00f49d8511d31f894606d306cb5b08e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 19:47:01 +0200 Subject: [PATCH 1544/2133] bump hwloc to 1.11.3, add missing hwloc easyconfig file --- .../hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb | 22 +++++++++++++++++++ .../OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 2 +- 2 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..54ea46766a --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +# numactl is a direct dependency of PGI +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index 8cd6dea646..be813ed50e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -18,7 +18,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify -dependencies = [('hwloc', '1.11.2')] +dependencies = [('hwloc', '1.11.3')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -- GitLab From ced0e99cf03255aa46d0855c8ee42cfe2e691835 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:18:33 +0200 Subject: [PATCH 1545/2133] add easyconfig ParaView-4.4.0-intel-2016a.eb --- .../p/ParaView/ParaView-4.4.0-intel-2016a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb new file mode 100644 index 0000000000..5961519cd4 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '4.4.0' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': False} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s-source.tar.gz"] + +patches = ['%(name)s-%(version)s_missingheader.patch'] + +dependencies = [ + ('Mesa', '11.2.1'), + ('libGLU', '9.0.0'), + ('libXt', '1.1.5'), + ('Qt', '4.8.7'), + ('libXext', '1.3.3'), + ('libX11', '1.6.3'), + ('zlib', '1.2.8'), +] + +builddependencies = [('CMake', '3.5.2')] + +separate_build_dir = True + +maxparallel = 4 + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +# Without internet connection turn off testing (uncomment the following line) +#configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From bb3540dfc10e41c0550bb4aa18610f15e8be76f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:23:40 +0200 Subject: [PATCH 1546/2133] modify easyconfig ParaView-4.4.0-intel-2016a.eb, add easyconfig libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb --- .../libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb | 27 +++++++++++++++++++ .../p/ParaView/ParaView-4.4.0-intel-2016a.eb | 3 +-- 2 files changed, 28 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..fe3cfb14d6 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesaver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesaver + +dependencies = [ + ('Mesa', mesaver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index 5961519cd4..dd7ed0db4e 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -16,8 +16,7 @@ sources = ["ParaView-v%(version)s-source.tar.gz"] patches = ['%(name)s-%(version)s_missingheader.patch'] dependencies = [ - ('Mesa', '11.2.1'), - ('libGLU', '9.0.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), ('libXt', '1.1.5'), ('Qt', '4.8.7'), ('libXext', '1.3.3'), -- GitLab From bdcebe8ebd643eedf64753a77bdb8a0500edf040 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 3 May 2016 11:29:46 +0200 Subject: [PATCH 1547/2133] DIAL with foss2016a --- .../d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb new file mode 100644 index 0000000000..9698cc436f --- /dev/null +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'DIAL' +version = '2011.06.06' + +homepage = 'http://www.bx.psu.edu/miller_lab/' +description = """ +DIAL (De novo Identification of Alleles) is a collection of programs to automate +the discovery of alleles for a species where we lack a reference sequence. The +SNPs/alleles are specifically selected for a low error rate in genotyping +assays. +""" + + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] + +patches = ['DIAL-Makefile.in.patch'] + +dependencies = [ + ('LASTZ', '1.02.00'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in [ + 'assemble', + 'assemble1', + 'assemble_illumina', + 'build_sff_index', + 'convertFastqFasta', + 'cull_components', + 'DIAL', + 'filter', + 'filter_clusters', + 'fish_clusters', + 'make_template', + 'masker', + 'partition', + 'remove_clones', + 'remove_clusters', + 'update', + 'update_clusters', + 'update_status', +]], + 'dirs': ["bin"] +} + +moduleclass = 'bio' -- GitLab From 4d95db4024048043a88926c1ab85b70103c54b1b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 3 May 2016 11:38:51 +0200 Subject: [PATCH 1548/2133] LASTZ with foss2016a --- .../l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb new file mode 100644 index 0000000000..6f1e587143 --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'LASTZ' +version = '1.02.00' + +homepage = 'http://www.bx.psu.edu/~rsharris/lastz/' +description = """ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle + sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS + sequencing technologies such as Roche 454. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] + +patches = ['LASTZ-Makefile.patch'] + +skipsteps=['configure'] + +installopts = 'installDir=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["lastz","lastz_D"]], + 'dirs': ["bin"] +} + +moduleclass = 'bio' -- GitLab From 86534840b088b9961b865fe76a0494db0932d37d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 3 May 2016 11:46:53 +0200 Subject: [PATCH 1549/2133] longlines --- .../easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb index 9698cc436f..3f508bfac5 100644 --- a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -4,14 +4,11 @@ name = 'DIAL' version = '2011.06.06' homepage = 'http://www.bx.psu.edu/miller_lab/' -description = """ -DIAL (De novo Identification of Alleles) is a collection of programs to automate -the discovery of alleles for a species where we lack a reference sequence. The -SNPs/alleles are specifically selected for a low error rate in genotyping -assays. +description = """DIAL (De novo Identification of Alleles) is a collection of programs + to automate the discovery of alleles for a species where we lack a reference sequence. + The SNPs/alleles are specifically selected for a low error rate in genotyping assays. """ - toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -- GitLab From bd6a68f0019b2a28271c533b904a43dea7518149 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:50:20 +0200 Subject: [PATCH 1550/2133] disable testing for ParaView --- easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index dd7ed0db4e..e9e923fc24 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -34,7 +34,7 @@ configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' # Without internet connection turn off testing (uncomment the following line) -#configopts += '-DBUILD_TESTING=OFF ' +configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) -- GitLab From a5acebaa141c7adea90c1ebc41016336c2c231bd Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 3 May 2016 11:53:50 +0200 Subject: [PATCH 1551/2133] comments exts --- .../BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 1e9c0c19f5..fdb264f023 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -18,12 +18,13 @@ dependencies = [ ('DB_File', '1.835', versionsuffix), ] -exts_list = [ - ('CGI', '4.28', { - 'source_tmpl': 'CGI-4.28.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], - }), -] +#exts_list = [ +# ('CGI', '4.28', { +# 'source_tmpl': 'CGI-4.28.tar.gz', +# 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], +# }), +#] + options = {'modulename': 'Bio::Perl'} moduleclass = 'bio' -- GitLab From 9b8e5bb3f71195e5ada26a6ebfa928b8772a03f7 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 3 May 2016 11:55:27 +0200 Subject: [PATCH 1552/2133] modify easyconfig Blitz++-0.10-foss-2016a.eb, modify easyconfig Blitz++-0.10-goolf-1.5.16.eb --- easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb | 2 ++ easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb index f91bad5dd3..f5aaed761c 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb @@ -17,4 +17,6 @@ sanity_check_paths = { 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], } +configopts = '--enable-shared' + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb index f75014e6f2..e75ab2de98 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb @@ -17,4 +17,6 @@ sanity_check_paths = { 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], } +configopts = '--enable-shared' + moduleclass = 'lib' -- GitLab From 9d63140391fe52ab6161f2df09171600fa04a875 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:57:35 +0200 Subject: [PATCH 1553/2133] add easyconfig grace-5.1.25-intel-2016a.eb, add easyconfig util-linux-2.28-intel-2016a.eb, add easyconfig motif-2.3.5-intel-2016a.eb, add easyconfig xbitmaps-1.1.1-intel-2016a.eb --- .../g/grace/grace-5.1.25-intel-2016a.eb | 29 ++++++++++++ .../m/motif/motif-2.3.5-intel-2016a.eb | 47 +++++++++++++++++++ .../util-linux/util-linux-2.28-intel-2016a.eb | 33 +++++++++++++ .../x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb | 19 ++++++++ 4 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb new file mode 100644 index 0000000000..e538b0ca3b --- /dev/null +++ b/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'grace' +version = '5.1.25' + +homepage = 'http://freecode.com/projects/grace' +description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" + +source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('motif', '2.3.5'), + ('netCDF', '4.4.0'), +] + +runtest = 'tests' + +# we also need to run make links right before or after make install. +installopts = 'links' + +sanity_check_paths = { + 'files': ['bin/xmgrace'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb new file mode 100644 index 0000000000..ed700e2d0b --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.5' + +homepage = 'http://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +# use -O1 to dance around icc segfaulting +toolchainopts = {'lowopt': True} + +sources = ['%(name)s-%(version)s-src.tgz'] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('libXt', '1.1.5'), + ('libXau', '1.0.8'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXdmcp', '1.1.2'), + ('libpng', '1.6.21'), + ('xbitmaps', '1.1.1'), + ('freetype', '2.6.3'), + ('libjpeg-turbo', '1.4.2'), + ('bzip2', '1.0.6'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('util-linux', '2.28'), +] + +preconfigopts = "./autogen.sh && " + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb new file mode 100644 index 0000000000..d86cc6a029 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.28' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb new file mode 100644 index 0000000000..a463f1ce79 --- /dev/null +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xbitmaps' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """provides bitmaps for x""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_DATA_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From f574411b83f9fda2f0dda5862b40ae1996aaa6f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 12:04:35 +0200 Subject: [PATCH 1554/2133] fix source URL for motif 2.3.5 --- easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb index ed700e2d0b..60a8ac80b7 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # use -O1 to dance around icc segfaulting toolchainopts = {'lowopt': True} -sources = ['%(name)s-%(version)s-src.tgz'] +sources = ['%(name)s-%(version)s.tgz'] source_urls = [SOURCEFORGE_SOURCE] dependencies = [ -- GitLab From 16f0c91739daa1cdf1cd19d283b29ae22a246d3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 12:09:34 +0200 Subject: [PATCH 1555/2133] really fix name of source tarball for motif 2.3.5 --- easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb index 60a8ac80b7..8072aeb7c2 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # use -O1 to dance around icc segfaulting toolchainopts = {'lowopt': True} -sources = ['%(name)s-%(version)s.tgz'] +sources = ['%(name)s-%(version)s.tar.gz'] source_urls = [SOURCEFORGE_SOURCE] dependencies = [ -- GitLab From 025a13b46c76146c6ddcb0c82b80b741c34e09e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 12:18:58 +0200 Subject: [PATCH 1556/2133] no autogen for motif 2.3.5 --- easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb index 8072aeb7c2..0cf658c9a2 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -34,8 +34,6 @@ builddependencies = [ ('util-linux', '2.28'), ] -preconfigopts = "./autogen.sh && " - # makefile is not parallel safe parallel = 1 -- GitLab From 17fed7291663dfab3144c3c71acbfa5461e73a24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 13:39:08 +0200 Subject: [PATCH 1557/2133] no need to limit parallel build for ParaView --- easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index e9e923fc24..838808a743 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -28,8 +28,6 @@ builddependencies = [('CMake', '3.5.2')] separate_build_dir = True -maxparallel = 4 - configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' -- GitLab From 4ef76e210cf81d007716d81489e3e951d67589eb Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 4 May 2016 13:34:30 +0200 Subject: [PATCH 1558/2133] Easyconfig for Gurobi 6.5.1 --- .../easyconfigs/g/Gurobi/Gurobi-6.5.1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb new file mode 100644 index 0000000000..4d3f74327c --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb @@ -0,0 +1,24 @@ +name = 'Gurobi' +version = '6.5.1' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +# Registration is required. +# source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] + +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", name, "%(namelower)s.lic") + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in ['grbprobe', 'grbtune', 'gurobi_cl', 'gurobi.sh']], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 53289060c2f14243de149b5e4146de0924c5427e Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 4 May 2016 13:36:14 +0200 Subject: [PATCH 1559/2133] Easyconfig for Gurobi 6.5.1 --- .../easyconfigs/g/Gurobi/Gurobi-6.5.1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb new file mode 100644 index 0000000000..4d3f74327c --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb @@ -0,0 +1,24 @@ +name = 'Gurobi' +version = '6.5.1' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +# Registration is required. +# source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] + +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", name, "%(namelower)s.lic") + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in ['grbprobe', 'grbtune', 'gurobi_cl', 'gurobi.sh']], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 596390a3f4ace66c6329792d3e3849d2d45dc4c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 May 2016 13:42:09 +0200 Subject: [PATCH 1560/2133] clean up binutils 2.26 easyconfigs to use binutils easyblock --- .../b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 20 ------------------- .../easyconfigs/b/binutils/binutils-2.26.eb | 20 ------------------- 2 files changed, 40 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb index ca71c5f04e..d7c829040f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.26' @@ -20,22 +18,4 @@ builddependencies = [ ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb index 5145e1becd..702b413120 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.26' @@ -18,22 +16,4 @@ builddependencies = [ ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' -- GitLab From 8580725e82c0690321e07d4588b0dfdac13968e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 May 2016 14:30:10 +0200 Subject: [PATCH 1561/2133] clean up binutils easyconfigs to use binutils easyblock --- .../binutils-2.22-goalf-1.1.0-no-OFED.eb | 14 ----------- .../binutils-2.22-gompi-1.4.12-no-OFED.eb | 14 ----------- .../b/binutils/binutils-2.22-goolf-1.4.10.eb | 14 ----------- .../b/binutils/binutils-2.22-goolf-1.5.14.eb | 11 --------- .../b/binutils/binutils-2.24-foss-2014b.eb | 13 ----------- .../b/binutils/binutils-2.24-intel-2014b.eb | 16 ------------- .../binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 23 +------------------ .../binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCC-4.9.3.eb | 23 +------------------ .../binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 22 +----------------- .../easyconfigs/b/binutils/binutils-2.25.1.eb | 22 +----------------- .../easyconfigs/b/binutils/binutils-2.25.eb | 22 +----------------- 15 files changed, 9 insertions(+), 273 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index bfc339020f..af12b0472e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,15 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 437f04c2a6..8035182b62 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,15 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index 5f76d89a06..de87300f7c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -23,15 +20,4 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb index 5dae8ebe27..d989a00acf 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,12 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%(version)s.tar.bz2'] source_urls = [GNU_SOURCE] -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb index 3d49fdcf03..9683cfc728 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.24' @@ -15,15 +13,4 @@ dependencies = [ ('zlib', '1.2.8'), ] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 77fb03962b..5d4b31cd73 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.24' @@ -15,18 +13,4 @@ dependencies = [ ('zlib', '1.2.8'), ] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -# disable warning/error #175 ("subscript out of range") -buildopts = 'CFLAGS="$CFLAGS -wd175"' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index c3ffc6e24a..08e10d150c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 418f81f5f1..ea9a13974b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -11,30 +9,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -# zlib required, but being linked instatically, so not a runtime dep builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 2e680c9ce3..9709696cf5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index b6d6a68fc6..7ccace8501 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -11,30 +9,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -# zlib required, but being linked instatically, so not a runtime dep builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index 6858b124b1..d6e68008e5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb index a9d4815d89..9ec7a3f3f3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,28 +13,10 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 5378940837..f411442d12 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,28 +13,10 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index 63837a712c..e3f5b15724 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25.1' @@ -14,26 +12,8 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index cfcfe38d3d..e08cd975ad 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,26 +13,8 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' -- GitLab From 60b7998227658378f64bdb37d17b2d93cec9954f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 14:35:38 +0200 Subject: [PATCH 1562/2133] Add libcroco --- .../l/libcroco/libcroco-0.6.11-intel-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb new file mode 100644 index 0000000000..29421c21ae --- /dev/null +++ b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libcroco' +version = '0.6.11' + +homepage = 'https://github.com/GNOME/libcroco' +description = """Libcroco is a standalone css2 parsing and manipulation library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/libcroco/%(version_major_minor)s/'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), + ('GLib', '2.48.0'), + ('XZ', '5.2.2',) +] + +sanity_check_paths = { + 'files': ['bin/csslint-%(version_major_minor)s', 'lib/libcroco-%%(version_major_minor)s.%s' % SHLIB_EXT, + 'lib/libcroco-%(version_major_minor)s.a'], + 'dirs': ['include/libcroco-%(version_major_minor)s', 'share'] +} + +moduleclass = 'lib' -- GitLab From 2b14bc7845376a3291b1a6ee367fde0cc6c866b1 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 14:36:11 +0200 Subject: [PATCH 1563/2133] Build shared FLTK and enable threads --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb index 97b3b63c16..226d6e353c 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb @@ -17,6 +17,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +configopts = '--enable-shared --enable-threads --enable-xft' dependencies = [ ('libX11', '1.6.3'), -- GitLab From f352cd263e6d396f3ee55d090ac2369d6f2fd1fe Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:01:57 +0200 Subject: [PATCH 1564/2133] Add librsvg --- .../l/librsvg/librsvg-2.40.15-intel-2016a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb new file mode 100644 index 0000000000..40a5c468bc --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.40.15' + +homepage = 'https://wiki.gnome.org/action/show/Projects/LibRsvg' +description = """librsvg is a library to render SVG files using cairo.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s'] + +dependencies = [ + ('Gdk-Pixbuf', '2.35.1'), + ('libcroco', '0.6.11'), + ('Pango', '1.40.1'), + ('cairo', '1.14.6', '-GLib-2.48.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'vis' -- GitLab From f5eb0bd2eaab60cf310f854add0143cd6c07a47d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:17:34 +0200 Subject: [PATCH 1565/2133] Make gettext build dep for XZ --- easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb index b717af018a..0d274e829e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb @@ -13,9 +13,6 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ ('gettext', '0.19.6'), ] -- GitLab From 6b794ab6f8552861afc6edb28e210a5ff3730a6c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:18:10 +0200 Subject: [PATCH 1566/2133] Add jwm --- .../j/jwm/jwm-2.3.5-intel-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb new file mode 100644 index 0000000000..46a293738e --- /dev/null +++ b/easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'JWM' +version = '2.3.5' + +homepage = 'https://joewing.net/projects/jwm/' +description = """JWM is a light-weight window manager for the X11 Window System.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['https://joewing.net/projects/jwm/releases'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libX11', '1.6.3'), + ('libXft', '2.3.2'), + ('libXext', '1.3.3'), + ('libXmu', '1.1.2'), + ('libXpm', '3.5.11'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), + ('libXinerama', '1.1.3'), + ('fontconfig', '2.11.95'), + ('cairo', '1.14.6', '-GLib-2.48.0'), + ('libcroco', '0.6.11'), + ('librsvg', '2.40.15'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'vis' -- GitLab From fb1473a41cc0fca45c09153b1c533a6ee4e07bec Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:30:37 +0200 Subject: [PATCH 1567/2133] Capitalize jwm --- .../jwm-2.3.5-intel-2016a.eb => JWM/JWM-2.3.5-intel-2016a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/j/{jwm/jwm-2.3.5-intel-2016a.eb => JWM/JWM-2.3.5-intel-2016a.eb} (100%) diff --git a/easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb similarity index 100% rename from easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb rename to easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb -- GitLab From 263190c2ecf45306f893665fd7a294b2f38dd75e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:37:57 +0200 Subject: [PATCH 1568/2133] Fix version hell --- .../j/JWM/JWM-2.3.5-intel-2016a.eb | 2 +- ...ft-2.3.2-intel-2016a-fontconfig-2.11.95.eb | 32 +++++++++++++++++++ 2 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb diff --git a/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb index 46a293738e..273e8bedca 100644 --- a/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb @@ -14,7 +14,7 @@ source_urls = ['https://joewing.net/projects/jwm/releases'] dependencies = [ ('bzip2', '1.0.6'), ('libX11', '1.6.3'), - ('libXft', '2.3.2'), + ('libXft', '2.3.2', '-fontconfig-2.11.95'), ('libXext', '1.3.3'), ('libXmu', '1.1.2'), ('libXpm', '3.5.11'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb new file mode 100644 index 0000000000..3c4a378321 --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' +versionsuffix = '-fontconfig-2.11.95' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXrender', '0.9.9'), + ('freetype', '2.6.3'), + ('fontconfig', '2.11.95'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From db94502b667bd318e0cd9b8124dc2cfa2d99ea2c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:49:56 +0200 Subject: [PATCH 1569/2133] Add sanity check --- easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb index 273e8bedca..754b3694f8 100644 --- a/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb @@ -28,8 +28,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['bin/jwm'], + 'dirs': ['etc', 'share'] } moduleclass = 'vis' -- GitLab From aa75dc672a73af64ccbbafe19281c4f415772167 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:51:20 +0200 Subject: [PATCH 1570/2133] FLTK: check of static and dynamic lib --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb index 226d6e353c..e045fbcd6c 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb @@ -31,7 +31,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/fltk-config', 'bin/fluid'], + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'libfltk.%s' % SHLIB_EXT], 'dirs': ['lib'], } -- GitLab From 78b5bbd0f7434449c304db593d6fa3c09a7ef9ab Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 16:00:37 +0200 Subject: [PATCH 1571/2133] Don't do GDK-pixbuf loader --- easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb index 40a5c468bc..9d059ba80c 100644 --- a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb @@ -11,6 +11,9 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_XZ] source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s'] +# this loader wants to install in the directory of Gdk-Pixbuf itself, so disable +configopts = '--disable-pixbuf-loader' + dependencies = [ ('Gdk-Pixbuf', '2.35.1'), ('libcroco', '0.6.11'), -- GitLab From 053e882d140f2227a4fb0da572fcce5014e80f7a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 16:11:17 +0200 Subject: [PATCH 1572/2133] Add sanity check --- .../easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb index 9d059ba80c..57726fc9cd 100644 --- a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb @@ -22,8 +22,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['bin/rsvg-convert', 'lib/librsvg-2.%s' % SHLIB_EXT, 'lib/librsvg-2.a'], + 'dirs': ['include/librsvg-2.0', 'share'] } moduleclass = 'vis' -- GitLab From 4f1e5b15a584305b53e92d193616e9a4f954cb2b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 16:44:35 +0200 Subject: [PATCH 1573/2133] Fix sanity check --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb index e045fbcd6c..859d8f39a4 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb @@ -31,7 +31,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'libfltk.%s' % SHLIB_EXT], + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], 'dirs': ['lib'], } -- GitLab From 52e2b45e866b5d6c1c3779d6f19ebba6a3c12aa8 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 10:55:13 -0400 Subject: [PATCH 1574/2133] bump to GLib 2.48.0 --- .../g/GLib/GLib-2.48.0-foss-2016a.eb | 33 +++++++++++++++++++ .../PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb new file mode 100644 index 0000000000..73ce1be6d6 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.48.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb index 9d7551949d..1438b0e86a 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.11'), - ('GLib', '2.47.5'), + ('GLib', '2.48.0'), ('GTS' ,'0.7.6'), ] -- GitLab From 61d8f74df864995f4a49d53ef64d108cd9ddf585 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 11:14:12 -0400 Subject: [PATCH 1575/2133] bump to mesa 11.2.1 --- ...bQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..3f7a781e6b --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,23 @@ +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('libGLU', '9.0.0', versionsuffix), +] + +builddependencies = [('Qt', '4.8.7', '-GLib-2.48.0')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' -- GitLab From 16181d207a81520c7b3d0b80143f37fb9a9e181f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 11:23:58 -0400 Subject: [PATCH 1576/2133] add Qt 4.8.7 with GLib-2.48.0 --- .../q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000..8616257c5c --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb @@ -0,0 +1,27 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +glib_ver = '2.48.0' +versionsuffix = '-GLib-%s' % glib_ver + +dependencies = [ + ('GLib', glib_ver), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXrender', '0.9.9'), +] + +moduleclass = 'devel' -- GitLab From c3b8ffb5250bcdba45838b4b54b402414f6d9697 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 11:53:26 -0400 Subject: [PATCH 1577/2133] bump to GLib 2.48.0 --- easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb index 6e89234d6b..cca1bedcdd 100644 --- a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb @@ -14,7 +14,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('GLib', '2.47.5'), + ('GLib', '2.48.0'), ] sanity_check_paths = { -- GitLab From 7e2777ca5529688af1eaf9595934fe727ca1b05d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 12:29:11 +0200 Subject: [PATCH 1578/2133] quickfixes --- .../d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 29 +++++-------------- 1 file changed, 7 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb index 3f508bfac5..a4838ae3d0 100644 --- a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -14,34 +14,19 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] -patches = ['DIAL-Makefile.in.patch'] +patches = ['DIAL-%(version)s_Makefile.in.patch'] dependencies = [ ('LASTZ', '1.02.00'), ] +binaries = [ 'assemble', 'assemble1', 'assemble_illumina', 'build_sff_index', 'convertFastqFasta', + 'cull_components', 'DIAL', 'filter', 'filter_clusters', 'fish_clusters', 'make_template', + 'masker', 'partition', 'remove_clones', 'remove_clusters', 'update', 'update_clusters', + 'update_status',] sanity_check_paths = { - 'files': ['bin/%s' % binfile for binfile in [ - 'assemble', - 'assemble1', - 'assemble_illumina', - 'build_sff_index', - 'convertFastqFasta', - 'cull_components', - 'DIAL', - 'filter', - 'filter_clusters', - 'fish_clusters', - 'make_template', - 'masker', - 'partition', - 'remove_clones', - 'remove_clusters', - 'update', - 'update_clusters', - 'update_status', -]], - 'dirs': ["bin"] + 'files': ['bin/%s' % bin for binfile in binaries], + 'dirs': ['bin'] } moduleclass = 'bio' -- GitLab From 8fc70c4034eaa8b0c805a15fa4cd50daf5fafa8e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:17:17 +0200 Subject: [PATCH 1579/2133] provided patch --- .../easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 2 +- .../easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch | 12 ++++++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb index 6f1e587143..e032219f9e 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] -patches = ['LASTZ-Makefile.patch'] +patches = ['LASTZ-1.02.00_Makefile.patch'] skipsteps=['configure'] diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch new file mode 100644 index 0000000000..e0aa55dbeb --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch @@ -0,0 +1,12 @@ +--- lastz-distrib-1.02.00/src/Makefile 2010-01-13 18:00:09.000000000 +0100 ++++ lastz-distrib-1.02.00/src/Makefile 2015-02-09 17:22:41.030256461 +0100 +@@ -28,7 +28,7 @@ + # + #--------- + +-definedForAll = -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE ++definedForAll = -Wall -Wextra -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE + + + VERSION_FLAGS= \ + -- GitLab From a2668ad34eeac9de4a4f5cb2e78272e9dd042329 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:20:41 +0200 Subject: [PATCH 1580/2133] quickfixes --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb index e032219f9e..76b32edded 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -16,12 +16,12 @@ source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] patches = ['LASTZ-1.02.00_Makefile.patch'] -skipsteps=['configure'] +skipsteps = ['configure'] installopts = 'installDir=%(installdir)s/bin' sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["lastz","lastz_D"]], + 'files': ["bin/%s" % binfile for binfile in ["lastz", "lastz_D"]], 'dirs': ["bin"] } -- GitLab From 1930b858c49360948b786786cbb6aeffc4e17d96 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:47:49 +0200 Subject: [PATCH 1581/2133] FFmpeg with foss2016a --- .../f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb new file mode 100644 index 0000000000..b93565bb4f --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.7' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.11.08'), + ('zlib', '1.2.8'), + ('x264', '20160114'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From a29a5c6c3bbe98becf368f5dff527ddf07b413e4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:51:38 +0200 Subject: [PATCH 1582/2133] FIAT with foss2016a --- .../FIAT-1.6.0-foss-2016a-Python-2.7.11.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..649eb41225 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '1.6.0' + +homepage = 'https://bitbucket.org/fenics-project/fiat' +description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order +instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating +arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +pyver = '2.7.11' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('sympy', '0.7.6.1', versionsuffix), +] + +options = {'modulename': name} + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'math' -- GitLab From 14050d83c1b95894071cb5da2fb4ea2ec1da3158 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 May 2016 14:24:43 +0200 Subject: [PATCH 1583/2133] disable necessary buildopts for binutils 2.24 w/ intel/2014b --- easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 5d4b31cd73..7598e76c07 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -13,4 +13,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# disable warning/error #175 ("subscript out of range") +buildopts = 'CFLAGS="$CFLAGS -wd175"' + moduleclass = 'tools' -- GitLab From 8292a831911188e5673f608d0de9abc0c81a4ca2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 May 2016 21:12:59 +0200 Subject: [PATCH 1584/2133] {toolchain}[dummy] intel/2016.03-GCC-5.3 --- .../h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb | 18 ++++++++++ .../i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb | 33 +++++++++++++++++ .../iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 18 ++++++++++ .../ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 33 +++++++++++++++++ .../i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb | 20 +++++++++++ ...11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb | 36 +++++++++++++++++++ ....181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 33 +++++++++++++++++ .../i/intel/intel-2016.03-GCC-5.3.eb | 26 ++++++++++++++ 8 files changed, 217 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb new file mode 100644 index 0000000000..7eaca67c16 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.03-GCC-5.3'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..d81ed4bdf9 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['d6f8529a44231e427219c8e025dec3b2'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..a1f40c75ae --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.3.210' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..703424d3e0 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..8e5a35ceef --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.03' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..82e5a9af1a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-5.3.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..cc0d58235f --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.3.0-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb new file mode 100644 index 0000000000..3de185ca63 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.03' +gcc_maj_min = '5.3' +versionsuffix = '-GCC-%s' % gcc_maj_min + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +gccver = '%s.0' % gcc_maj_min +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' -- GitLab From 892391bd9820632cb41dd723b2d9a46ae8ec6462 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 7 May 2016 23:46:07 +0100 Subject: [PATCH 1585/2133] Initial version of annovar for foss-2016a --- ...nnovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..af32067597 --- /dev/null +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'annovar' +version = '2016Feb01' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://annovar.openbioinformatics.org/en/latest/' +description = """ ANNOVAR is an efficient software tool to utilize update-to-date information + to functionally annotate genetic variants detected from diverse genomes (including human + genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# Registration required for download +# http://www.openbioinformatics.org/annovar/annovar_download_form.php +sources = ['%(name)s.latest.tar.gz'] + +dependencies = [('Perl', '5.22.1')] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'dirs': ["example", "humandb"], +} + +moduleclass = 'bio' -- GitLab From 64b203ccd0ade8375d5f1a698ec9b07adb88ae9c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 7 May 2016 23:48:44 +0100 Subject: [PATCH 1586/2133] add easyconfig annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb --- ...nnovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..af32067597 --- /dev/null +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'annovar' +version = '2016Feb01' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://annovar.openbioinformatics.org/en/latest/' +description = """ ANNOVAR is an efficient software tool to utilize update-to-date information + to functionally annotate genetic variants detected from diverse genomes (including human + genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# Registration required for download +# http://www.openbioinformatics.org/annovar/annovar_download_form.php +sources = ['%(name)s.latest.tar.gz'] + +dependencies = [('Perl', '5.22.1')] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'dirs': ["example", "humandb"], +} + +moduleclass = 'bio' -- GitLab From 09b4e9468c5dd27612574fa2da9448e66dd37a2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 May 2016 07:29:48 +0200 Subject: [PATCH 1587/2133] fix checksums for icc/ifort 2016.3 and imkl 11.3.3 --- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb index d81ed4bdf9..2192bcc506 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] -checksums = ['d6f8529a44231e427219c8e025dec3b2'] +checksums = ['b256c5573d4bba3692c9c4a6ac994d1c'] gccver = '5.3.0' binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index 703424d3e0..b354753609 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] -checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] +checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] gccver = '5.3.0' binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb index 82e5a9af1a..09806746b2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-5.3.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['536dbd82896d6facc16de8f961d17d65'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] dontcreateinstalldir = 'True' -- GitLab From e1d1dbbfa433cf1e5c52482d274fba80c8219468 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 09:22:01 +0200 Subject: [PATCH 1588/2133] {toolchain}[dummy] foss/2016.04 --- .../f/FFTW/FFTW-3.3.4-gompi-2016.04.eb | 34 +++++++++++++ easybuild/easyconfigs/f/foss/foss-2016.04.eb | 35 +++++++++++++ .../easyconfigs/g/gompi/gompi-2016.04.eb | 20 ++++++++ .../easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb | 18 +++++++ .../h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb | 23 +++++++++ .../numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb | 23 +++++++++ ...BLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 51 +++++++++++++++++++ .../OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb | 32 ++++++++++++ ...pi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb | 25 +++++++++ 9 files changed, 261 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2016.04.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2016.04.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb new file mode 100644 index 0000000000..aeee54992e --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2016.04'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.04.eb b/easybuild/easyconfigs/f/foss/foss-2016.04.eb new file mode 100644 index 0000000000..b70b879a23 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016.04.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016.04' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.3.0-2.26' + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('OpenMPI', '1.10.2', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb new file mode 100644 index 0000000000..b978fd902a --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.04' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.3.0-2.26' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC 5.3.0 and binutils 2.26 + ('OpenMPI', '1.10.2', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb new file mode 100644 index 0000000000..e65fa73eda --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2016.04'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..5a122dc923 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..d7d6d78efa --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..d8f2e33a19 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.18' + +lapackver = '3.6.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..4502f5c9f4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.11.3')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..326e2d8f43 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2016.04'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blassuff = '-LAPACK-3.6.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '5.3.0-2.26'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From d70cc438be3667d0aed78dc8ac353bbae6a3ad2d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 11:15:21 +0200 Subject: [PATCH 1589/2133] modify easyconfig Mathematica-10.4.1.eb --- .../m/Mathematica/Mathematica-10.4.1.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb new file mode 100644 index 0000000000..9d13deaf53 --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb @@ -0,0 +1,14 @@ +name = 'Mathematica' +version = '10.4.1' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%(version)s_LINUX.sh'] + +license_server = 'license.example.com' + +moduleclass = 'math' -- GitLab From 176ad0202e8ea0ec6bff115ce32aa1cbe5449d77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 12:59:05 +0200 Subject: [PATCH 1590/2133] add easyconfig FLANN-1.8.4-intel-2016a-Python-2.7.11.eb --- .../FLANN-1.8.4-intel-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..2072207364 --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.8.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cs.ubc.ca/research/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www.cs.ubc.ca/research/flann/uploads/FLANN/'] +sources = ['flann-%(version)s-src.zip'] + +builddependencies = [('CMake', '3.5.2')] +dependencies = [ + ('Python', '2.7.11'), +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/doc/flann', 'share/flann/python'], +} +sanity_check_commands = [('python', '-c "import pyflann"')] + +moduleclass = '' -- GitLab From a85f8ccc6a4f2eec679db0cbb58d270c32f0d0c0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 13:50:48 +0200 Subject: [PATCH 1591/2133] rm FIAT config --- .../FIAT-1.6.0-foss-2016a-Python-2.7.11.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index 649eb41225..0000000000 --- a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'FIAT' -version = '1.6.0' - -homepage = 'https://bitbucket.org/fenics-project/fiat' -description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order -instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating -arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] -sources = [SOURCELOWER_TAR_GZ] - -pyver = '2.7.11' -versionsuffix = '-Python-%s' % pyver - -dependencies = [ - ('Python', pyver), - ('sympy', '0.7.6.1', versionsuffix), -] - -options = {'modulename': name} - -pyshortver = '.'.join(pyver.split('.')[:2]) -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'math' -- GitLab From b34ef4de8733009684425ad8f39f0480f561a19e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:21:45 +0200 Subject: [PATCH 1592/2133] updated NASM and x264 --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb index b93565bb4f..0badebf4eb 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb @@ -12,9 +12,9 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ - ('NASM', '2.11.08'), + ('NASM', '2.12.01'), ('zlib', '1.2.8'), - ('x264', '20160114'), + ('x264', '20160430'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' -- GitLab From a88a6c7339fc37a4c19a29f58dc1ca32654d8383 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:24:38 +0200 Subject: [PATCH 1593/2133] NASM with foss 2016a --- .../n/NASM/NASM-2.12.01-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb new file mode 100644 index 0000000000..3097f4cb0e --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.01' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 0839e877fbd375b3c22f3901ed9e7870346343f4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:27:02 +0200 Subject: [PATCH 1594/2133] x264 with foss2016a --- .../x/x264/x264-20160430-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb new file mode 100644 index 0000000000..5f7b69a6bc --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160430' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 5fb8dea52cb48755a96ff45156087c5071e3fcf5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:28:15 +0200 Subject: [PATCH 1595/2133] for foss --- easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb index 5f7b69a6bc..7a55229c71 100644 --- a/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb +++ b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb @@ -7,7 +7,7 @@ homepage = 'http://www.videolan.org/developers/x264.html' description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.""" -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [ 'https://download.videolan.org/pub/videolan/x264/snapshots/', -- GitLab From 8caf1e4defeaff863d5b7205f6b1576e6837d914 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:31:35 +0200 Subject: [PATCH 1596/2133] FLASH with foss 2016a --- .../f/FLASH/FLASH-1.2.11-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb b/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb new file mode 100644 index 0000000000..5212c8b658 --- /dev/null +++ b/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'FLASH' +version = '1.2.11' + +homepage = 'https://ccb.jhu.edu/software/FLASH/' +description = """FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software + tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to + merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. + The resulting longer reads can significantly improve genome assemblies. They can also improve + transcriptome assembly when FLASH is used to merge RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://download.sourceforge.net/%(namelower)spage'] +sources = [SOURCE_TAR_GZ] + +files_to_copy = [(['flash'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/flash'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 486cc49fa3b8fda9c1a1d48d581e5decbe837fb8 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:50:56 +0200 Subject: [PATCH 1597/2133] Yasm with foss 2016a --- .../y/Yasm/Yasm-1.3.0-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb new file mode 100644 index 0000000000..fd9ab5e210 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From cc7240533ac882ca7bfc16fffa56d51c6fa4365d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 15:19:19 +0200 Subject: [PATCH 1598/2133] provided author and explaination for patch --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch index e0aa55dbeb..39bfb5c655 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch @@ -1,3 +1,6 @@ +# Remove use of -Werror because Werror is not used (discussed in http://seqanswers.com/forums/showthread.php?t=20113). +# Using -Werror gives warnings which result in a failure of the installation. +# Author: Fokke Dijkstra - Rijksuniversiteit Groningen (RUG) --- lastz-distrib-1.02.00/src/Makefile 2010-01-13 18:00:09.000000000 +0100 +++ lastz-distrib-1.02.00/src/Makefile 2015-02-09 17:22:41.030256461 +0100 @@ -28,7 +28,7 @@ -- GitLab From 2e74be2bf1817e6e33b78b68b394223cde42a32b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:07:40 +0200 Subject: [PATCH 1599/2133] add easyconfig PCL-1.7.2-intel-2016a-Python-2.7.11.eb, add easyconfig VTK-6.3.0-intel-2016a-Python-2.7.11.eb, add easyconfig Eigen-3.2.8-intel-2016a.eb --- .../e/Eigen/Eigen-3.2.8-intel-2016a.eb | 14 +++++ .../PCL-1.7.2-intel-2016a-Python-2.7.11.eb | 33 ++++++++++ .../VTK-6.3.0-intel-2016a-Python-2.7.11.eb | 60 +++++++++++++++++++ 3 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb new file mode 100644 index 0000000000..ec8373b9eb --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.8' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..6c685288a4 --- /dev/null +++ b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'PCL' +version = '1.7.2' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://pointclouds.org/' +description = """The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and + point cloud processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PointCloudLibrary/pcl/archive/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.5.2')] +dependencies = [ + ('Boost', '1.60.0', versionsuffix), + ('Eigen', '3.2.8'), + ('FLANN', '1.8.4', versionsuffix), + ('VTK', '6.3.0', versionsuffix), + ('Qhull', '2015.2'), +] + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include/pcl-%(version_major_minor)s/pcl', 'lib', 'share/pcl-%(version_major_minor)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1302e71e57 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,60 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '6.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.5.2')] + +mesaver = '11.0.8' +dependencies = [ + ('Python', '2.7.11'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', + 'mkg3states', 'ParseOGLExt']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' -- GitLab From da8956afd380f0e489f882180c6efea70d2d3955 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:23:20 +0200 Subject: [PATCH 1600/2133] drop toolchainopts from Eigen easyconfigs, since it is headers-only --- easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb | 1 - .../easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb | 1 - 22 files changed, 22 deletions(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb index a9cf345767..447fdcc2f1 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb index 57fad2e4e7..3cc61b8643 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb index 04a48d1f60..f64ca17dc1 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb index 34c32694d7..ad92c7352d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb index eda95916d0..c2159638f2 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb @@ -19,7 +19,6 @@ description = """Eigen is a C++ template library for linear algebra: toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb index ab4f378feb..0db2cb2232 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb index 92042e0a82..ad65bdfc92 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb index 5e8553cde7..8868b07c82 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb index bf81409418..0a2271f035 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb index 934d581d37..0dd48816d2 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb index 890a8a4839..9e7b9cf60d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb index 024205f8b6..7cbefdf8ab 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb index bca769f27d..81edc7d68b 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb index ab03a385a5..b3c186165b 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb index 9cca953ebc..d9a3a23dd0 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'foss', 'version': '2015a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb index d9ce74d1cf..fcb13a817f 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb index 5ec6f45b74..8648dbd440 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'dummy', 'version': ''} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb index ec09959b74..59832233f0 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb index 6d4de9bbd8..d79ef2b7af 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'dummy', 'version': ''} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb index a45d43c1fa..7d8ebf1a32 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb index 16eecd14b8..499d24c76f 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb index 5e2d4fc5a2..f02fff458c 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] -- GitLab From 01924fc6212f07e9a18cd600576f2a1672ee8442 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 16:46:57 +0200 Subject: [PATCH 1601/2133] quickfix --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb index 76b32edded..10dacf3472 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] -patches = ['LASTZ-1.02.00_Makefile.patch'] +patches = ['LASTZ-%(version)s_Makefile.patch'] skipsteps = ['configure'] -- GitLab From aacbf6070779e6cd532ce03bea9aee2da65ddc87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:47:51 +0200 Subject: [PATCH 1602/2133] modify easyconfig PCL-1.7.2-intel-2016a-Python-2.7.11.eb, modify easyconfig VTK-6.3.0-intel-2016a-Python-2.7.11.eb --- .../easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb | 2 +- .../easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb index 6c685288a4..2aa0797158 100644 --- a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ dependencies = [ ('Qhull', '2015.2'), ] -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts = '-DCMAKE_BUILD_TYPE=Release ' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb index 1302e71e57..55d38284a0 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb @@ -33,7 +33,6 @@ sources = [ builddependencies = [('CMake', '3.5.2')] -mesaver = '11.0.8' dependencies = [ ('Python', '2.7.11'), ('libGLU', '9.0.0', '-Mesa-11.2.1'), -- GitLab From b83826fbddbf3a82d2852de3a0ff3b372d7cafb2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:56:18 +0200 Subject: [PATCH 1603/2133] modify easyconfig Eigen-3.2.8-intel-2016a.eb --- easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb index ec8373b9eb..3ba31dc38d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] -- GitLab From 2cb4f18e397665dca42a2855989d8dc1c873f82d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:00:48 +0200 Subject: [PATCH 1604/2133] fix moduleclass in FLANN easyconfig --- .../f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb index 2072207364..82bf05536d 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb @@ -31,4 +31,4 @@ sanity_check_paths = { } sanity_check_commands = [('python', '-c "import pyflann"')] -moduleclass = '' +moduleclass = 'lib' -- GitLab From 85d18715306f40b7df042be06ace371577d0ddcc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:03:13 +0200 Subject: [PATCH 1605/2133] check moduleclass for all easyconfigs --- test/easyconfigs/easyconfigs.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index db5060f0b6..2d23e93e64 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -49,6 +49,7 @@ from easybuild.framework.easyconfig.easyconfig import get_easyblock_class from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, process_easyconfig from easybuild.tools import config +from easybuild.tools.config import build_option from easybuild.tools.filetools import write_file from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS @@ -263,8 +264,9 @@ def template_easyconfig_test(self, spec): fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) self.assertEqual(expected_subdir, subdir, fail_msg) - # sanity check for software name - self.assertTrue(ec['name'], name) + # sanity check for software name, moduleclass + self.assertEqual(ec['name'], name) + self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) -- GitLab From 8d70f76effbf87f18b59050f70ab2ac317a87e10 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 9 May 2016 17:05:41 +0200 Subject: [PATCH 1606/2133] Set additional environment variables needed by MDSplus --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 5 +++++ ...MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index b1dbee0965..111f00bfda 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -27,4 +27,9 @@ preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' parallel = 1 +modextravars = { + 'MDSPLUS_DIR': '%(installdir)s', + 'MDS_PATH': '%(installdir)s/tdi', +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb index a5aa488ebe..25d836f8e5 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -27,4 +27,9 @@ preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' parallel = 1 +modextravars = { + 'MDSPLUS_DIR': '%(installdir)s', + 'MDS_PATH': '%(installdir)s/tdi', +} + moduleclass = 'data' -- GitLab From e0ec35666ff58976a80b06e8f48abbdaecbee7fc Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 17:25:00 +0200 Subject: [PATCH 1607/2133] GMAP-GSNAP with foss2016a --- .../GMAP-GSNAP-2016-05-01-foss-2016a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb new file mode 100644 index 0000000000..a44b2320e8 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2016-04-04' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] + +# with these deps you can use standard compressed files +# to support files in gobby format take a look at README for extra dependencies +# http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# you can change the MAX_READLENGTH for GSNAP with something like this. +# details in the README http://research-pub.gene.com/gmap/src/README +#configopts = 'MAX_READLENGTH=250' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c0da370258d724be5c96dbdebecaf64eee8d6359 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 17:33:50 +0200 Subject: [PATCH 1608/2133] drop double line --- .../b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index 2abd2af08c..a42f248efe 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -12,7 +12,6 @@ name = 'Biopython' version = '1.65' versionsuffix = "-Python-%(pyver)s" - homepage = 'http://www.biopython.org' description = """Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to @@ -35,4 +34,4 @@ sanity_check_paths = { options = {'modulename': 'Bio'} -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From 48e0528837d5a104c655550c908631e367632b41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:51:00 +0200 Subject: [PATCH 1609/2133] add easyconfig FFmpeg-3.0.2-intel-2016a.eb --- .../f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb new file mode 100644 index 0000000000..fb0c75a29b --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.0.2' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('x264', '20160430'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From 6a9be36285ea30558bf51ebf212608de44f13806 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:51:29 +0200 Subject: [PATCH 1610/2133] add easyconfig SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb --- ...iteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000..63fe3bdb3b --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb @@ -0,0 +1,24 @@ +name = 'SuiteSparse' +version = '4.5.2' + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' + +maxparallel = 1 + +moduleclass = 'numlib' -- GitLab From 083f6097e67a16f6817ca9d6f3cbfa7438b2ccc2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 9 May 2016 18:20:47 +0100 Subject: [PATCH 1611/2133] Add checksum and enforce renaming of tarball to EasyBuild standards --- .../a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index af32067597..eacaffe6ed 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,9 @@ toolchain = {'name': 'foss', 'version': '2016a'} # Registration required for download # http://www.openbioinformatics.org/annovar/annovar_download_form.php -sources = ['%(name)s.latest.tar.gz'] +# rename after download to %(name)s-%(version)s.tar.gz +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['2b26e514c54a847bfdcf4ce57e43f95c'] dependencies = [('Perl', '5.22.1')] -- GitLab From 013bc31badbb395d57449e5284215e61f826610d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 9 May 2016 19:10:28 +0100 Subject: [PATCH 1612/2133] add easyconfig FastQC-0.11.5-Java-1.7.0_80.eb, add easyconfig FastQC-0.11.5-Java-1.8.0_74.eb --- .../f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb | 32 +++++++++++++++++++ .../f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb create mode 100644 easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb new file mode 100644 index 0000000000..f6dbacc9e2 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] + +patches = ['FastQC_shebang.patch'] + +dependencies = [('Java', '1.7.0_80')] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] + +sanity_check_paths = { + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb new file mode 100644 index 0000000000..7b8be6500d --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] + +patches = ['FastQC_shebang.patch'] + +dependencies = [('Java', '1.8.0_74')] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] + +sanity_check_paths = { + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' -- GitLab From fadd32eacf74fa74fd4e065d57704eedd9414853 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 10 May 2016 10:55:45 +0200 Subject: [PATCH 1613/2133] version update --- .../g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb index a44b2320e8..84e054bf9c 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb @@ -6,7 +6,7 @@ easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' -version = '2016-04-04' +version = '2016-05-01' homepage = 'http://research-pub.gene.com/gmap/' description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences -- GitLab From f449aad70457a4ebd314b927e634397c0f1822c4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 10 May 2016 11:08:03 +0200 Subject: [PATCH 1614/2133] added newline --- easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb index a4838ae3d0..9f8127a929 100644 --- a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -24,6 +24,7 @@ binaries = [ 'assemble', 'assemble1', 'assemble_illumina', 'build_sff_index', 'c 'cull_components', 'DIAL', 'filter', 'filter_clusters', 'fish_clusters', 'make_template', 'masker', 'partition', 'remove_clones', 'remove_clusters', 'update', 'update_clusters', 'update_status',] + sanity_check_paths = { 'files': ['bin/%s' % bin for binfile in binaries], 'dirs': ['bin'] -- GitLab From 2a0d756f82d1828bd5273bebcfa7afcd70405efa Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 May 2016 11:13:50 +0200 Subject: [PATCH 1615/2133] Add ESMF-7.0.0-foss-2016a.eb --- .../e/ESMF/ESMF-7.0.0-foss-2016a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb new file mode 100644 index 0000000000..c589117471 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb @@ -0,0 +1,29 @@ +name = 'ESMF' +version = '7.0.0' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] + +patches = ['ESMF-6.1.1_libopts.patch'] + +dependencies = [ + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.3'), + ('netCDF-C++', '4.2'), +] + +prebuildopts = 'ESMF_NETCDF_LIBS="`ncconfig --libs` `nf-config --flibs` `ncxx4-config --libs`" ' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ESMF_NETCDF_LIBS="`ncconfig --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' -- GitLab From cf69c6050935d504b0c9c4f02adc049658264197 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 May 2016 11:25:25 +0200 Subject: [PATCH 1616/2133] Add netCDF/netCDF-4.4.0-foss-2016a.eb --- .../n/netCDF/netCDF-4.4.0-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb new file mode 100644 index 0000000000..39406d6275 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.47.0'), + ('Szip', '2.1'), +] + +builddependencies = [ + ('CMake', '3.4.3'), + ('Doxygen', '1.8.11'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From 786cde88a922411b67d07e0f550506e3fee7c0de Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 May 2016 11:24:57 +0200 Subject: [PATCH 1617/2133] Add netCDF-Fortran-4.4.3-foss-2016a.eb --- .../netCDF-Fortran-4.4.3-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-foss-2016a.eb new file mode 100644 index 0000000000..98a102fb28 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-foss-2016a.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +version = '4.4.3' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' -- GitLab From c115f4819900be51344d675f979f591b6614126d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 May 2016 11:24:35 +0200 Subject: [PATCH 1618/2133] Add netCDF-C++-4.2-foss-2016a.eb --- .../n/netCDF-C++/netCDF-C++-4.2-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-foss-2016a.eb new file mode 100644 index 0000000000..5f23071cc5 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++' +version = '4.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['netcdf-cxx-%(version)s.tar.gz'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.4.0')] + +sanity_check_paths = { + 'files': ['include/ncvalues.h', 'include/netcdfcpp.h', 'include/netcdf.hh', 'lib/libnetcdf_c++.a', 'lib/libnetcdf_c++.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 40530fc95d74286b986af08eb4f7d9c7daeee848 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 10 May 2016 12:24:21 +0200 Subject: [PATCH 1619/2133] added patch --- easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch b/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch new file mode 100644 index 0000000000..d5a95a417e --- /dev/null +++ b/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch @@ -0,0 +1,11 @@ +--- DIAL/src/Makefile.in 2015-02-10 14:10:33.143293723 +0100 ++++ DIAL/src/Makefile.in 2015-02-10 14:10:39.462384572 +0100 +@@ -246,7 +246,7 @@ + @DEBUG_FALSE@@PROFILE_FALSE@@TESTING_TRUE@OPTIMIZATIONS = -ggdb + @DEBUG_FALSE@@PROFILE_TRUE@OPTIMIZATIONS = -ggdb -pg -DNDEBUG -O2 -funroll-all-loops $(ARCH) + @DEBUG_TRUE@OPTIMIZATIONS = -ggdb -DDEBUG +-AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall -Werror \ ++AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall \ + -Wunused-variable -Wunused-parameter -Wreturn-type -Wswitch \ + -Wcast-align -Winline -Wnested-externs -Wextra $(OPTIMIZATIONS) \ + -std=c99 -- GitLab From b7381a539153e3f39aa2ef23704649522cc2a2bc Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 10 May 2016 12:28:41 +0200 Subject: [PATCH 1620/2133] provided patch --- .../d/DIAL/DIAL-2011.06.06_Makefile.in.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch new file mode 100644 index 0000000000..0f365be126 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch @@ -0,0 +1,13 @@ +# Remove use of -Werror because Werror is not used (discussed in http://seqanswers.com/forums/showthread.php?t=20113). +# Using -Werror gives warnings which result in a failure of the installation. +# Author: Fokke Dijkstra - Rijksuniversiteit Groningen (RUG)--- DIAL/src/Makefile.in 2015-02-10 14:10:33.143293723 +0100 ++++ DIAL/src/Makefile.in 2015-02-10 14:10:39.462384572 +0100 +@@ -246,7 +246,7 @@ + @DEBUG_FALSE@@PROFILE_FALSE@@TESTING_TRUE@OPTIMIZATIONS = -ggdb + @DEBUG_FALSE@@PROFILE_TRUE@OPTIMIZATIONS = -ggdb -pg -DNDEBUG -O2 -funroll-all-loops $(ARCH) + @DEBUG_TRUE@OPTIMIZATIONS = -ggdb -DDEBUG +-AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall -Werror \ ++AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall \ + -Wunused-variable -Wunused-parameter -Wreturn-type -Wswitch \ + -Wcast-align -Winline -Wnested-externs -Wextra $(OPTIMIZATIONS) \ + -std=c99 -- GitLab From fa6d81bf60bb2cb4f1f582a8577b718d0e151665 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 12:53:28 +0200 Subject: [PATCH 1621/2133] Change to bundle, include CGI --- .../BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 29 ++++++++++++------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index fdb264f023..3e3a66a690 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -1,4 +1,4 @@ -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.6.924' @@ -10,21 +10,30 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] -sources = ['release-%s.tar.gz' % version.replace('.', '-')] +# this is a bundle of Perl modules packages +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") dependencies = [ ('Perl', '5.22.1'), ('DB_File', '1.835', versionsuffix), ] -#exts_list = [ -# ('CGI', '4.28', { -# 'source_tmpl': 'CGI-4.28.tar.gz', -# 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], -# }), -#] +exts_list = [ + ('CGI', '4.28', { + 'source_tmpl': 'CGI-4.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + }), + (name, version, { + 'modulename': 'Bio::Perl', + 'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'), + 'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'], + }), +] -options = {'modulename': 'Bio::Perl'} +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' +} moduleclass = 'bio' + -- GitLab From ea4d86d83894b1ec5cae01517b40c0a46df6f55d Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 12:56:36 +0200 Subject: [PATCH 1622/2133] Small change in comment --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 3e3a66a690..bd7bcac177 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -10,7 +10,7 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'foss', 'version': '2016a'} -# this is a bundle of Perl modules packages +# this is a bundle of Perl modules exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") -- GitLab From 5442266f3d9b5f6f62514c323f29b2dfd3724f96 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 13:02:34 +0200 Subject: [PATCH 1623/2133] Comment about CGI --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index bd7bcac177..796b828449 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -20,6 +20,7 @@ dependencies = [ ] exts_list = [ + # CGI has been removed from the Perl core since version 5.22. ('CGI', '4.28', { 'source_tmpl': 'CGI-4.28.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], -- GitLab From 6d2ee53436d7ffd21309097fd057bb8a99ddec77 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 13:04:17 +0200 Subject: [PATCH 1624/2133] Comment about CGI --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 796b828449..d62e2cbb88 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -20,7 +20,7 @@ dependencies = [ ] exts_list = [ - # CGI has been removed from the Perl core since version 5.22. + # CGI has been removed from the Perl core since version 5.22 ('CGI', '4.28', { 'source_tmpl': 'CGI-4.28.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], -- GitLab From 08cf383bee8935e7091cdec693c1fbba153ae5cd Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 10 May 2016 11:15:28 -0400 Subject: [PATCH 1625/2133] PGI: uncomment sanity checks; they now work with framework PR #1754 --- .../OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index be813ed50e..95cc4d76a5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -31,10 +31,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } -#sanity_check_commands = [ -# ('mpicc --version | grep pgcc', ''), -# ('mpicxx --version | grep pgc++', ''), -# ('mpifort --version | grep pgfortran', ''), -#] +sanity_check_commands = [ + ('mpicc --version | grep pgcc', ''), + ('mpicxx --version | grep pgc++', ''), + ('mpifort --version | grep pgfortran', ''), +] moduleclass = 'mpi' -- GitLab From a4703d9def18a0867167a45f1244c593099b1a79 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 10 May 2016 13:05:38 -0400 Subject: [PATCH 1626/2133] GraphicsMagick: add include/GraphicsMagick to CPATH as that is the include path. --- .../g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb | 2 ++ .../g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb | 2 ++ .../g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb index 513feabb7e..b7e2be06e2 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb @@ -14,4 +14,6 @@ source_urls = [ ] sources = [SOURCE_TAR_GZ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb index 6fa3747197..bd06dcc281 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb @@ -32,4 +32,6 @@ dependencies = [ ('zlib', '1.2.8'), ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb index ea37c3e81c..de4cfae31e 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb @@ -32,4 +32,6 @@ dependencies = [ ('zlib', '1.2.8'), ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' -- GitLab From 7184d0c0ddec1f80515700b43193c9721315b429 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Tue, 10 May 2016 15:33:50 -0400 Subject: [PATCH 1627/2133] add easyconfig CGAL 4.8 for foss 2016a and dependencies --- .../CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb | 33 ++++++++++++++++ .../e/expat/expat-2.1.1-foss-2016a.eb | 16 ++++++++ .../fontconfig-2.11.95-foss-2016a.eb | 22 +++++++++++ .../intltool-0.51.0-foss-2016a-Perl-5.22.1.eb | 25 ++++++++++++ .../libxkbcommon-0.6.1-foss-2016a.eb | 32 +++++++++++++++ .../m/MPFR/MPFR-3.1.4-foss-2016a.eb | 26 +++++++++++++ .../easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb | 39 +++++++++++++++++++ .../XKeyboardConfig-2.17-foss-2016a.eb | 36 +++++++++++++++++ .../XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb | 27 +++++++++++++ .../xcb-util-image-0.4.0-foss-2016a.eb | 23 +++++++++++ .../xcb-util-keysyms-0.4.0-foss-2016a.eb | 24 ++++++++++++ .../xcb-util-renderutil-0.3.9-foss-2016a.eb | 23 +++++++++++ .../xcb-util-wm-0.4.1-foss-2016a.eb | 23 +++++++++++ .../x/xcb-util/xcb-util-0.4.0-foss-2016a.eb | 24 ++++++++++++ 14 files changed, 373 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f4633df398 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +name = 'CGAL' +version = '4.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['e31e7039b5cdc74ac7b106db8ba644f3'] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('MPFR', '3.1.4'), + ('Qt5', '5.6.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.5.2'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000..1a58effe3d --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.1' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb new file mode 100644 index 0000000000..93a5699fb5 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.95' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.1'), + ('freetype', '2.6.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..e0b8aa4117 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.22.1' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.44', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb new file mode 100644 index 0000000000..5f450a0988 --- /dev/null +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxkbcommon' +version = '0.6.1' + +homepage = 'http://xkbcommon.org/' +description = """xkbcommon is a library to handle keyboard descriptions, + including loading them from disk, parsing them and handling their state. + It's mainly meant for client toolkits, window systems, + and other system applications.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xkbcommon.org/download/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libxcb', '1.11.1'), + ('XKeyboardConfig', '2.17'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': ['lib/libxkbcommon%s.so' % x for x in ['', '-x11']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb new file mode 100644 index 0000000000..fe347368b1 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.0')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb new file mode 100644 index 0000000000..27b1514a37 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.6.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +dependencies = [ + ('GLib', '2.48.0'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXi', '1.7.6'), + ('xcb-util', '0.4.0'), + ('xcb-util-image', '0.4.0'), + ('xcb-util-keysyms', '0.4.0'), + ('xcb-util-renderutil', '0.3.9'), + ('xcb-util-wm', '0.4.1'), + ('libxkbcommon', '0.6.1'), + ('libXrender', '0.9.9'), + ('fontconfig', '2.11.95'), + ('freetype', '2.6.3'), + ('libXfixes', '5.0.1'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('libXrandr', '1.5.0'), + ('libpng', '1.6.21'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb new file mode 100644 index 0000000000..10d7fbd3ea --- /dev/null +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'XKeyboardConfig' +version = '2.17' + +homepage = 'http://www.freedesktop.org/wiki/Software/XKeyboardConfig/' +description = """The non-arch keyboard configuration database for X Window. + The goal is to provide the consistent, well-structured, + frequently released open source of X keyboard configuration data + for X Window System implementations (free, open source and commercial). + The project is targeted to XKB-based systems.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://ftp.x.org/pub/individual/data/xkeyboard-config/'] +sources = ['xkeyboard-config-%(version)s.tar.bz2'] + +builddependencies = [ + ('libxslt', '1.1.28'), + ('gettext', '0.19.7'), + ('intltool', '0.51.0', '-Perl-5.22.1'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +# see http://www.linuxfromscratch.org/blfs/view/svn/x/xkeyboard-config.html +configopts = '--with-xkb-rules-symlink=xorg ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/X11/xkb'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..71416dbf17 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.44' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1'), + ('expat', '2.1.1') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb new file mode 100644 index 0000000000..bb023fe417 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-image' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-image package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('xcb-util', '0.4.0'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-image.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb new file mode 100644 index 0000000000..000b28f309 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-keysyms' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-keysyms package contains a library for + handling standard X key constants and conversion to/from keycodes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-keysyms.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb new file mode 100644 index 0000000000..fd3484fb38 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-renderutil' +version = '0.3.9' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-renderutil package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-render-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb new file mode 100644 index 0000000000..d412a4babf --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-wm' +version = '0.4.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-%s.so' % x for x in ['ewmh', 'icccm']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb new file mode 100644 index 0000000000..78a0c3a9b7 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util package provides additional extensions to the XCB library, + many that were previously found in Xlib, but are not part of core X protocol""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From dfabd2e04531e4f26aa54f3d487e36da8774b93c Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Tue, 10 May 2016 15:40:40 -0400 Subject: [PATCH 1628/2133] add easyconfig boost_versionsuffix --- .../Boost-1.60.0-foss-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a913c20849 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.60.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 37dfc06cc929c2bd313f65dcd50f57a08f6dedc8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 09:36:09 +0200 Subject: [PATCH 1629/2133] clean up dummy bzip2 easyconfig, define buildopts rather than defining and via os.environ --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb index 4d95eeaef2..7ae9aaf98a 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb @@ -12,8 +12,8 @@ toolchainopts = {'pic': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.bzip.org/%(version)s/'] -import os -os.environ['CC'] = 'gcc' -os.environ['CFLAGS'] = '-O3 -fPIC' +buildopts = "CC=gcc CFLAGS='-Wall -Winline -O3 -fPIC -g $(BIGFILES)'" + +with_shared_libs = False moduleclass = 'tools' -- GitLab From f6d376f8e12af48220b36c23b3542df2d1a15bd0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 09:37:39 +0200 Subject: [PATCH 1630/2133] clean up dummy bzip2 easyconfig, define buildopts rather than defining $CC and $CFLAGS via os.environ --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb index 7ae9aaf98a..460cd7abe7 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb @@ -14,6 +14,7 @@ source_urls = ['http://www.bzip.org/%(version)s/'] buildopts = "CC=gcc CFLAGS='-Wall -Winline -O3 -fPIC -g $(BIGFILES)'" +# disable building of shared libraries, doesn't work everywhere (e.g. on OS X, where 'gcc' is actually Clang...) with_shared_libs = False moduleclass = 'tools' -- GitLab From cd98ac1f5b3372ad1346ce99048059b4ed435a40 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 11 May 2016 12:34:44 +0200 Subject: [PATCH 1631/2133] Include patch that fixes bug in build-score/configure, which breaks builds involving multiple toolchains (e.g., compiling Score-P for Intel against Cube built with GGGcore) --- .../s/Score-P/Score-P-2.0.1-foss-2016a.eb | 7 +++ .../Score-P-2.0.1_fix_score_configure.patch | 52 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index 66303634bd..feeade9e0a 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -24,8 +24,15 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = ['scorep-%(version)s.tar.gz'] source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] +# Backported fix to prevent build-score/configure from picking up CFLAGS etc.; +# included in Score-P 2.0.2 and above +patches = [ + 'Score-P-2.0.1_fix_score_configure.patch', +] + checksums = [ '031a82fa26e2c9412e55d964f92fc9e9', # scorep-2.0.1.tar.gz + 'e5bfc115b9013b87a294a3bd84db02ed', # Score-P-2.0.1_fix_score_configure.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch new file mode 100644 index 0000000000..c387be0132 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch @@ -0,0 +1,52 @@ +--- build-score/configure.orig 2016-05-11 09:21:03.716441529 +0200 ++++ build-score/configure 2016-05-11 09:38:14.651525955 +0200 +@@ -735,6 +735,7 @@ afs_srcdir + AFS_PACKAGE_TO_TOP + AFS_PACKAGE_NAME + AFS_PACKAGE_name ++CXXFLAGS_FOR_BUILD_SCORE + target_alias + host_alias + build_alias +@@ -790,6 +791,7 @@ enable_libtool_lock + ac_precious_vars='build_alias + host_alias + target_alias ++CXXFLAGS_FOR_BUILD_SCORE + CC + CFLAGS + LDFLAGS +@@ -1444,6 +1446,8 @@ Optional Packages: + compiler's sysroot if not specified). + + Some influential environment variables: ++ CXXFLAGS_FOR_BUILD_SCORE ++ C++ compiler flags for building scorep-score + CC C compiler command + CFLAGS C compiler flags + LDFLAGS linker flags, e.g. -L if you have libraries in a +@@ -2363,6 +2367,24 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu + + + ++# Compilers etc. are set according to Cube installation (see below), ++# so ignore environment variables set in the environment. ++{ CC=; unset CC;} ++{ CFLAGS=; unset CFLAGS;} ++{ LDFLAGS=; unset LDFLAGS;} ++{ LIBS=; unset LIBS;} ++{ CPPFLAGS=; unset CPPFLAGS;} ++{ LT_SYS_LIBRARY_PATH=; unset LT_SYS_LIBRARY_PATH;} ++{ CPP=; unset CPP;} ++{ CXX=; unset CXX;} ++{ CXXFLAGS=; unset CXXFLAGS;} ++{ CXXCPP=; unset CXXCPP;} ++ ++ ++if test "x${ac_cv_env_CXXFLAGS_FOR_BUILD_SCORE_set}" = xset; then : ++ CXXFLAGS="${ac_cv_env_CXXFLAGS_FOR_BUILD_SCORE_value}" ++fi ++ + + + -- GitLab From a7042f4afe607a698be30c08bcd74918118486df Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 11 May 2016 12:48:07 +0200 Subject: [PATCH 1632/2133] Bump PDT to 3.22 --- .../p/PDT/{PDT-3.21-foss-2016a.eb => PDT-3.22-foss-2016a.eb} | 4 ++-- easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/PDT/{PDT-3.21-foss-2016a.eb => PDT-3.22-foss-2016a.eb} (92%) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.22-foss-2016a.eb similarity index 92% rename from easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb rename to easybuild/easyconfigs/p/PDT/PDT-3.22-foss-2016a.eb index a48bf0f63e..c1c3137a73 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.22-foss-2016a.eb @@ -11,7 +11,7 @@ ## name = 'PDT' -version = '3.21' +version = '3.22' homepage = 'http://www.cs.uoregon.edu/research/pdt/' description = """Program Database Toolkit (PDT) is a framework for analyzing source @@ -26,7 +26,7 @@ sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] checksums = [ - '3092ca0d8833b69992c17e63ae66c263', # pdtoolkit-3.21.tar.gz + '982d667617802962a1f7fe6c4c31184f', # pdtoolkit-3.22.tar.gz ] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index feeade9e0a..c013f5f3e6 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -43,7 +43,7 @@ dependencies = [ ('OPARI2', '2.0'), ('OTF2', '2.0'), ('PAPI', '5.4.3'), - ('PDT', '3.21'), + ('PDT', '3.22'), ] configopts = '--enable-shared' -- GitLab From 6569ffa0d96ffcf7dfe5545df6567d0eb19d2b51 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 May 2016 14:00:02 +0200 Subject: [PATCH 1633/2133] {bio}[foss-2016a] Kraken 0.10.5-beta (REVIEW) --- .../Jellyfish/Jellyfish-1.1.11-foss-2016a.eb | 25 +++++++++++ ...aken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 43 +++++++++++++++++++ .../Kraken/Kraken_0.10.5-beta_makefile.patch | 12 ++++++ 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb new file mode 100644 index 0000000000..8e2a518511 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '1.1.11' + +homepage = 'http://www.cbcb.umd.edu/software/jellyfish/' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cbcb.umd.edu/software/jellyfish/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..ad490e94ef --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PackedBinary' + +name = 'Kraken' +version = '0.10.5-beta' +versionsuffix='-Perl-%(perlver)s' + +homepage = 'http://ccb.jhu.edu/software/kraken/' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +#Part is compiled with CXX, the rest is in Perl +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://ccb.jhu.edu/software/kraken/dl/'] +sources = [SOURCELOWER_TGZ] + +patches = ['Kraken_%(version)s_makefile.patch'] + +dependencies = [ + ('Perl', '5.22.1'), + ('Jellyfish', '1.1.11'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken.sh %(installdir)s' + +sanity_check_paths = { + 'files': ['add_to_library.sh', 'build_kraken_db.sh', 'check_for_jellyfish.sh', 'classify', 'clean_db.sh', + 'cp_into_tempfile.pl', 'db_shrink', 'db_sort', 'download_genomic_library.sh', + 'download_taxonomy.sh', 'kraken', 'kraken-build', 'kraken-filter', 'krakenlib.pm', + 'kraken-mpa-report', 'kraken-report', 'kraken-translate', 'make_seqid_to_taxid_map', + 'read_merger.pl', 'report_gi_numbers.pl', 'set_lcas', 'shrink_db.sh', + 'standard_installation.sh', 'upgrade_db.sh', 'verify_gi_numbers.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch b/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch new file mode 100644 index 0000000000..4a0bc26aa6 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch @@ -0,0 +1,12 @@ +#Pick CXX and CXXFLAGS from EasyBuild via pre-defined variables +#May 11th 2016 by B. Hajgato (Free Uninrrsity Brussels, VUB) +--- kraken-0.10.5-beta/src/Makefile.orig 2015-02-18 12:38:00.000000000 +0100 ++++ kraken-0.10.5-beta/src/Makefile 2016-05-11 13:33:39.370016057 +0200 +@@ -1,5 +1,5 @@ +-CXX = g++ +-CXXFLAGS = -Wall -fopenmp -O3 ++CXX ?= g++ ++CXXFLAGS ?= -Wall -fopenmp -O3 + PROGS = db_sort set_lcas classify make_seqid_to_taxid_map db_shrink + + .PHONY: all install clean -- GitLab From e6a548baeec911151b309f32cc10404060136fb6 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 11 May 2016 15:04:52 +0200 Subject: [PATCH 1634/2133] Add OpenSSL-1.0.2g-GCCcore-4.9.3.eb to work with minimal toolchains --- .../o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..29256de39d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.2g' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From ee694e1b8f698196b590aaee777130a1feb3de1f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 11 May 2016 16:09:49 +0200 Subject: [PATCH 1635/2133] Add tmux-2.2-GCCcore-4.9.3.eb --- .../t/tmux/tmux-2.2-GCCcore-4.9.3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..a8b6500ba3 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '2.2' + +homepage = 'http://tmux.sourceforge.net/' +description = """tmux is a terminal multiplexer. It lets you switch easily +between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + +dependencies = [ + ('ncurses', '6.0'), + ('libevent', '2.0.22'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 8a22b902332cf5110c9055b9df18c2d720522d93 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 11 May 2016 16:10:06 +0200 Subject: [PATCH 1636/2133] Add libevent-2.0.22-GCCcore-4.9.3.eb --- .../libevent/libevent-2.0.22-GCCcore-4.9.3.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..2de9d3663c --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.0.22' + +homepage = 'http://libevent.org/' +description = """The libevent API provides a mechanism to execute a callback function when a specific + event occurs on a file descriptor or after a timeout has been reached. + Furthermore, libevent also support callbacks due to signals or regular timeouts.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = [ + 'https://github.com/downloads/%(name)s/%(name)s/', + 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', +] +sources = ['%(name)s-%(version)s-stable.tar.gz'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + +moduleclass = 'lib' -- GitLab From f280305bef61512ee04bf405afee98cb1d9e2802 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 May 2016 16:20:40 +0200 Subject: [PATCH 1637/2133] add wget dependency to Kraken --- .../g/gnutls/gnutls-3.4.11-foss-2016a.eb | 40 +++++++++++++++++++ .../g/guile/guile-1.8.8-foss-2016a.eb | 32 +++++++++++++++ ...aken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 1 + .../l/libidn/libidn-1.32-foss-2016a.eb | 19 +++++++++ .../l/libtasn1/libtasn1-4.7-foss-2016a.eb | 22 ++++++++++ .../libunistring-0.9.3-foss-2016a.eb | 24 +++++++++++ .../n/nettle/nettle-3.1.1-foss-2016a.eb | 28 +++++++++++++ .../p/p11-kit/p11-kit-0.23.2-foss-2016a.eb | 29 ++++++++++++++ .../w/wget/wget-1.17.1-foss-2016a.eb | 35 ++++++++++++++++ 9 files changed, 230 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb new file mode 100644 index 0000000000..fbf5215dd8 --- /dev/null +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'gnutls' +version = '3.4.11' + +homepage = 'http://www.gnutls.org/' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCE_TAR_XZ] + +guilever = '1.8.8' +guileshortver = '.'.join(guilever.split('.')[:2]) +dependencies = [ + ('GMP', '6.1.0'), + ('nettle', '3.1.1'), + ('guile', guilever), + ('libtasn1', '4.7'), + ('libidn', '1.32'), + ('p11-kit', '0.23.2'), +] + +configopts = "--with-guile-site-dir=$EBROOTGUILE --enable-openssl-compatibility " + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['certtool', 'crywrap', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]] + + ['lib/guile/%s/guile-gnutls-v-2.so' % guileshortver], + 'dirs': ['include/gnutls'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb new file mode 100644 index 0000000000..132fe56abf --- /dev/null +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.0'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.29'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb index ad490e94ef..4bb09cbfe2 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -25,6 +25,7 @@ patches = ['Kraken_%(version)s_makefile.patch'] dependencies = [ ('Perl', '5.22.1'), ('Jellyfish', '1.1.11'), + ('wget', '1.17.1'), ] install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb new file mode 100644 index 0000000000..be095e8cc2 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.32' + +homepage = 'http://www.gnu.org/software/libidn' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb new file mode 100644 index 0000000000..0a37b2e392 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.7' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. + It was written by Fabio Fiorina, and has been shipped as part of GnuTLS + for some time but is now a proper GNU package.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb new file mode 100644 index 0000000000..052063704a --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb new file mode 100644 index 0000000000..fc3be53324 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.1.1' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb new file mode 100644 index 0000000000..75ecf0ad6a --- /dev/null +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'p11-kit' +version = '0.23.2' + +homepage = 'http://p11-glue.freedesktop.org/p11-kit.html' +description = """Provides a way to load and enumerate PKCS#11 modules. + Provides a standard configuration setup for installing + PKCS#11 modules in such a way that they're discoverable. + Also solves problems with coordinating the use of PKCS#11 + by different components or libraries living in the same process.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://p11-glue.freedesktop.org/releases/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libtasn1', '4.7'), + ('libffi', '3.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/p11-kit', 'bin/trust'] + + ['lib/libp11-kit.%s' % SHLIB_EXT], + 'dirs': ['include/p11-kit-1/p11-kit'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb new file mode 100644 index 0000000000..855ecb2068 --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.17.1' + +homepage = 'https://www.gnu.org/software/wget/' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('gnutls', '3.4.11'), + ('PCRE', '8.38'), + ('libidn', '1.32'), + ('zlib', '1.2.8'), + #('OpenSSL', '1.0.1s'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +#Optionally, you can use OpenSSL insted of gnutls +#configopts = '--with-ssl=openssl ' +# +#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/wget'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 7a5bbbf4be73ddcce4a1e18aa9dd2363fb5ce7f7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 May 2016 16:32:43 +0200 Subject: [PATCH 1638/2133] use os dep gnutls --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 855ecb2068..6ca8a613aa 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -14,7 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] dependencies = [ - ('gnutls', '3.4.11'), + #('gnutls', '3.4.11'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date gnutls for security reasons ('PCRE', '8.38'), ('libidn', '1.32'), ('zlib', '1.2.8'), @@ -26,6 +27,7 @@ dependencies = [ #configopts = '--with-ssl=openssl ' # #osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('gnutls')] sanity_check_paths = { 'files': ['bin/wget'], -- GitLab From 38cacab3b3d32d4b13267a167a6681e01a122d8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 16:53:18 +0200 Subject: [PATCH 1639/2133] add easyconfig Wannier90-2.0.1-intel-2016a.eb --- .../Wannier90/Wannier90-2.0.1-intel-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb new file mode 100644 index 0000000000..5f4964f921 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '2.0.1' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] + +patches = ['Wannier90_2x_ignore_makesys.patch'] + +prebuildopts = 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' + +# build program and library +buildopts = "all" + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' -- GitLab From 47ee49d3fe6431cb7a0f1b20a8778569f9c5db65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 16:53:43 +0200 Subject: [PATCH 1640/2133] add easyconfig FLEUR-0.26e-intel-2016a.eb --- .../f/FLEUR/FLEUR-0.26e-intel-2016a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb new file mode 100644 index 0000000000..39ac2cdb63 --- /dev/null +++ b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'FLEUR' +version = '0.26e' + +homepage = 'http://www.flapw.de/' +description = """FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, + based on density-functional theory.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +# dowload requires registration, see http://www.flapw.de/pm/index.php?n=FLEUR.Downloads +sources = ['v%s.tgz' % version.split('.')[1]] + +builddependencies = [('imake', '1.0.7')] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), + ('HDF5', '1.8.16'), +# ('Wannier90', '2.0.1'), # only needed if '#define wann' is added to Imakefile +] + +# define hardware platform to be 'parallel intel compiler, 64 bit, use scalapack') +prebuildopts = "sed -i 's/^#define jureca/#define linux_evp_64/g' Imakefile && " +# don't specialize for systems with structural symmetry +prebuildopts += "sed -i 's/^#define inversion//g' Imakefile && " +# no need to jump through hoops to make compilation work with older Fortran compilers +prebuildopts += "sed -i 's/^#define f_90//g' Imakefile && " + +prebuildopts += "imake && " +buildopts = 'FC="$FC" FFLAGS="$FFLAGS -r8 -assume byterecl" HDFROOT=$EBROOTHDF5 fleur.x inpgen.x' + +# parallel build tends to fail +parallel = 1 + +files_to_copy = [(['fleur.x', 'inpgen.x'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fleur.x', 'bin/inpgen.x'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From d4b275db57e76944ce1f2ffd4e54e9610ef7f221 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 11 May 2016 12:19:16 -0400 Subject: [PATCH 1641/2133] improve Yade easyconfig --- .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 45 ++++++------------- 1 file changed, 13 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 5e5fa25372..6f3e1611f8 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -18,53 +18,34 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Loki', '0.1.7'), ('Boost', '1.60.0', versionsuffix), - ('GL2PS', '1.3.9'), - ('Python', '2.7.11'), + ('GL2PS', '1.3.9', '-Mesa-11.2.1'), + ('Python', '2.7.11'), ('IPython', '3.2.3', versionsuffix), ('PyGTS', '0.3.1', versionsuffix), ('Eigen', '3.2.7'), ('minieigen', '0.5.3', versionsuffix), - ('Qt', '4.8.7'), + ('Qt', '4.8.7', '-GLib-2.48.0'), ('GTS', '0.7.6'), - ('libQGLViewer', '2.6.3'), - ('GDB', '7.10.1', versionsuffix), - ('zlib', '1.2.8'), - # optional -# ('CGAL', '4.7'), + ('libQGLViewer', '2.6.3', '-Mesa-11.2.1'), + ('zlib', '1.2.8'), + ('CGAL', '4.8', versionsuffix), ] -builddependencies = [('CMake', '3.4.3')] +builddependencies = [('CMake', '3.5.2')] separate_build_dir = True configopts = '-DENABLE_GUI=OFF ' configopts += '-DENABLE_VTK=OFF ' -configopts += '-DENABLE_CGAL=OFF' configopts += '-DENABLE_LINSOLV=OFF ' configopts += '-DENABLE_PFVFLOW=OFF ' -configopts += '-DQGLVIEWER_INCLUDE_DIR=$EBROOTLIBQGLVIEWER/include ' +configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include ' +configopts += '-DGMP_LIBRARIES=$EBROOTGMP/lib ' +configopts += '-DGMPXX_LIBRARIES=$EBROOTGMP/lib ' -# In case you want disable some Yade features -# configopts = '-OPTION_1 = OFF -OPTION_2 = OFF ...' - -# options available, -# ENABLE_GUI: enable GUI option (ON by default) -# ENABLE_CGAL: enable CGAL option (ON by default) -# ENABLE_VTK: enable VTK-export option (ON by default) -# ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default) -# ENABLE_GTS: enable GTS-option (ON by default) -# ENABLE_GL2PS: enable GL2PS-option (ON by default) -# ENABLE_LINSOLV: enable LINSOLV-option (ON by default) -# ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default) -# ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default) -# ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default) -# ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013] for details (OFF by default) -# ENABLE_MASK_ARBITRARY: enable MASK_ARBITRARY option (OFF by default) -# ENABLE_PROFILING: enable profiling, e.g., shows some more metrics, which can define bottlenecks of the code (OFF by default) -# runtimePREFIX: used for packaging, when install directory is not the same as runtime directory (/usr/local by default) -# CHUNKSIZE: specifiy the chunk size if you want several sources to be compiled at once. Increases compilation speed but RAM-consumption during compilation as well (1 by default) -# VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) -# USE_QT5: use QT5 for GUI, experimental (OFF by default) +#to disable CGAL uncomment the following line: +#configopts += '-DENABLE_CGAL=OFF ' sanity_check_paths = { 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], -- GitLab From b34283cba9fb1d3ccea409d2e7fc8a885fe13d30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 20:30:33 +0200 Subject: [PATCH 1642/2133] fix remark, enable r8 toolchain option, add imake easyconfig to resolve dep --- .../f/FLEUR/FLEUR-0.26e-intel-2016a.eb | 4 ++-- .../i/imake/imake-1.0.7-intel-2016a.eb | 21 +++++++++++++++++++ 2 files changed, 23 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb index 39ac2cdb63..d7d711211d 100644 --- a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb @@ -8,7 +8,7 @@ description = """FLEUR is a feature-full, freely available FLAPW (full potential based on density-functional theory.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'r8': True} # dowload requires registration, see http://www.flapw.de/pm/index.php?n=FLEUR.Downloads sources = ['v%s.tgz' % version.split('.')[1]] @@ -30,7 +30,7 @@ prebuildopts += "sed -i 's/^#define inversion//g' Imakefile && " prebuildopts += "sed -i 's/^#define f_90//g' Imakefile && " prebuildopts += "imake && " -buildopts = 'FC="$FC" FFLAGS="$FFLAGS -r8 -assume byterecl" HDFROOT=$EBROOTHDF5 fleur.x inpgen.x' +buildopts = 'FC="$FC" FFLAGS="$FFLAGS" HDFROOT=$EBROOTHDF5 fleur.x inpgen.x' # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb new file mode 100644 index 0000000000..dd473f56b9 --- /dev/null +++ b/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'imake' +version = '1.0.7' + +homepage = 'http://www.x.org/' +description = """imake is a Makefile-generator that is intended to make it easier to develop software + portably for multiple systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['ftp://artfiles.org/x.org/pub/individual/util/'] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['ccmakedep', 'cleanlinks', 'imake', 'makeg', 'mergelib', + 'mkdirhier', 'mkhtmlindex', 'revpath', 'xmkmf']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 0129924d39247c5ade82b7d9a4a32b9f41557ec8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 21:59:27 +0200 Subject: [PATCH 1643/2133] {toolchain}[pompi/2016.04] HPL 2.1 --- .../h/HPL/HPL-2.1-pomkl-2016.04.eb | 23 +++++++++++ .../hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb | 22 ++++++++++ .../i/imkl/imkl-11.3.3.210-pompi-2016.04.eb | 36 +++++++++++++++++ .../n/numactl/numactl-2.0.11-GCCcore-5.3.0.eb | 25 ++++++++++++ .../OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb | 40 +++++++++++++++++++ .../p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb | 25 ++++++++++++ .../easyconfigs/p/pomkl/pomkl-2016.04.eb | 20 ++++++++++ .../easyconfigs/p/pompi/pompi-2016.04.eb | 19 +++++++++ 8 files changed, 210 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb create mode 100644 easybuild/easyconfigs/p/pompi/pompi-2016.04.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb new file mode 100644 index 0000000000..7d18ed0de8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb @@ -0,0 +1,23 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'pomkl', 'version': '2016.04'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +# needs to include -ldl or else we get +# .../libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' +import os +os.environ['LIBS'] = '-ldl' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..1b876ae44f --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +# numactl is a direct dependency of PGI +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb new file mode 100644 index 0000000000..ab281bf6b1 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'pompi', 'version': '2016.04'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..a7cf283740 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +builddependencies = [('binutils', '2.26')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..017a48c7e4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify + +dependencies = [('hwloc', '1.11.3')] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +sanity_check_commands = [ + ('mpicc --version | grep pgcc', ''), + ('mpicxx --version | grep pgc++', ''), + ('mpifort --version | grep pgfortran', ''), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..09bd42b128 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '16.4' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['3804dc13b8cf3d50aa16fb56e2682dd7'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb b/easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb new file mode 100644 index 0000000000..1c27eb7962 --- /dev/null +++ b/easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'pomkl' +version = '2016.04' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.4' +gccsuff = '-GCC-5.3.0-2.26' + +dependencies = [ + ('PGI', compver, gccsuff), + ('OpenMPI', '1.10.2', '', ('PGI', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('pompi', '%s' % (version))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/p/pompi/pompi-2016.04.eb b/easybuild/easyconfigs/p/pompi/pompi-2016.04.eb new file mode 100644 index 0000000000..b7e500bb5f --- /dev/null +++ b/easybuild/easyconfigs/p/pompi/pompi-2016.04.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'pompi' +version = '2016.04' +pgisuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.4' + +dependencies = [ + ('PGI', compver, pgisuffix), + ('OpenMPI', '1.10.2', '', ('PGI', '%s%s' % (compver, pgisuffix))), +] + +moduleclass = 'toolchain' -- GitLab From 8bad3a4379147aea0fe99cdf2b994dc67c053ce2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 22:01:45 +0200 Subject: [PATCH 1644/2133] drop duplicate empty line --- .../o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 1 - .../o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index 95cc4d76a5..3dfb0c023b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb index 017a48c7e4..274fb15e1f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support -- GitLab From 99a8ea6b43e676485d7a62cdc44c389bfd1d78ff Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 11 May 2016 17:07:44 -0400 Subject: [PATCH 1645/2133] compiler finds eigen include-path automatic, no needs patch --- ...inieigen-0.5.3-foss-2016a-Python-2.7.11.eb | 5 +--- .../m/minieigen/minieigen-0.5.3_Eigen.patch | 24 ------------------- 2 files changed, 1 insertion(+), 28 deletions(-) delete mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb index bcc3a6db18..6bb8c242f7 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'minieigen' version = '0.5.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://launchpad.net/minieigen/' description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" @@ -11,10 +12,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] -patches = ['minieigen-0.5.3_Eigen.patch'] - -versionsuffix = '-Python-%(pyver)s' - dependencies = [ ('Boost', '1.60.0', versionsuffix), ('Eigen', '3.2.7'), diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch deleted file mode 100644 index 95775909f2..0000000000 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -ru minieigen-0.5.3.orig/setup.py minieigen-0.5.3/setup.py ---- minieigen-0.5.3.orig/setup.py 2015-09-18 12:15:40.000000000 -0400 -+++ minieigen-0.5.3/setup.py 2016-04-28 14:12:46.507198765 -0400 -@@ -1,6 +1,6 @@ - # encoding: utf-8 - from distutils.core import setup,Extension --import sys, glob -+import os, sys, glob - - # vectorization is currently broken and experimental ONLY - vectorize=False -@@ -19,10 +19,11 @@ - # * https://bugs.launchpad.net/panda3d/+bug/919237 - define_macros+=[('EIGEN_DONT_VECTORIZE',None)] - else: -+ eigen_prefix = os.environ.get('EBROOTEIGEN', 'EBROOTEIGEN_NOT_DEFINED') - py3k=(sys.version_info[0]==3) - libraries=['boost_python-py3%d'%sys.version_info[1] if py3k else 'boost_python'] - library_dirs=[] -- include_dirs=['/usr/include/eigen3','/usr/local/include/eigen3','minieigen'] -+ include_dirs=['%s/include/eigen3' % eigen_prefix, 'minieigen'] - - setup(name='minieigen', - version='0.5.3', -- GitLab From 9fdbee0e78675e3587889e8fd9f5a1ea20fdf256 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 11 May 2016 17:10:39 -0400 Subject: [PATCH 1646/2133] improve Yade and Loki easyconfig --- .../l/Loki/Loki-0.1.7-foss-2016a.eb | 7 ++++--- .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 20 +++++++------------ 2 files changed, 11 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb index 990683c5b7..07ee053893 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb @@ -4,17 +4,18 @@ name = 'Loki' version = '0.1.7' homepage = 'http://loki-lib.sourceforge.net/' -description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms. """ +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and + idioms. """ toolchain = {'name': 'foss', 'version': '2016a'} -installopts = "prefix=%(installdir)s" - source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] sources = [SOURCELOWER_TAR_GZ] skipsteps = ['configure'] +installopts = "prefix=%(installdir)s" + sanity_check_paths={ 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], 'dirs': ['include/loki'], diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 6f3e1611f8..6ca7251d44 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -15,10 +15,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] sources = [SOURCELOWER_TAR_GZ] +mesaver = '11.2.1' dependencies = [ ('Loki', '0.1.7'), ('Boost', '1.60.0', versionsuffix), - ('GL2PS', '1.3.9', '-Mesa-11.2.1'), + ('GL2PS', '1.3.9', '-Mesa-%s' % mesaver), ('Python', '2.7.11'), ('IPython', '3.2.3', versionsuffix), ('PyGTS', '0.3.1', versionsuffix), @@ -26,7 +27,7 @@ dependencies = [ ('minieigen', '0.5.3', versionsuffix), ('Qt', '4.8.7', '-GLib-2.48.0'), ('GTS', '0.7.6'), - ('libQGLViewer', '2.6.3', '-Mesa-11.2.1'), + ('libQGLViewer', '2.6.3', '-Mesa-%s' % mesaver), ('zlib', '1.2.8'), ('CGAL', '4.8', versionsuffix), ] @@ -35,20 +36,13 @@ builddependencies = [('CMake', '3.5.2')] separate_build_dir = True -configopts = '-DENABLE_GUI=OFF ' -configopts += '-DENABLE_VTK=OFF ' -configopts += '-DENABLE_LINSOLV=OFF ' -configopts += '-DENABLE_PFVFLOW=OFF ' +configopts = '-DENABLE_GUI=OFF -DENABLE_VTK=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' -configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include ' -configopts += '-DGMP_LIBRARIES=$EBROOTGMP/lib ' -configopts += '-DGMPXX_LIBRARIES=$EBROOTGMP/lib ' - -#to disable CGAL uncomment the following line: -#configopts += '-DENABLE_CGAL=OFF ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' sanity_check_paths = { - 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', + 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], 'dirs': ['lib/x86_64-linux-gnu/yade-%(version)s/py/yade'], } -- GitLab From ffd9ea76ab826db4b79c77d1901733df17239d59 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 May 2016 07:38:23 +0200 Subject: [PATCH 1647/2133] Use OpenSSL --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 6ca8a613aa..969681ed3b 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -23,11 +23,11 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -#Optionally, you can use OpenSSL insted of gnutls -#configopts = '--with-ssl=openssl ' -# -#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -osdependencies = [('gnutls')] +configopts = '--with-ssl=openssl ' + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +#Optionally, you can use gnutls (default) instead of OpenSSL +#osdependencies = [('gnutls-devel', 'gnutls-dev), 'libgnutls-devel')] sanity_check_paths = { 'files': ['bin/wget'], -- GitLab From f4491d2ac003c2e3b16e422b837043762403c720 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 May 2016 09:29:40 +0200 Subject: [PATCH 1648/2133] Type corrected in the comment --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 969681ed3b..462167df50 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -26,8 +26,8 @@ dependencies = [ configopts = '--with-ssl=openssl ' osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -#Optionally, you can use gnutls (default) instead of OpenSSL -#osdependencies = [('gnutls-devel', 'gnutls-dev), 'libgnutls-devel')] +#Optionally, you can use gnutls (default) instead of OpenSSL +#osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] sanity_check_paths = { 'files': ['bin/wget'], -- GitLab From b4850c38476a83f68723becde0c0d16646849551 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 May 2016 09:32:05 +0200 Subject: [PATCH 1649/2133] extra comment --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 462167df50..bbebd9aa83 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -26,7 +26,8 @@ dependencies = [ configopts = '--with-ssl=openssl ' osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -#Optionally, you can use gnutls (default) instead of OpenSSL +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. #osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] sanity_check_paths = { -- GitLab From a8c17069e073d203c1187cef09c1495efe2c33d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 10:19:12 +0200 Subject: [PATCH 1650/2133] remove hack in HPL pomkl easyconfig for linking with -ldl --- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb index 73bc06cddb..9552b4d653 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb @@ -15,9 +15,4 @@ source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] # fix Make dependencies, so parallel build also works patches = ['HPL_parallel-make.patch'] -# needs to include -ldl or else we get -# .../libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' -import os -os.environ['LIBS'] = '-ldl' - moduleclass = 'tools' -- GitLab From 3fbfc03ba64a14c5c803d6761009142a490e5015 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 10:57:41 +0200 Subject: [PATCH 1651/2133] {chem}[intel/2016a] NBO 1.1 --- .../easyconfigs/n/NBO/NBO-1.1_MKL95.patch | 505 ++++++++++++++++++ easybuild/easyconfigs/n/NBO/NBO.eb | 27 + 2 files changed, 532 insertions(+) create mode 100644 easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch create mode 100644 easybuild/easyconfigs/n/NBO/NBO.eb diff --git a/easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch b/easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch new file mode 100644 index 0000000000..1bde9b006b --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch @@ -0,0 +1,505 @@ +fix using BLAS95/LAPACK95 interface for recent Intel MKL versions +author: Kenneth Hoste (HPC-UGent) +diff -ru periodic_nbo.orig/matutil.f90 periodic_nbo/matutil.f90 +--- periodic_nbo.orig/matutil.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/matutil.f90 2016-05-12 10:17:54.673546000 +0200 +@@ -93,7 +93,7 @@ + END FUNCTION matdet + + FUNCTION matsqrt_real(dmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matsqrt_real, vecs +@@ -115,14 +115,14 @@ + FORALL (i=1:n1) matsqrt_real(i,i) = SQRT(abs(vals(i))) + !matsqrt_real = MATMUL(vecs, MATMUL(matsqrt_real, TRANSPOSE(vecs))) + +- CALL DGEMM_MKL95(vecs,matsqrt_real,dummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,vecs,matsqrt_real,'N','T',1.d0,0.d0) ++ CALL DGEMM(vecs,matsqrt_real,dummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(dummy,vecs,matsqrt_real,'N','T',1.d0,0.d0) + + + END FUNCTION matsqrt_real + + FUNCTION matsqrt_complex(cmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + COMPLEX*16 , DIMENSION(SIZE(cmat,1),SIZE(cmat,2)) :: matsqrt_complex, vecs +@@ -140,13 +140,13 @@ + FORALL (i=1:n1) matsqrt_complex(i,i) = SQRT(abs(vals(i))) + !matsqrt_complex = MATMUL(vecs, MATMUL(matsqrt_complex, TRANSPOSE(CONJG(vecs)))) + +- CALL ZGEMM_MKL95(vecs,matsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(dummy,vecs,matsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(vecs,matsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(dummy,vecs,matsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + + END FUNCTION matsqrt_complex + + FUNCTION matinvsqrt_real(dmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matinvsqrt_real, vecs +@@ -164,13 +164,13 @@ + FORALL (i=1:n1) matinvsqrt_real(i,i) = 1.d0/SQRT(abs(vals(i))) + !matinvsqrt_real = MATMUL(vecs, MATMUL(matinvsqrt_real, TRANSPOSE(vecs))) + +- CALL DGEMM_MKL95(vecs,matinvsqrt_real,dummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,vecs,matinvsqrt_real,'N','T',1.d0,0.d0) ++ CALL DGEMM(vecs,matinvsqrt_real,dummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(dummy,vecs,matinvsqrt_real,'N','T',1.d0,0.d0) + + END FUNCTION matinvsqrt_real + + FUNCTION matinvsqrt_complex(cmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + COMPLEX*16 , DIMENSION(SIZE(cmat,1),SIZE(cmat,2)) :: matinvsqrt_complex, vecs +@@ -199,13 +199,13 @@ + + !matinvsqrt_complex = MATMUL(vecs, MATMUL(matinvsqrt_complex, TRANSPOSE(CONJG(vecs)))) + +- CALL ZGEMM_MKL95(vecs,matinvsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(dummy,vecs,matinvsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(vecs,matinvsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(dummy,vecs,matinvsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + + END FUNCTION matinvsqrt_complex + + FUNCTION matexp(dmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matexp, vecs +@@ -222,8 +222,8 @@ + matexp = 0.d0 + FORALL (i=1:n1) matexp(i,i) = EXP(vals(i)) + !matexp = MATMUL(vecs, MATMUL(matexp, TRANSPOSE(vecs))) +- CALL DGEMM_MKL95(vecs,matexp,dummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,vecs,matexp,'N','T',1.d0,0.d0) ++ CALL DGEMM(vecs,matexp,dummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(dummy,vecs,matexp,'N','T',1.d0,0.d0) + + END FUNCTION matexp + +@@ -246,8 +246,8 @@ + + ! solves the generalized eigenvalue equations D c=S c*lambda + SUBROUTINE diag_general(dmat,smat,dvals,dvecs) +- USE MKL95_BLAS +- USE MKL95_LAPACK ++ USE BLAS95 ++ USE LAPACK95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat, smat, dvecs + REAL*8 , DIMENSION(:) :: dvals +@@ -277,14 +277,14 @@ + + ! transform to the coordinates of the normal eigensystem + !dmat = MATMUL(TRANSPOSE(shalfi),MATMUL(dmat,shalfi)) +- CALL DGEMM_MKL95(shalfi,dmat,dummy,'T','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,shalfi,dmat,'N','N',1.d0,0.d0) ++ CALL DGEMM(shalfi,dmat,dummy,'T','N',1.d0,0.d0) ++ CALL DGEMM(dummy,shalfi,dmat,'N','N',1.d0,0.d0) + ! get the normal eigenvalues and vectors + call jacobi(dmat,n1,n1,dvals,dvecs,nrot) + ! transform the eigenvectors BACK to the original coordinate system + !dvecs = MATMUL(shalfi, dvecs) + dummy = dvecs +- CALL DGEMM_MKL95(shalfi,dummy,dvecs,'N','N',1.d0,0.d0) ++ CALL DGEMM(shalfi,dummy,dvecs,'N','N',1.d0,0.d0) + CALL eigsrt(dvals,dvecs,n1,n1) + + !WRITE(6,*)'Eigenvalues' +@@ -294,7 +294,7 @@ + END SUBROUTINE diag_general + + FUNCTION matinv_real(dmat) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matinv_real +@@ -306,12 +306,12 @@ + IF (n1.NE.n2) STOP 'Attempting to invert a non-square matrix' + + matinv_real=dmat +- CALL DGETRF_MKL95(matinv_real,ipiv,info) +- CALL DGETRI_MKL95(matinv_real,ipiv,info) ++ CALL DGETRF(matinv_real,ipiv,info) ++ CALL DGETRI(matinv_real,ipiv,info) + END FUNCTION matinv_real + + FUNCTION matinv_complex(cmat) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + COMPLEX*16 , DIMENSION(SIZE(cmat,1),SIZE(cmat,2)) :: matinv_complex +@@ -328,7 +328,7 @@ + + + !evecs = cmat +- !CALL ZHEEV_MKL95(evecs,evals,'V','U',INFO) ++ !CALL ZHEEV(evecs,evals,'V','U',INFO) + !DO info=1,SIZE(evals,1) + ! WRITE(6,'(F10.5)')evals(info) + !ENDDO +@@ -337,8 +337,8 @@ + + + matinv_complex=cmat +- CALL ZGETRF_MKL95(matinv_complex,ipiv,info) +- CALL ZGETRI_MKL95(matinv_complex,ipiv,info) ++ CALL ZGETRF(matinv_complex,ipiv,info) ++ CALL ZGETRI(matinv_complex,ipiv,info) + END FUNCTION matinv_complex + + FUNCTION outer_product(x,y) +@@ -351,7 +351,7 @@ + + !Fortran 90 wrappers for diag routines + SUBROUTINE matdiag_real(dmat,evals,evecs) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1)) :: evals +@@ -363,7 +363,7 @@ + IF (n1.NE.n2) STOP 'Attempting to diagonalize a non-square matrix' + + evecs=dmat +- !CALL dsyev_mkl95(evecs,evals,'V','U',info) ++ !CALL dsyev(evecs,evals,'V','U',info) + CALL diag(dmat,n1,n1,evals,evecs) + + !WRITE(6,*)'using real symmetrizing routine' +@@ -373,7 +373,7 @@ + END SUBROUTINE matdiag_real + + SUBROUTINE matdiag_complex(cmat,evals,evecs) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + REAL*8 , DIMENSION(SIZE(cmat,1)) :: evals +@@ -389,11 +389,11 @@ + + evecs=cmat + +- CALL zheev_mkl95(evecs,evals,'V','U',info) ++ CALL zheev(evecs,evals,'V','U',info) + IF (info.NE.0) STOP 'Error in matdiag_complex' + + !dummy=cmat +- !CALL ZGESVD_MKL95(dummy,sing_value,u_matrix,v_matrix) ++ !CALL ZGESVD(dummy,sing_value,u_matrix,v_matrix) + + + !IF( evals(1) .LE. -1.d-13 )WRITE(6,*)'WHOOOOOOOOOAAAAAAAAAAAAAAA!!! Negative eigenvalues' +@@ -436,31 +436,31 @@ + END FUNCTION matiden + + FUNCTION matunitary_trans_real(A,U) RESULT(Ap) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:) :: A,U + REAL*8,DIMENSION(SIZE(U,1),SIZE(U,1)) :: Ap + REAL*8,DIMENSION(SIZE(A,1),SIZE(U,1)) :: dummy + + !Ap=MATMUL(U,MATMUL(A,TRANSPOSE(U))) +- CALL DGEMM_MKL95(A,U,dummy,'N','T',1.d0,0.d0) +- CALL DGEMM_MKL95(U,dummy,Ap,'N','N',1.d0,0.d0) ++ CALL DGEMM(A,U,dummy,'N','T',1.d0,0.d0) ++ CALL DGEMM(U,dummy,Ap,'N','N',1.d0,0.d0) + END FUNCTION matunitary_trans_real + + FUNCTION matunitary_trans_complex(A,U) RESULT(Ap) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16,DIMENSION(:,:) :: A,U + COMPLEX*16,DIMENSION(SIZE(U,1),SIZE(U,1)) :: Ap + COMPLEX*16,DIMENSION(SIZE(A,1),SIZE(U,1)) :: dummy + + !Ap=MATMUL(U,MATMUL(A,CONJG(TRANSPOSE(U)))) +- CALL ZGEMM_MKL95(A,U,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(U,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(A,U,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(U,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + END FUNCTION matunitary_trans_complex + + FUNCTION matunitary_trans_complex2(A,U) RESULT(Ap) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16,DIMENSION(:,:) :: A + REAL*8,DIMENSION(:,:) :: U +@@ -470,8 +470,8 @@ + + U_comp = U + !Ap=MATMUL(U,MATMUL(A,TRANSPOSE(U))) +- CALL ZGEMM_MKL95(A,U_comp,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(U_comp,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(A,U_comp,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(U_comp,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + END FUNCTION matunitary_trans_complex2 + + +diff -ru periodic_nbo.orig/nbo.f90 periodic_nbo/nbo.f90 +--- periodic_nbo.orig/nbo.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/nbo.f90 2016-05-12 09:55:32.463039731 +0200 +@@ -1,6 +1,6 @@ + MODULE nbo + USE nbo_shared +- USE MKL95_BLAS ++ USE BLAS95 + PRIVATE + PUBLIC :: do_nbo, output + +@@ -336,7 +336,7 @@ + !IF( jg /= ig )Pi = Pi - outer_product(bond_coeff(:,2*ibondorlp+1-inbo,jg),bond_coeff(:,2*ibondorlp+1-inbo,jg)) + !proj_dummy = P + !P = MATMUL(Pi,P) +- !CALL DGEMM_MKL95(Pi,proj_dummy,P,'N','N',1.d0,0.d0) ++ !CALL DGEMM(Pi,proj_dummy,P,'N','N',1.d0,0.d0) + + rhoat=0.d0 + rhoat(iifirst:iilast,iifirst:iilast)=inp%rho0(ifirst:ilast,ifirst:ilast,ig,ispin) +@@ -379,8 +379,8 @@ + + !Now project out all of the bonding and antibonding density, to leave solely the dentisy associated with Rydberg states + !inp%rho0(:,:,1) = MATMUL(P,(MATMUL(inp%rho0(:,:,1),P))) +- !CALL DGEMM_MKL95(inp%rho0(:,:,1),P,proj_dummy,'N','N',1.d0,0.d0) +- !CALL DGEMM_MKL95(P,proj_dummy,inp%rho0(:,:,1),'N','N',1.d0,0.d0) ++ !CALL DGEMM(inp%rho0(:,:,1),P,proj_dummy,'N','N',1.d0,0.d0) ++ !CALL DGEMM(P,proj_dummy,inp%rho0(:,:,1),'N','N',1.d0,0.d0) + + + !PRINT *, 'made it to doing rydberg search' +@@ -552,7 +552,7 @@ + Pi=Pi-outer_product(lpcontrib,lpcontrib) + Pdummy=P + !P=MATMUL(Pi,P) +- CALL DGEMM_MKL95(Pi,Pdummy,P,'N','N',1.d0,0.d0) ++ CALL DGEMM(Pi,Pdummy,P,'N','N',1.d0,0.d0) + + !IF( occ > core_thresh*DBLE(3-inp%nspins) )THEN + ! PRINT *, 'Removing CR from atom',iatom +@@ -563,8 +563,8 @@ + !PRINT * + + !inp%rho0(:,:,1) = MATMUL(P,(MATMUL(inp%rho0(:,:,1),P))) +- CALL DGEMM_MKL95(inp%rho0(:,:,1,ispin),P,Pdummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(P,Pdummy,inp%rho0(:,:,1,ispin),'N','N',1.d0,0.d0) ++ CALL DGEMM(inp%rho0(:,:,1,ispin),P,Pdummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(P,Pdummy,inp%rho0(:,:,1,ispin),'N','N',1.d0,0.d0) + + + END SUBROUTINE do_1c_search +@@ -966,7 +966,7 @@ + + FUNCTION schmidt_orthog_matrix(S,n) RESULT(Os) + USE matutil +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:) :: S + REAL*8,DIMENSION(n,n) :: Sinv +@@ -981,7 +981,7 @@ + !onto the remaining basis function n+1:nbasis + Sinv=matinv(S(1:n,1:n)) + !proj=MATMUL(Sinv,S(1:n,n+1:nbasis)) +- CALL DGEMM_MKL95(Sinv,S(1:n,n+1:nbasis),proj,'N','N',1.d0,0.d0) ++ CALL DGEMM(Sinv,S(1:n,n+1:nbasis),proj,'N','N',1.d0,0.d0) + + !Now do gs orthogonalization using those projections + Os=0.d0 +diff -ru periodic_nbo.orig/nbo_shared.f90 periodic_nbo/nbo_shared.f90 +--- periodic_nbo.orig/nbo_shared.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/nbo_shared.f90 2016-05-12 09:55:32.463039731 +0200 +@@ -151,7 +151,7 @@ + !Calculates the number of electrons in the unit cell + ! + SUBROUTINE calc_nelec(inp,is_orthog) +- USE MKL95_BLAS ++ USE BLAS95 + USE matutil + IMPLICIT NONE + TYPE(nbo_input) :: inp +@@ -167,9 +167,9 @@ + + DO ispin=1,inp%nspins + DO ik=1,nk +- CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),inp%sk(:,:,ik),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(inp%rhok(:,:,ik,ispin),inp%sk(:,:,ik),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + nelec=nelec+inp%kpt_wt(ik)*mattrace(nelec_dummy) +- CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + nenergy=nenergy+inp%kpt_wt(ik)*mattrace(nelec_dummy) + ENDDO + ENDDO +diff -ru periodic_nbo.orig/periodic_matutil.f90 periodic_nbo/periodic_matutil.f90 +--- periodic_nbo.orig/periodic_matutil.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/periodic_matutil.f90 2016-05-12 09:55:32.463039731 +0200 +@@ -41,7 +41,7 @@ + !Multiples two periodic matrices. + ! + FUNCTION periodic_matmul(a,b) RESULT(c) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:,:), INTENT(in) :: a,b + REAL*8,DIMENSION(SIZE(a,1),SIZE(a,2),SIZE(a,3)) :: c +@@ -101,7 +101,7 @@ + !$OMP END CRITICAL + IF (idg.GT.0.AND.normab.GT.thresh) THEN + ! c(:,:,ig)=c(:,:,ig)+MATMUL(a(:,:,igp),b(:,:,idg)) +- CALL DGEMM_MKL95(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) ++ CALL DGEMM(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) + !$OMP CRITICAL + imul=imul+1 + !$OMP END CRITICAL +@@ -118,7 +118,7 @@ + END FUNCTION periodic_matmul + + FUNCTION periodic_matvecmul(a,b) RESULT(c) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:,:), INTENT(in) :: a + REAL*8,DIMENSION(:,:), INTENT(IN) :: b +@@ -165,7 +165,7 @@ + IF (idg.GT.0) THEN + !WRITE(6,*)'non zero matrix',idg,indexg(:,idg) + c(:,ig)=c(:,ig)+MATMUL(a(:,:,idg),b(:,igp)) +- !CALL DGEMM_MKL95(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) ++ !CALL DGEMM(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) + imul=imul+1 + ENDIF + +diff -ru periodic_nbo.orig/pre_nao.f90 periodic_nbo/pre_nao.f90 +--- periodic_nbo.orig/pre_nao.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/pre_nao.f90 2016-05-12 10:18:03.939451000 +0200 +@@ -1,5 +1,5 @@ + MODULE pre_nao +- USE MKL95_BLAS ++ USE BLAS95 + PRIVATE + PUBLIC :: do_pre_nao + +@@ -18,7 +18,7 @@ + USE matutil + USE periodic_matutil + USE nbo_shared +- USE mkl95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + + TYPE(nbo_input) :: inp +@@ -135,9 +135,9 @@ + num_elec = 0.d0 + DO ispin=1,nspins + DO ik=1,nk +- CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),energy_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),energy_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + energy_sum = energy_sum + inp%kpt_wt(ik)*mattrace(energy_test) +- !CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),sk(:,:,ik),elec_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ !CALL ZGEMM(inp%rhok(:,:,ik,ispin),sk(:,:,ik),elec_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + num_elec = num_elec + inp%kpt_wt(ik)*mattrace(inp%rhok(:,:,ik,ispin)) !sk should be the identity matrix now + ENDDO + ENDDO +@@ -193,8 +193,8 @@ + !$OMP PARALLEL DEFAULT(PRIVATE) SHARED(nk,rhok,sk) + !$OMP DO SCHEDULE(STATIC) + DO ik=1,nk +- CALL ZGEMM_MKL95(rhok(:,:,ik),sk(:,:,ik),dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL zGEMM_MKL95(sk(:,:,ik),dummy,rhok(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(rhok(:,:,ik),sk(:,:,ik),dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL zGEMM(sk(:,:,ik),dummy,rhok(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + ENDDO + !$OMP END DO NOWAIT + !$OMP END PARALLEL +@@ -298,7 +298,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),TRANSPOSE(N)) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),TRANSPOSE(N)) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(N,dummy,idenk(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(N,dummy,idenk(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) + ENDDO + !$OMP END DO NOWAIT + !$OMP END PARALLEL +@@ -365,7 +365,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Os) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Os) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Step 3c: Restoration of natural character of NRB + !(Omitted; doesn't seem important at all) +@@ -451,7 +451,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Ow) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Ow) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !WRITE(6,*)'hi occ ryd orthog' + +@@ -461,7 +461,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Ow) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Ow) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Finally with the low occupancy NRB + !Here we first do a Gram-Schmidt orthogonalization of the low occupancy states to the remainder +@@ -469,7 +469,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Os) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Os) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !WRITE(6,*)'lo occ ryd orthog' + +@@ -480,7 +480,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Ow) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Ow) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Now restore the expected order of the basis functions + sk(:,:,ik)=remap_matrix(sk(:,:,ik),irydbasisremap,.TRUE.) +@@ -656,7 +656,7 @@ + !onto the remaining basis function n+1:nbasis + Sinv=matinv(S(1:n,1:n)) + !proj=MATMUL(Sinv,S(1:n,n+1:nbasis)) +- CALL ZGEMM_MKL95(Sinv,S(1:n,n+1:nbasis),proj,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Sinv,S(1:n,n+1:nbasis),proj,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Now do gs orthogonalization using those projections + Os=0.d0 +@@ -707,7 +707,7 @@ + nbasis=SIZE(N,1) + IF (PRESENT(S)) THEN + !overlap=MATMUL(matsqrt(S),N) +- CALL DGEMM_MKL95(matsqrt(S),N,overlap,'N','N',1.d0,0.d0) ++ CALL DGEMM(matsqrt(S),N,overlap,'N','N',1.d0,0.d0) + ELSE + overlap=N + ENDIF diff --git a/easybuild/easyconfigs/n/NBO/NBO.eb b/easybuild/easyconfigs/n/NBO/NBO.eb new file mode 100644 index 0000000000..c629f66838 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'NBO' +version = '1.1' + +homepage = 'http://schmidt.chem.wisc.edu/nbosoftware' +description = """Generalized Natural Bond Orbital algorithm to handle systems characterized by periodic symmetry.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://schmidt.chem.wisc.edu/sites/schmidt.chem.wisc.edu/files/'] +sources = ['periodic_nbo_v.%(version)s.tgz'] + +patches = ['NBO-%(version)s_MKL95.patch'] + +buildopts = 'FC="$FC" LD="$FC" FFLAGS="$FFLAGS -I$LAPACK_INC_DIR/intel64/ilp64" ' +buildopts += 'LDFLAGS="$FFLAGS $LDFLAGS $LIBLAPACK -lmkl_blas95_ilp64 -lmkl_lapack95_ilp64"' + +files_to_copy = [(['nbo.exe'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/nbo.exe'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From e6233dc104ac2488f8a7ea35ec3f5df51f8de4c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 11:10:16 +0200 Subject: [PATCH 1652/2133] fix filename of NBO easyconfig --- easybuild/easyconfigs/n/NBO/{NBO.eb => NBO-1.1-intel-2016a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/n/NBO/{NBO.eb => NBO-1.1-intel-2016a.eb} (100%) diff --git a/easybuild/easyconfigs/n/NBO/NBO.eb b/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb similarity index 100% rename from easybuild/easyconfigs/n/NBO/NBO.eb rename to easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb -- GitLab From 36481d302c326fb888f18395e9485de0369211c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 11:42:34 +0200 Subject: [PATCH 1653/2133] remove hack in HPL pomkl easyconfig for linking with -ldl --- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb index 7d18ed0de8..4d48990b54 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb @@ -15,9 +15,4 @@ source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] # fix Make dependencies, so parallel build also works patches = ['HPL_parallel-make.patch'] -# needs to include -ldl or else we get -# .../libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' -import os -os.environ['LIBS'] = '-ldl' - moduleclass = 'tools' -- GitLab From daf6705c34074fd88288abd68b8d470ffb390e3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 14:29:59 +0200 Subject: [PATCH 1654/2133] also build projection.exe tool in NBO easyconfig --- .../easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb | 18 +- .../n/NBO/projection-1.1.2_MKL95.patch | 212 ++++++++++++++++++ 2 files changed, 226 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch diff --git a/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb b/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb index c629f66838..a0ff978b52 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb @@ -10,17 +10,27 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'openmp': True} source_urls = ['http://schmidt.chem.wisc.edu/sites/schmidt.chem.wisc.edu/files/'] -sources = ['periodic_nbo_v.%(version)s.tgz'] +sources = [ + 'periodic_nbo_v.%(version)s.tgz', + 'projection_v.1.1.2.tgz', +] -patches = ['NBO-%(version)s_MKL95.patch'] +patches = [ + 'NBO-%(version)s_MKL95.patch', + ('projection-1.1.2_MKL95.patch', '..'), +] + +prebuildopts = "cd %(builddir)s/projection && " +prebuildopts += 'make FFLAGS="$FFLAGS -I$LAPACK_INC_DIR/intel64/ilp64" && ' +prebuildopts += "cd %(builddir)s/periodic_nbo && " buildopts = 'FC="$FC" LD="$FC" FFLAGS="$FFLAGS -I$LAPACK_INC_DIR/intel64/ilp64" ' buildopts += 'LDFLAGS="$FFLAGS $LDFLAGS $LIBLAPACK -lmkl_blas95_ilp64 -lmkl_lapack95_ilp64"' -files_to_copy = [(['nbo.exe'], 'bin')] +files_to_copy = [(['%(builddir)s/periodic_nbo/nbo.exe', '%(builddir)s/projection/projection.exe'], 'bin')] sanity_check_paths = { - 'files': ['bin/nbo.exe'], + 'files': ['bin/nbo.exe', 'bin/projection.exe'], 'dirs': [], } diff --git a/easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch b/easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch new file mode 100644 index 0000000000..f12e3ac7a4 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch @@ -0,0 +1,212 @@ +fix using BLAS95/LAPACK95 interface for recent Intel MKL versions +author: Kenneth Hoste (HPC-UGent) +diff -ru projection.orig/bloch_overlap.f90 projection/bloch_overlap.f90 +--- projection.orig/bloch_overlap.f90 2015-04-15 18:05:39.000000000 +0200 ++++ projection/bloch_overlap.f90 2016-05-12 13:58:53.000000000 +0200 +@@ -18,8 +18,8 @@ + ! Kudin and Scuseria, Chem. Phys. Lett.; 289, 611-616 (1998) + + SUBROUTINE bloch_space_overlap(AO_basis,index_l) +- USE mkl95_lapack +- USE mkl95_blas ++ USE LAPACK95 ++ USE BLAS95 + IMPLICIT NONE + + TYPE(AO_function), DIMENSION(:) :: AO_basis +@@ -189,9 +189,9 @@ + bloch_s_inv(:,:,ik) = bloch_s_mat(:,:,ik) + IF( SVD )THEN + !SVD inversion method, more robust but slow +- CALL ZGESVD_MKL95(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,work_array,'A') ++ CALL ZGESVD(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,work_array,'A') + !Previously used SVD routine, has numerical instability wrt really small values +- !CALL ZGESDD_MKL95(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,'A') ++ !CALL ZGESDD(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,'A') + + !This loop is the equivalent of multiplying the inverse of the singular values matrix by adjoint of the u matrix + DO j=1,s_dim +@@ -202,16 +202,16 @@ + inv_dummy(j,:) = 0.d0 + ENDIF + ENDDO +- CALL ZGEMM_MKL95(v_matrix,inv_dummy,bloch_s_inv(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(v_matrix,inv_dummy,bloch_s_inv(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) + ELSE + !LU decompostion inversion method, fast but easily suffers from instability due to linear dependency +- CALL ZGETRF_MKL95(bloch_s_inv(:,:,ik),IPIV,INFO) ++ CALL ZGETRF(bloch_s_inv(:,:,ik),IPIV,INFO) + IF( INFO /= 0 )THEN + WRITE(6,*)'The inverese of the overlap matrix for kpt',ik,'could not be computed' + WRITE(6,*)'INFO value output from ZGETRF',INFO + STOP + ENDIF +- CALL ZGETRI_MKL95(bloch_s_inv(:,:,ik),IPIV) ++ CALL ZGETRI(bloch_s_inv(:,:,ik),IPIV) + ENDIF + + !WRITE(6,*)'inverse for kpoint',ik +@@ -248,7 +248,7 @@ + !IF there are linear dependencies the best bet is to just 'trim' the basis set of its most diffuse functions. + !In periodic systems there is no 'edge' and these diffuse functions are largely uneccessary. + SUBROUTINE check_linear_depend(input_mat,eig_min) +- USE mkl95_lapack ++ USE LAPACK95 + IMPLICIT NONE + + COMPLEX*16,DIMENSION(:,:),INTENT(IN) :: input_mat +@@ -262,7 +262,7 @@ + + test_mat = input_mat + +- CALL ZHEEV_MKL95(test_mat,eigval,'V','U',INFO) ++ CALL ZHEEV(test_mat,eigval,'V','U',INFO) + + IF( INFO .NE. 0 )THEN + WRITE(6,*)'Calculating eigenvalues in check_linear_depend failed' +diff -ru projection.orig/projection_main.f90 projection/projection_main.f90 +--- projection.orig/projection_main.f90 2015-03-04 17:07:27.000000000 +0100 ++++ projection/projection_main.f90 2016-05-12 13:58:57.000000000 +0200 +@@ -4,7 +4,7 @@ + USE rd_basis + USE bloch_overlap + USE PAW +- USE mkl95_blas ++ USE BLAS95 + IMPLICIT NONE + + CHARACTER(128) :: basis_fn, VASP_fn, NBO_fn +@@ -145,28 +145,28 @@ + !Then for each basis function, nu, the contribution of the planewaves is calculated for all bands at one using vector-matrix multiplication + DO ispin=1,nspins + !each computation is SUM(nu) S-1{mu,nu} * (SUM(g) *c(a,g)) +- CALL ZGEMV_MKL95(pw_coeff(:,:,ik,ispin),AO_PW_overlap(:,ik),proj_matrix(nu,:,ik,ispin),(1.d0,0.d0),(0.d0,0.d0),'T') ++ CALL ZGEMV(pw_coeff(:,:,ik,ispin),AO_PW_overlap(:,ik),proj_matrix(nu,:,ik,ispin),(1.d0,0.d0),(0.d0,0.d0),'T') + ENDDO + ENDDO + + DO ispin=1,nspins + ! !Calculation of planewave contributions to band coeff's are done at once using matrix multiplication + ! !each computation is SUM(nu) S-1{mu,nu} * (SUM(g) *c(a,g)) +-! CALL ZGEMM_MKL95(AO_PW_overlap(:,:,ik),pw_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++! CALL ZGEMM(AO_PW_overlap(:,:,ik),pw_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + ! + ! !Since band is simply summation of PW AND PAW, PAW contirbution is simply added to PW's +-! IF( PAW_pseudo ) CALL ZGEMM_MKL95(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(1.d0,0.d0)) ++! IF( PAW_pseudo ) CALL ZGEMM(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(1.d0,0.d0)) + ! + ! !Band overlaps are finally multiplied by inverse of overlap matrix to complete projection + ! !The use of the inverse of the overlap matrix is necessary due to the non-orthogonality of the AO-basis +-! CALL ZGEMM_MKL95(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++! CALL ZGEMM(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Since band is simply summation of PW AND PAW, PAW contirbution is simply added to PW's +- IF( PAW_pseudo ) CALL ZGEMM_MKL95(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik,ispin),'N','N',(1.d0,0.d0),(1.d0,0.d0)) ++ IF( PAW_pseudo ) CALL ZGEMM(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik,ispin),'N','N',(1.d0,0.d0),(1.d0,0.d0)) + + !Band overlaps are finally multiplied by inverse of overlap matrix to complete projection + !The use of the inverse of the overlap matrix is necessary due to the non-orthogonality of the AO-basis +- CALL ZGEMM_MKL95(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik,ispin),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik,ispin),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + ENDDO + +@@ -208,19 +208,19 @@ + coeff_dummy(:,iband) = bloch_band_coeff(:,iband,ik,ispin) * weight(iband,ik,ispin) + ENDDO + !Matrix muliplication is used to calculate the density matrix +- CALL ZGEMM_MKL95(coeff_dummy,bloch_band_coeff(:,:,ik,ispin),bloch_density(:,:,ik,ispin),'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(coeff_dummy,bloch_band_coeff(:,:,ik,ispin),bloch_density(:,:,ik,ispin),'N','C',(1.d0,0.d0),(0.d0,0.d0)) + + !FOCK MATRIX + !Matrix multiplication is used to convert the Fock matrix into the projected basis + ! F{mu,nu} = SUM(fock_coeff{nu,iband}*F{iband,iband}*CONJG(fock_coeff{nu,iband})) + !First the nonorthogonality of the bloch orbtials must be addressed since the MO->AO transform is not unitary + !coeff's must be multiplied by Overlap matrix +- CALL ZGEMM_MKL95(bloch_s_mat(:,:,ik),bloch_band_coeff(:,:,ik,ispin),coeff_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_s_mat(:,:,ik),bloch_band_coeff(:,:,ik,ispin),coeff_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + !Then the trnsformation is simply a unitary transform using the new coefficients + DO iband=1,nbands + fock_dummy(iband,:) = eig(iband,ik,ispin)*CONJG(coeff_dummy(:,iband)) + ENDDO +- CALL ZGEMM_MKL95(coeff_dummy,fock_dummy,bloch_fock(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(coeff_dummy,fock_dummy,bloch_fock(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + ENDDO + ENDDO + +@@ -235,12 +235,12 @@ + energy_sum = 0.d0 + DO ispin=1,nspins + DO ik=1,nkpts +- CALL ZGEMM_MKL95(bloch_density(:,:,ik,ispin),bloch_s_mat(:,:,ik),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_density(:,:,ik,ispin),bloch_s_mat(:,:,ik),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + n_elec_dummy = n_elec_dummy*kpt_wt(ik) + DO nu=1,s_dim + num_elec = num_elec + n_elec_dummy(nu,nu) + ENDDO +- CALL ZGEMM_MKL95(bloch_density(:,:,ik,ispin),bloch_fock(:,:,ik,ispin),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_density(:,:,ik,ispin),bloch_fock(:,:,ik,ispin),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + n_elec_dummy = n_elec_dummy*kpt_wt(ik) + DO nu=1,s_dim + energy_sum = energy_sum + n_elec_dummy(nu,nu) +@@ -271,7 +271,7 @@ + !This subrotuine computes the overlap matrices of the projected bands in the AO basis. + !This information is also used to calculate the spillover (quantify how much of band density is lost in projection + SUBROUTINE calc_spillover(r_mat,band_coeff) +- USE mkl95_blas ++ USE BLAS95 + USE rd_wavefunction + USE projection_shared + IMPLICIT NONE +@@ -345,8 +345,8 @@ + + !Overlap of projected bands is computed using matrix mulitplication + !Each overlap is equal to SUM(mu) SUM(nu) c*S{mu,nu}c +- CALL ZGEMM_MKL95(bloch_s_mat(:,:,ik),band_coeff(:,:,ik,ispin),r_mat_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(band_coeff(:,:,ik,ispin),r_mat_dummy,r_mat(:,:,ik,ispin),'C','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_s_mat(:,:,ik),band_coeff(:,:,ik,ispin),r_mat_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(band_coeff(:,:,ik,ispin),r_mat_dummy,r_mat(:,:,ik,ispin),'C','N',(1.d0,0.d0),(0.d0,0.d0)) + + + !Then the norm of each band at each k-point is analyzed to make sure the norm is appropriate +diff -ru projection.orig/projection_shared.f90 projection/projection_shared.f90 +--- projection.orig/projection_shared.f90 2015-04-15 17:50:44.000000000 +0200 ++++ projection/projection_shared.f90 2016-05-12 13:59:00.000000000 +0200 +@@ -94,8 +94,8 @@ + !The bands are in the same original AO basis + !The orhtogonalizing matrix is constructed as W(WSW)^-1/2, where S is the 'overlap_mat' and W is a diagonal matrix containing the occupancy of each band + SUBROUTINE do_OWSO(overlap_mat,band_occ,band_coeff) +- USE mkl95_BLAS +- USE mkl95_LAPACK ++ USE BLAS95 ++ USE LAPACK95 + IMPLICIT NONE + + COMPLEX*16,DIMENSION(:,:),INTENT(IN) :: overlap_mat !Input overlap matrix, used to construct orthogonalizing matrix +@@ -145,7 +145,7 @@ + + !Now obtain the eigenvectors to obtain the square root matrix + eigvec = sym_weight +- CALL ZHEEV_MKL95(eigvec,eigval,'V','U',INFO) ++ CALL ZHEEV(eigvec,eigval,'V','U',INFO) + IF( INFO /= 0 )THEN + WRITE(6,*)'The eigenvalues of the overlap matrix could not be computed' + WRITE(6,*)'INFO on exit of ZHEEV',INFO +@@ -156,7 +156,7 @@ + DO iband=1,nbands + sym_weight(iband,:) = CONJG(eigvec(:,iband)) / SQRT(eigval(iband)) !Sym_weight is now just a dummy matrix for use in the BLAS routine + ENDDO +- CALL ZGEMM_MKL95(eigvec,sym_weight,sqrt_inv,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(eigvec,sym_weight,sqrt_inv,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + + !To obtain the orthogonlaizing matrix an additional multiplication by the weight matrix must be applied from the left +@@ -168,7 +168,7 @@ + !Now the bands can finally be orhtogonalized + !Note that the original coefficients are lost. They are currently unused but this will have to be rewritten if they become necessary. + coeff_dummy = band_coeff +- CALL ZGEMM_MKL95(coeff_dummy,sqrt_inv,band_coeff,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(coeff_dummy,sqrt_inv,band_coeff,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + + -- GitLab From 81cb6797e4686ceaf9b0606870cce5f4518fd9ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 17:41:26 +0200 Subject: [PATCH 1655/2133] add easyconfig CheMPS2-1.7-rc2-intel-2016a.eb --- .../c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb new file mode 100644 index 0000000000..a6d4195a03 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.7-rc2' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('GSL', '2.1'), + ('HDF5', '1.8.16') +] + +buildopts = 'VERBOSE=1' + +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' -- GitLab From a7c1b9ba4615973a4383146119a9f64f90dadea6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 17:44:43 +0200 Subject: [PATCH 1656/2133] remove VERBOSE=1 from buildopts for CheMPS2 --- easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb | 2 -- easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb index aab739ed19..c318ed2f59 100644 --- a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb @@ -19,8 +19,6 @@ dependencies = [ ('HDF5', '1.8.16') ] -buildopts = 'VERBOSE=1' - runtest = 'test' separate_build_dir = True diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb index a6d4195a03..d7f97d6e59 100644 --- a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb @@ -19,8 +19,6 @@ dependencies = [ ('HDF5', '1.8.16') ] -buildopts = 'VERBOSE=1' - runtest = 'test' separate_build_dir = True -- GitLab From eaf991faae5eecdef7bd8c7e67741ad667cd6515 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 12:28:10 -0400 Subject: [PATCH 1657/2133] add VTK and SuiteSparse easyconfig it are necessary for fluid coupling module in yade, improve Yade easyconfig (sanity-check) --- ...uiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb | 27 +++++++++++ .../VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb | 48 +++++++++++++++++++ .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 30 +++++++----- 3 files changed, 93 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000..69daf4f59c --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb @@ -0,0 +1,27 @@ +name = 'SuiteSparse' +version = '4.5.2' + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +preconfigopts += 'LAPACK="$LIBLAPACK" ' +prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +prebuildopts += 'LAPACK="$LIBLAPACK" ' +preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +preinstallopts += 'LAPACK="$LIBLAPACK" ' + +maxparallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..e96c03e7a3 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'VTK' +version = '6.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('Python', '2.7.11'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), + ('libXt', '1.1.5'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', + 'mkg3states', 'ParseOGLExt']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 6ca7251d44..74cf92bc23 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -17,33 +17,39 @@ sources = [SOURCELOWER_TAR_GZ] mesaver = '11.2.1' dependencies = [ - ('Loki', '0.1.7'), ('Boost', '1.60.0', versionsuffix), + ('CGAL', '4.8', versionsuffix), + ('Eigen', '3.2.7'), + ('GDB', '7.10.1', versionsuffix), ('GL2PS', '1.3.9', '-Mesa-%s' % mesaver), - ('Python', '2.7.11'), + ('GTS', '0.7.6'), ('IPython', '3.2.3', versionsuffix), - ('PyGTS', '0.3.1', versionsuffix), - ('Eigen', '3.2.7'), + ('libQGLViewer', '2.6.3', '-Mesa-%s' % mesaver), + ('Loki', '0.1.7'), + ('matplotlib', '1.5.1', versionsuffix), ('minieigen', '0.5.3', versionsuffix), + ('PyGTS', '0.3.1', versionsuffix), + ('Python', '2.7.11'), ('Qt', '4.8.7', '-GLib-2.48.0'), - ('GTS', '0.7.6'), - ('libQGLViewer', '2.6.3', '-Mesa-%s' % mesaver), - ('zlib', '1.2.8'), - ('CGAL', '4.8', versionsuffix), + ('SQLite', '3.9.2'), + ('SuiteSparse', '4.5.2', '-METIS-5.1.0'), + ('VTK', '6.3.0', versionsuffix), + ('zlib', '1.2.8'), ] builddependencies = [('CMake', '3.5.2')] separate_build_dir = True -configopts = '-DENABLE_GUI=OFF -DENABLE_VTK=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' +configopts = '-DENABLE_GUI=OFF ' configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' sanity_check_paths = { - 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', - 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], - 'dirs': ['lib/x86_64-linux-gnu/yade-%(version)s/py/yade'], + 'files': [('bin/yade-%(version)s', 'bin/yade-%(version)s-batch'), + ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, + 'lib64/yade-%%(version)s/libyade.%s' %SHLIB_EXT)], + 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } moduleclass = 'devel' -- GitLab From d4c24166c7296977a365409e36ffbab0e5f1bd80 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 12 May 2016 18:30:42 +0200 Subject: [PATCH 1658/2133] Update SuiteSparse EasyConfig files after update of the EasyBlock --- .../SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb | 4 ---- .../SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb | 4 ---- 2 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb index ac231b59ef..be2d19e2ca 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb @@ -15,10 +15,6 @@ metis_ver = '5.1.0' versionsuffix = '-%s-%s' % (metis, metis_ver) dependencies = [(metis, metis_ver)] -preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' - maxparallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb index 63fe3bdb3b..8f26d75a93 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb @@ -15,10 +15,6 @@ metis_ver = '5.1.0' versionsuffix = '-%s-%s' % (metis, metis_ver) dependencies = [(metis, metis_ver)] -preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' - maxparallel = 1 moduleclass = 'numlib' -- GitLab From b9f2c26ddab0d6ceb7aaa7769e17fa5e8e902fa2 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 12:32:35 -0400 Subject: [PATCH 1659/2133] fix santy_check_paths --- .../easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 74cf92bc23..771c1391cd 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -46,7 +46,7 @@ configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' sanity_check_paths = { - 'files': [('bin/yade-%(version)s', 'bin/yade-%(version)s-batch'), + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, 'lib64/yade-%%(version)s/libyade.%s' %SHLIB_EXT)], 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], -- GitLab From 14c7469bfad8a9e8a5db7bf1415794928f835e16 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 13:28:27 -0400 Subject: [PATCH 1660/2133] add matplotlib-freetype-2.6.3 easyconfig to resolve conflict dependencies --- ...foss-2016a-Python-2.7.11-freetype-2.6.3.eb | 44 +++++++++++++++++++ .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb new file mode 100644 index 0000000000..d74aeaeeca --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s-freetype-2.6.3' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.3'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 771c1391cd..3ae713b3be 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -26,7 +26,7 @@ dependencies = [ ('IPython', '3.2.3', versionsuffix), ('libQGLViewer', '2.6.3', '-Mesa-%s' % mesaver), ('Loki', '0.1.7'), - ('matplotlib', '1.5.1', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3'), ('minieigen', '0.5.3', versionsuffix), ('PyGTS', '0.3.1', versionsuffix), ('Python', '2.7.11'), -- GitLab From e7c51d2166ef05e976a4be67fae383e22298f09f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 14:26:52 -0400 Subject: [PATCH 1661/2133] avoid hardcoding the freetype version in two places --- ...plotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb index d74aeaeeca..528d8a13cb 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -2,7 +2,6 @@ easyblock = 'Bundle' name = 'matplotlib' version = '1.5.1' -versionsuffix = '-Python-%(pyver)s-freetype-2.6.3' homepage = 'http://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of @@ -14,9 +13,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' +freetype_ver = '2.6.3' +versionsuffix = '-Python-%%(pyver)s-freetype-%s' % freetype_ver + dependencies = [ ('Python', '2.7.11'), - ('freetype', '2.6.3'), + ('freetype', freetype_ver), ('libpng', '1.6.21'), ] -- GitLab From e13db3b9bef67a50ea0f1c44236caa20592eb199 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 16:07:16 -0400 Subject: [PATCH 1662/2133] improve matplotlib and remove SuiteSparse easyconfig --- ...foss-2016a-Python-2.7.11-freetype-2.6.3.eb | 1 + ...uiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb | 27 ------------------- .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 5 ++-- 3 files changed, 3 insertions(+), 30 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb index 528d8a13cb..c9dd3410c4 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -30,6 +30,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb deleted file mode 100644 index 69daf4f59c..0000000000 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'SuiteSparse' -version = '4.5.2' - -homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' -description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" - -toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'opt': True, 'unroll': True, 'pic': True} - -source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] -sources = [SOURCE_TAR_GZ] - -metis = 'METIS' -metis_ver = '5.1.0' -versionsuffix = '-%s-%s' % (metis, metis_ver) -dependencies = [(metis, metis_ver)] - -preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -preconfigopts += 'LAPACK="$LIBLAPACK" ' -prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -prebuildopts += 'LAPACK="$LIBLAPACK" ' -preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -preinstallopts += 'LAPACK="$LIBLAPACK" ' - -maxparallel = 1 - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 3ae713b3be..dfcea93ba1 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -31,8 +31,7 @@ dependencies = [ ('PyGTS', '0.3.1', versionsuffix), ('Python', '2.7.11'), ('Qt', '4.8.7', '-GLib-2.48.0'), - ('SQLite', '3.9.2'), - ('SuiteSparse', '4.5.2', '-METIS-5.1.0'), + ('SQLite', '3.9.2'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), ] @@ -41,7 +40,7 @@ builddependencies = [('CMake', '3.5.2')] separate_build_dir = True -configopts = '-DENABLE_GUI=OFF ' +configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' -- GitLab From 4742855b22f00d063e0c39a9334340a2c6f0b699 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 16:50:22 -0400 Subject: [PATCH 1663/2133] add modextrapaths in Yade easyconfig --- .../y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index dfcea93ba1..f94f281e77 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -44,6 +44,12 @@ configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'PYTHONPATH': ['lib/x86_64-linux-gnu/yade-%(version)s/py', 'lib64/yade-%(version)s/py'], +} + sanity_check_paths = { 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, -- GitLab From 0d740a9f0879dc7e077305bef87a3a479c4e8eda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 11:00:37 +0200 Subject: [PATCH 1664/2133] use %(pyshortver)s rather than hardcoding 2.7 in VTK easyconfigs --- .../easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb | 2 +- .../easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb index 4be27d99f6..94b031902b 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb @@ -48,7 +48,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%s.%s " % (pyshortver, SHLIB_EXT) configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%s " % pyshortver -preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " preinstallopts += "export PYTHONPATH=%%(installdir)s/lib/python%s/site-packages:$PYTHONPATH && " % pyshortver modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb index 55d38284a0..e549b2e963 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb @@ -43,7 +43,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -- GitLab From a732161e4dce6dec6b86026064ac2bb30707e9f7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 13 May 2016 12:54:06 +0200 Subject: [PATCH 1665/2133] try to patch --- easybuild/easyconfigs/r/RSEM/Makefile | 173 +++++++ easybuild/easyconfigs/r/RSEM/Makefile.orig | 173 +++++++ .../r/RSEM/RSEM-1.2.30-foss-2016a.eb | 57 +++ .../r/RSEM/RSEM-1.2.30_boost.patch | 23 + .../r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch | 162 +++++++ easybuild/easyconfigs/r/RSEM/sam/Makefile | 314 +++++++++++++ .../easyconfigs/r/RSEM/sam/Makefile.orig | 314 +++++++++++++ easybuild/easyconfigs/r/RSEM/sam/diff | 23 + easybuild/easyconfigs/r/RSEM/sam/hts/Makefile | 426 ++++++++++++++++++ .../easyconfigs/r/RSEM/sam/hts/Makefile.orig | 426 ++++++++++++++++++ easybuild/easyconfigs/r/RSEM/sam/hts/diff | 18 + 11 files changed, 2109 insertions(+) create mode 100644 easybuild/easyconfigs/r/RSEM/Makefile create mode 100644 easybuild/easyconfigs/r/RSEM/Makefile.orig create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch create mode 100644 easybuild/easyconfigs/r/RSEM/sam/Makefile create mode 100644 easybuild/easyconfigs/r/RSEM/sam/Makefile.orig create mode 100644 easybuild/easyconfigs/r/RSEM/sam/diff create mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/Makefile create mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig create mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/diff diff --git a/easybuild/easyconfigs/r/RSEM/Makefile b/easybuild/easyconfigs/r/RSEM/Makefile new file mode 100644 index 0000000000..921b40b1b3 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/Makefile @@ -0,0 +1,173 @@ +SAMTOOLS = samtools-1.3 +HTSLIB = htslib-1.3 + +ifneq ($(cygwin), true) + SAMTOOLS_MAKEFILE = Makefile +else + SAMTOOLS_MAKEFILE = Makefile.cygwin +endif + +# overridable, defaulting to local copy +BOOST = ${EBROOTBOOST} + +# Compilation variables +CXX = g++ +CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) +CPPFLAGS = + +LDFLAGS = +LDLIBS = + +# Installation variables +INSTALL = install +INSTALL_PROGRAM = $(INSTALL) -p +INSTALL_DATA = $(INSTALL) -p -m 644 +INSTALL_DIR = $(INSTALL) -d +STRIP ?=strip + +prefix ?= /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin + +# Auxiliary variables for compilation +SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h +SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a +CONFIGURE = ./configure + +OBJS1 = parseIt.o +OBJS2 = extractRef.o synthesisRef.o preRef.o buildReadIndex.o wiggle.o tbam2gbam.o bam2wig.o bam2readdepth.o getUnique.o samValidator.o scanForPairedEndReads.o SamHeader.o +OBJS3 = EM.o Gibbs.o calcCI.o simulation.o + +PROGS1 = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads +PROGS2 = rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads +PROGS3 = rsem-run-gibbs rsem-calculate-credibility-intervals + +PROGRAMS = $(PROGS1) $(PROGS2) $(PROGS3) + +# Auxiliary variables for installation +SCRIPTS = rsem-prepare-reference rsem-calculate-expression rsem-refseq-extract-primary-assembly rsem-gff3-to-gtf rsem-plot-model \ + rsem-plot-transcript-wiggles rsem-gen-transcript-plots rsem-generate-data-matrix \ + extract-transcript-to-gene-map-from-trinity convert-sam-for-rsem + + + + +.PHONY : all ebseq clean + +all : $(PROGRAMS) $(SAMTOOLS)/samtools + +$(SAMTOOLS)/samtools : + cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools + +$(SAMLIBS) : $(SAMTOOLS)/samtools + + +# Compile objects +$(OBJS1) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O2 -c -o $@ $< + +$(OBJS2) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -c -o $@ $< + +$(OBJS3) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -ffast-math -c -o $@ $< + + +# Generate executables +$(PROGS1) : + $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) + +$(PROGS2) : + $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -L$(EBROOTZLIB)/lib -lz + +$(PROGS3) : + $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) + + +# Dependencies for executables +rsem-extract-reference-transcripts : extractRef.o +rsem-synthesis-reference-transcripts : synthesisRef.o +rsem-preref : preRef.o +rsem-build-read-index : buildReadIndex.o +rsem-simulate-reads : simulation.o + +rsem-parse-alignments : parseIt.o $(SAMLIBS) +rsem-run-em : EM.o SamHeader.o $(SAMLIBS) +rsem-tbam2gbam : tbam2gbam.o SamHeader.o $(SAMLIBS) +rsem-bam2wig : bam2wig.o wiggle.o $(SAMLIBS) +rsem-bam2readdepth : bam2readdepth.o wiggle.o $(SAMLIBS) +rsem-get-unique : getUnique.o $(SAMLIBS) +rsem-sam-validator : samValidator.o $(SAMLIBS) +rsem-scan-for-paired-end-reads : scanForPairedEndReads.o $(SAMLIBS) + +rsem-run-gibbs : Gibbs.o +rsem-calculate-credibility-intervals : calcCI.o $(LDLIBS) + +# Dependencies for objects +parseIt.o : parseIt.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h + +extractRef.o : extractRef.cpp utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h +synthesisRef.o : synthesisRef.cpp utils.h my_assert.h Transcript.h Transcripts.h +preRef.o : preRef.cpp utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h +buildReadIndex.o : buildReadIndex.cpp utils.h +wiggle.o: wiggle.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h wiggle.h +tbam2gbam.o : tbam2gbam.cpp $(SAMHEADERS) utils.h Transcripts.h Transcript.h BamConverter.h sam_utils.h SamHeader.hpp my_assert.h bc_aux.h +bam2wig.o : bam2wig.cpp utils.h my_assert.h wiggle.h +bam2readdepth.o : bam2readdepth.cpp utils.h my_assert.h wiggle.h +getUnique.o : getUnique.cpp $(SAMHEADERS) sam_utils.h utils.h +samValidator.o : samValidator.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h +scanForPairedEndReads.o : scanForPairedEndReads.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h +SamHeader.o : SamHeader.cpp $(SAMHEADERS) SamHeader.hpp + +EM.o : EM.cpp $(SAMHEADERS) utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_utils.h SamHeader.hpp sampling.h $(BOOST)/boost/random.hpp WriteResults.h +Gibbs.o : Gibbs.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h +calcCI.o : calcCI.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h +simulation.o : simulation.cpp utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h $(BOOST)/boost/random.hpp WriteResults.h + +# Dependencies for header files +Transcript.h : utils.h +Transcripts.h : utils.h my_assert.h Transcript.h +BowtieRefSeqPolicy.h : RefSeqPolicy.h +RefSeq.h : utils.h +Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h +SingleRead.h : Read.h +SingleReadQ.h : Read.h +PairedEndRead.h : Read.h SingleRead.h +PairedEndReadQ.h : Read.h SingleReadQ.h +PairedEndHit.h : SingleHit.h +HitContainer.h : GroupInfo.h +sam_utils.h : $(SAMHEADERS) Transcript.h Transcripts.h +SamParser.h : $(SAMHEADERS) sam_utils.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h +simul.h : $(BOOST)/boost/random.hpp +ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h +SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h +SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h +PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h +PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h +HitWrapper.h : HitContainer.h +BamWriter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h +sampling.h : $(BOOST)/boost/random.hpp +WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h +bc_aux.h : $(SAMHEADERS) +BamConverter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h bc_aux.h Transcript.h Transcripts.h +Buffer.h : my_assert.h +SamHeader.hpp : $(SAMHEADERS) + +# Compile EBSeq +ebseq : + cd EBSeq && $(MAKE) all + +# Install RSEM +install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) + $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) + $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools + $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools + $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) + $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm + +# Clean +clean : + rm -f *.o *~ $(PROGRAMS) + cd $(SAMTOOLS) && $(MAKE) clean-all + cd EBSeq && $(MAKE) clean diff --git a/easybuild/easyconfigs/r/RSEM/Makefile.orig b/easybuild/easyconfigs/r/RSEM/Makefile.orig new file mode 100644 index 0000000000..09d2223b23 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/Makefile.orig @@ -0,0 +1,173 @@ +SAMTOOLS = samtools-1.3 +HTSLIB = htslib-1.3 + +ifneq ($(cygwin), true) + SAMTOOLS_MAKEFILE = Makefile +else + SAMTOOLS_MAKEFILE = Makefile.cygwin +endif + +# overridable, defaulting to local copy +BOOST = . + +# Compilation variables +CXX = g++ +CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) +CPPFLAGS = + +LDFLAGS = +LDLIBS = + +# Installation variables +INSTALL = install +INSTALL_PROGRAM = $(INSTALL) -p +INSTALL_DATA = $(INSTALL) -p -m 644 +INSTALL_DIR = $(INSTALL) -d +STRIP ?=strip + +prefix ?= /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin + +# Auxiliary variables for compilation +SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h +SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a +CONFIGURE = ./configure + +OBJS1 = parseIt.o +OBJS2 = extractRef.o synthesisRef.o preRef.o buildReadIndex.o wiggle.o tbam2gbam.o bam2wig.o bam2readdepth.o getUnique.o samValidator.o scanForPairedEndReads.o SamHeader.o +OBJS3 = EM.o Gibbs.o calcCI.o simulation.o + +PROGS1 = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads +PROGS2 = rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads +PROGS3 = rsem-run-gibbs rsem-calculate-credibility-intervals + +PROGRAMS = $(PROGS1) $(PROGS2) $(PROGS3) + +# Auxiliary variables for installation +SCRIPTS = rsem-prepare-reference rsem-calculate-expression rsem-refseq-extract-primary-assembly rsem-gff3-to-gtf rsem-plot-model \ + rsem-plot-transcript-wiggles rsem-gen-transcript-plots rsem-generate-data-matrix \ + extract-transcript-to-gene-map-from-trinity convert-sam-for-rsem + + + + +.PHONY : all ebseq clean + +all : $(PROGRAMS) $(SAMTOOLS)/samtools + +$(SAMTOOLS)/samtools : + cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools + +$(SAMLIBS) : $(SAMTOOLS)/samtools + + +# Compile objects +$(OBJS1) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O2 -c -o $@ $< + +$(OBJS2) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -c -o $@ $< + +$(OBJS3) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -ffast-math -c -o $@ $< + + +# Generate executables +$(PROGS1) : + $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) + +$(PROGS2) : + $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lz + +$(PROGS3) : + $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) + + +# Dependencies for executables +rsem-extract-reference-transcripts : extractRef.o +rsem-synthesis-reference-transcripts : synthesisRef.o +rsem-preref : preRef.o +rsem-build-read-index : buildReadIndex.o +rsem-simulate-reads : simulation.o + +rsem-parse-alignments : parseIt.o $(SAMLIBS) +rsem-run-em : EM.o SamHeader.o $(SAMLIBS) +rsem-tbam2gbam : tbam2gbam.o SamHeader.o $(SAMLIBS) +rsem-bam2wig : bam2wig.o wiggle.o $(SAMLIBS) +rsem-bam2readdepth : bam2readdepth.o wiggle.o $(SAMLIBS) +rsem-get-unique : getUnique.o $(SAMLIBS) +rsem-sam-validator : samValidator.o $(SAMLIBS) +rsem-scan-for-paired-end-reads : scanForPairedEndReads.o $(SAMLIBS) + +rsem-run-gibbs : Gibbs.o +rsem-calculate-credibility-intervals : calcCI.o + +# Dependencies for objects +parseIt.o : parseIt.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h + +extractRef.o : extractRef.cpp utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h +synthesisRef.o : synthesisRef.cpp utils.h my_assert.h Transcript.h Transcripts.h +preRef.o : preRef.cpp utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h +buildReadIndex.o : buildReadIndex.cpp utils.h +wiggle.o: wiggle.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h wiggle.h +tbam2gbam.o : tbam2gbam.cpp $(SAMHEADERS) utils.h Transcripts.h Transcript.h BamConverter.h sam_utils.h SamHeader.hpp my_assert.h bc_aux.h +bam2wig.o : bam2wig.cpp utils.h my_assert.h wiggle.h +bam2readdepth.o : bam2readdepth.cpp utils.h my_assert.h wiggle.h +getUnique.o : getUnique.cpp $(SAMHEADERS) sam_utils.h utils.h +samValidator.o : samValidator.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h +scanForPairedEndReads.o : scanForPairedEndReads.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h +SamHeader.o : SamHeader.cpp $(SAMHEADERS) SamHeader.hpp + +EM.o : EM.cpp $(SAMHEADERS) utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_utils.h SamHeader.hpp sampling.h $(BOOST)/boost/random.hpp WriteResults.h +Gibbs.o : Gibbs.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h +calcCI.o : calcCI.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h +simulation.o : simulation.cpp utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h $(BOOST)/boost/random.hpp WriteResults.h + +# Dependencies for header files +Transcript.h : utils.h +Transcripts.h : utils.h my_assert.h Transcript.h +BowtieRefSeqPolicy.h : RefSeqPolicy.h +RefSeq.h : utils.h +Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h +SingleRead.h : Read.h +SingleReadQ.h : Read.h +PairedEndRead.h : Read.h SingleRead.h +PairedEndReadQ.h : Read.h SingleReadQ.h +PairedEndHit.h : SingleHit.h +HitContainer.h : GroupInfo.h +sam_utils.h : $(SAMHEADERS) Transcript.h Transcripts.h +SamParser.h : $(SAMHEADERS) sam_utils.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h +simul.h : $(BOOST)/boost/random.hpp +ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h +SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h +SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h +PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h +PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h +HitWrapper.h : HitContainer.h +BamWriter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h +sampling.h : $(BOOST)/boost/random.hpp +WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h +bc_aux.h : $(SAMHEADERS) +BamConverter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h bc_aux.h Transcript.h Transcripts.h +Buffer.h : my_assert.h +SamHeader.hpp : $(SAMHEADERS) + +# Compile EBSeq +ebseq : + cd EBSeq && $(MAKE) all + +# Install RSEM +install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) + $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) + $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools + $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools + $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) + $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm + +# Clean +clean : + rm -f *.o *~ $(PROGRAMS) + cd $(SAMTOOLS) && $(MAKE) clean-all + cd EBSeq && $(MAKE) clean diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb new file mode 100644 index 0000000000..0daeb572d1 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb @@ -0,0 +1,57 @@ +easyblock = 'MakeCp' + +name = 'RSEM' +version = '1.2.30' + +homepage = 'http://deweylab.github.io/RSEM/' +description = """RNA-Seq by Expectation-Maximization""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] + +#patches = ['RSEM-%(version)s_boost.patch'] + +dependencies = [ + ('ncurses', '6.0'), +] + +list_of_executables = [ + "rsem_perl_utils.pm", + "rsem-bam2readdepth", + "rsem-bam2wig", + "rsem-build-read-index", + "rsem-calculate-credibility-intervals", + "rsem-calculate-expression", + "rsem-control-fdr", + "rsem-extract-reference-transcripts", + "rsem-generate-data-matrix", + "rsem-generate-ngvector", + "rsem-gen-transcript-plots", + "rsem-get-unique", + "rsem-gff3-to-gtf", + "rsem-parse-alignments", + "rsem-plot-model", + "rsem-plot-transcript-wiggles", + "rsem-prepare-reference", + "rsem-preref", + "rsem-refseq-extract-primary-assembly", + "rsem-run-ebseq", + "rsem-run-em", + "rsem-run-gibbs", + "rsem-sam-validator", + "rsem-scan-for-paired-end-reads", + "rsem-simulate-reads", + "rsem-synthesis-reference-transcripts", + "rsem-tbam2gbam", +] + +files_to_copy = [(list_of_executables, "bin"), "WHAT_IS_NEW"] + +sanity_check_paths = { + 'files': ['''"bin/%s" % x for x in list_of_executables'''], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch new file mode 100644 index 0000000000..5782cb6a2d --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch @@ -0,0 +1,23 @@ +--- samtools-1.3/Makefile.orig 2016-05-13 11:39:28.000000000 +0200 ++++ samtools-1.3/Makefile 2016-05-13 11:42:52.000000000 +0200 +@@ -21,9 +21,9 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++#CC = gcc + CPPFLAGS = +-CFLAGS = -g -Wall -O2 ++#CFLAGS = -g -Wall -O2 + LDFLAGS = + LIBS = + +@@ -83,7 +83,7 @@ + # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally + ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz -ldl $(LIBS) ++ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch new file mode 100644 index 0000000000..206ac1fda2 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch @@ -0,0 +1,162 @@ +#Use EB provided libz and use EB provided CXX and CXXFLAGS +# January 11, 2016 by B. Hajgato (Vrije Ubiversiteit Brussel) +--- Makefile.orig 2016-01-08 02:23:01.000000000 +0100 ++++ Makefile 2016-01-18 12:02:56.406105229 +0100 +@@ -1,6 +1,6 @@ +-CC = g++ +-CFLAGS = -Wall -c -I. +-COFLAGS = -Wall -O3 -ffast-math -c -I. ++#CC = g++ ++#CFLAGS = -Wall -c -I. ++COFLAGS = ${CXXFLAGS} -Wall -c -I. + PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads + + .PHONY : all ebseq clean +@@ -8,6 +8,8 @@ + all : $(PROGRAMS) + + sam/libbam.a : ++ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i sam/Makefile ++ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i sam/bcftools/Makefile + cd sam ; ${MAKE} all + + Transcript.h : utils.h +@@ -15,10 +17,10 @@ + Transcripts.h : utils.h my_assert.h Transcript.h + + rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp +- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts ++ $(CXX) -Wall ${CXXFLAGS} extractRef.cpp -o rsem-extract-reference-transcripts + + rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp +- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts ++ $(CXX) -Wall ${CXXFLAGS} synthesisRef.cpp -o rsem-synthesis-reference-transcripts + + BowtieRefSeqPolicy.h : RefSeqPolicy.h + +@@ -28,10 +30,10 @@ + + + rsem-preref : preRef.o +- $(CC) preRef.o -o rsem-preref ++ $(CXX) preRef.o -o rsem-preref + + preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp +- $(CC) $(COFLAGS) preRef.cpp ++ $(CXX) $(COFLAGS) preRef.cpp + + + SingleRead.h : Read.h +@@ -52,14 +54,14 @@ + + + rsem-parse-alignments : parseIt.o sam/libbam.a +- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread ++ $(CXX) -o rsem-parse-alignments parseIt.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread + + parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp +- $(CC) -Wall -O2 -c -I. parseIt.cpp ++ $(CXX) $(COFLAGS) parseIt.cpp + + + rsem-build-read-index : utils.h buildReadIndex.cpp +- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index ++ $(CXX) ${CXXFLAGS} buildReadIndex.cpp -o rsem-build-read-index + + + simul.h : boost/random.hpp +@@ -87,57 +89,57 @@ + WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h + + rsem-run-em : EM.o sam/libbam.a +- $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread ++ $(CXX) -o rsem-run-em EM.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread + + EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp +- $(CC) $(COFLAGS) EM.cpp ++ $(CXX) $(COFLAGS) EM.cpp + + bc_aux.h : sam/bam.h + + BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h + + rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a +- $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall tbam2gbam.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp +- $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall bam2wig.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp +- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h +- $(CC) $(COFLAGS) wiggle.cpp ++ $(CXX) $(COFLAGS) wiggle.cpp + + rsem-simulate-reads : simulation.o +- $(CC) -o rsem-simulate-reads simulation.o ++ $(CXX) -o rsem-simulate-reads simulation.o + + simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp +- $(CC) $(COFLAGS) simulation.cpp ++ $(CXX) $(COFLAGS) simulation.cpp + + rsem-run-gibbs : Gibbs.o +- $(CC) -o rsem-run-gibbs Gibbs.o -lpthread ++ $(CXX) -o rsem-run-gibbs Gibbs.o -lpthread + + #some header files are omitted + Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp +- $(CC) $(COFLAGS) Gibbs.cpp ++ $(CXX) $(COFLAGS) Gibbs.cpp + + Buffer.h : my_assert.h + + rsem-calculate-credibility-intervals : calcCI.o +- $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread ++ $(CXX) -o rsem-calculate-credibility-intervals calcCI.o -lpthread + + #some header files are omitted + calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp +- $(CC) $(COFLAGS) calcCI.cpp ++ $(CXX) $(COFLAGS) calcCI.cpp + + rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a +- $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall getUnique.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a +- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall samValidator.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a +- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall scanForPairedEndReads.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + ebseq : + cd EBSeq ; ${MAKE} all +--- sam/Makefile.orig 2016-01-08 02:23:01.000000000 +0100 ++++ sam/Makefile 2016-01-18 12:08:43.769066188 +0100 +@@ -1,7 +1,7 @@ +-CC= gcc ++#CC= gcc + CFLAGS_EXTRA= + #CFLAGS_EXTRA= -L/usr/include/ncurses +-CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) ++#CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) + #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib + DFLAGS_EXTRA= + #DFLAGS_EXTRA= -Dexpl=exp -Dlogl=log +--- sam/bcftools/Makefile.orig 2016-01-08 02:23:01.000000000 +0100 ++++ sam/bcftools/Makefile 2016-01-18 12:09:10.076063429 +0100 +@@ -1,5 +1,5 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc ++#CC= gcc ++#CFLAGS= -g -Wall -O2 #-m64 #-arch ppc + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE + LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o + OMISC= .. \ No newline at end of file diff --git a/easybuild/easyconfigs/r/RSEM/sam/Makefile b/easybuild/easyconfigs/r/RSEM/sam/Makefile new file mode 100644 index 0000000000..c7e392d67c --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/Makefile @@ -0,0 +1,314 @@ +# Makefile for samtools, utilities for the Sequence Alignment/Map format. +# +# Copyright (C) 2008-2015 Genome Research Ltd. +# Portions copyright (C) 2010-2012 Broad Institute. +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. + +#CC = gcc +CPPFLAGS = +#CFLAGS = -g -Wall -O2 +LDFLAGS = +LIBS = + +DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE +LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o +AOBJS= bam_index.o bam_plcmd.o sam_view.o \ + bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o \ + bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ + bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o \ + cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ + faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \ + bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ + bam_quickcheck.o bam_addrprg.o + +prefix = /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin +datarootdir = $(prefix)/share +mandir = $(datarootdir)/man +man1dir = $(mandir)/man1 + +MKDIR_P = mkdir -p +INSTALL = install -p +INSTALL_PROGRAM = $(INSTALL) +INSTALL_DATA = $(INSTALL) -m 644 +INSTALL_DIR = $(MKDIR_P) -m 755 + + +PROGRAMS = samtools + +BUILT_MISC_PROGRAMS = \ + misc/ace2sam misc/maq2sam-long misc/maq2sam-short \ + misc/md5fa misc/md5sum-lite misc/wgsim + +MISC_PROGRAMS = \ + $(BUILT_MISC_PROGRAMS) \ + misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ + misc/interpolate_sam.pl misc/novo2sam.pl \ + misc/plot-bamstats misc/psl2sam.pl \ + misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \ + misc/soap2sam.pl \ + misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl + +BUILT_TEST_PROGRAMS = \ + test/merge/test_bam_translate \ + test/merge/test_rtrans_build \ + test/merge/test_trans_tbl_init \ + test/split/test_count_rg \ + test/split/test_expand_format_string \ + test/split/test_filter_header_rg \ + test/split/test_parse_args \ + test/vcf-miniview + +all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) + +# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally +ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) +ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) + +# Usually config.mk and config.h are generated by running configure +# or config.status, but if those aren't used create defaults here. + +config.mk: + @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ + +config.h: + echo '/* Basic config.h generated by Makefile */' > $@ + echo '#define HAVE_CURSES' >> $@ + echo '#define HAVE_CURSES_H' >> $@ + +include config.mk + + +PACKAGE_VERSION = 1.3 + +# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git +# description of the working tree: either a release tag with the same value +# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. +# $(shell), :=, etc are GNU Make-specific. If you don't have GNU Make, +# comment out this conditional. +ifneq "$(wildcard .git)" "" +PACKAGE_VERSION := $(shell git describe --always --dirty) + +# Force version.h to be remade if $(PACKAGE_VERSION) has changed. +version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) +endif + +# If you don't have GNU Make but are building from a Git repository, you may +# wish to replace this with a rule that always rebuilds version.h: +# version.h: force +# echo '#define SAMTOOLS_VERSION "`git describe --always --dirty`"' > $@ +version.h: + echo '#define SAMTOOLS_VERSION "$(PACKAGE_VERSION)"' > $@ + +print-version: + @echo $(PACKAGE_VERSION) + + +.SUFFIXES: .c .o + +.c.o: + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< + + +lib:libbam.a + +libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +samtools: $(AOBJS) libbam.a $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) + +bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) +bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h +bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) +bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) +sam_h = sam.h $(htslib_sam_h) $(bam_h) +sam_opts_h = sam_opts.h $(htslib_hts_h) +sample_h = sample.h $(htslib_kstring_h) + +bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h +bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h +bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) +bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) +bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) +bam_aux.o: bam_aux.c $(bam_h) +bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) +bam_color.o: bam_color.c $(bam_h) +bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) +bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h +bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) +bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) +bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) +bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) +bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) +bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h +bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) +bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) +bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) +bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) +bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h +bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) +bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) +bam_tview_html.o: bam_tview_html.c $(bam_tview_h) +bam_flags.o: bam_flags.c $(htslib_sam_h) +bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) +bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h +bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) +bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) +cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) +dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) +errmod.o: errmod.c errmod.h $(htslib_ksort_h) +kprobaln.o: kprobaln.c kprobaln.h +padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) +phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) +sam.o: sam.c $(htslib_faidx_h) $(sam_h) +sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) +sam_opts.o: sam_opts.c $(sam_opts_h) +sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) +sample.o: sample.c $(sample_h) $(htslib_khash_h) +stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) +stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) + + +# test programs + +# For tests that might use it, set $REF_PATH explicitly to use only reference +# areas within the test suite (or set it to ':' to use no reference areas). +# (regression.sh sets $REF_PATH to a subdirectory itself.) +check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) + REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_rtrans_build + test/merge/test_trans_tbl_init + cd test/mpileup && ./regression.sh mpileup.reg + cd test/mpileup && ./regression.sh depth.reg + test/split/test_count_rg + test/split/test_expand_format_string + test/split/test_filter_header_rg + test/split/test_parse_args + + +test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) + +test_test_h = test/test.h $(htslib_sam_h) + +test/merge/test_bam_translate.o: test/merge/test_bam_translate.c bam_sort.o $(test_test_h) +test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c bam_sort.o +test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c bam_sort.o +test/split/test_count_rg.o: test/split/test_count_rg.c bam_split.o $(test_test_h) +test/split/test_expand_format_string.o: test/split/test_expand_format_string.c bam_split.o $(test_test_h) +test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c bam_split.o $(test_test_h) +test/split/test_parse_args.o: test/split/test_parse_args.c bam_split.o $(test_test_h) +test/test.o: test/test.c $(htslib_sam_h) $(test_test_h) +test/vcf-miniview.o: test/vcf-miniview.c $(htslib_vcf_h) + + +# misc programs + +misc/ace2sam: misc/ace2sam.o + $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) + +misc/maq2sam-short: misc/maq2sam-short.o + $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) + +misc/maq2sam-long: misc/maq2sam-long.o + $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) + +misc/md5fa: misc/md5fa.o $(HTSLIB) + $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) + +misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) + $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) + +misc/wgsim: misc/wgsim.o + $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) + +misc/ace2sam.o: misc/ace2sam.c $(htslib_kstring_h) $(htslib_kseq_h) +misc/md5fa.o: misc/md5fa.c $(htslib_kseq_h) $(htslib_hts_h) +misc/md5sum-lite.o: misc/md5sum-lite.c $(htslib_hts_h) +misc/wgsim.o: misc/wgsim.c $(htslib_kseq_h) + +misc/maq2sam-short.o: misc/maq2sam.c + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c + +misc/maq2sam-long.o: misc/maq2sam.c + $(CC) $(CFLAGS) -DMAQ_LONGREADS $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c + + +install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) + $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) + $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) + + +testclean: + -rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* + -cd test/dat && rm -f test_input_*.bam.bai + -cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam* + +mostlyclean: testclean + -rm -f *.o misc/*.o test/*.o test/*/*.o version.h + +clean: mostlyclean + -rm -f $(PROGRAMS) libbam.a $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) + +distclean: clean + -rm -f config.cache config.h config.log config.mk config.status + -rm -f TAGS + +clean-all: clean clean-htslib + + +tags: + ctags -f TAGS *.[ch] misc/*.[ch] + + +force: + + +.PHONY: all check clean clean-all distclean force install +.PHONY: lib mostlyclean print-version tags test testclean diff --git a/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig b/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig new file mode 100644 index 0000000000..525288c2c8 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig @@ -0,0 +1,314 @@ +# Makefile for samtools, utilities for the Sequence Alignment/Map format. +# +# Copyright (C) 2008-2015 Genome Research Ltd. +# Portions copyright (C) 2010-2012 Broad Institute. +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. + +CC = gcc +CPPFLAGS = +CFLAGS = -g -Wall -O2 +LDFLAGS = +LIBS = + +DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE +LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o +AOBJS= bam_index.o bam_plcmd.o sam_view.o \ + bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o \ + bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ + bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o \ + cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ + faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \ + bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ + bam_quickcheck.o bam_addrprg.o + +prefix = /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin +datarootdir = $(prefix)/share +mandir = $(datarootdir)/man +man1dir = $(mandir)/man1 + +MKDIR_P = mkdir -p +INSTALL = install -p +INSTALL_PROGRAM = $(INSTALL) +INSTALL_DATA = $(INSTALL) -m 644 +INSTALL_DIR = $(MKDIR_P) -m 755 + + +PROGRAMS = samtools + +BUILT_MISC_PROGRAMS = \ + misc/ace2sam misc/maq2sam-long misc/maq2sam-short \ + misc/md5fa misc/md5sum-lite misc/wgsim + +MISC_PROGRAMS = \ + $(BUILT_MISC_PROGRAMS) \ + misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ + misc/interpolate_sam.pl misc/novo2sam.pl \ + misc/plot-bamstats misc/psl2sam.pl \ + misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \ + misc/soap2sam.pl \ + misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl + +BUILT_TEST_PROGRAMS = \ + test/merge/test_bam_translate \ + test/merge/test_rtrans_build \ + test/merge/test_trans_tbl_init \ + test/split/test_count_rg \ + test/split/test_expand_format_string \ + test/split/test_filter_header_rg \ + test/split/test_parse_args \ + test/vcf-miniview + +all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) + +# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally +ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) +ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +ALL_LIBS = -lz -ldl $(LIBS) + +# Usually config.mk and config.h are generated by running configure +# or config.status, but if those aren't used create defaults here. + +config.mk: + @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ + +config.h: + echo '/* Basic config.h generated by Makefile */' > $@ + echo '#define HAVE_CURSES' >> $@ + echo '#define HAVE_CURSES_H' >> $@ + +include config.mk + + +PACKAGE_VERSION = 1.3 + +# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git +# description of the working tree: either a release tag with the same value +# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. +# $(shell), :=, etc are GNU Make-specific. If you don't have GNU Make, +# comment out this conditional. +ifneq "$(wildcard .git)" "" +PACKAGE_VERSION := $(shell git describe --always --dirty) + +# Force version.h to be remade if $(PACKAGE_VERSION) has changed. +version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) +endif + +# If you don't have GNU Make but are building from a Git repository, you may +# wish to replace this with a rule that always rebuilds version.h: +# version.h: force +# echo '#define SAMTOOLS_VERSION "`git describe --always --dirty`"' > $@ +version.h: + echo '#define SAMTOOLS_VERSION "$(PACKAGE_VERSION)"' > $@ + +print-version: + @echo $(PACKAGE_VERSION) + + +.SUFFIXES: .c .o + +.c.o: + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< + + +lib:libbam.a + +libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +samtools: $(AOBJS) libbam.a $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) + +bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) +bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h +bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) +bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) +sam_h = sam.h $(htslib_sam_h) $(bam_h) +sam_opts_h = sam_opts.h $(htslib_hts_h) +sample_h = sample.h $(htslib_kstring_h) + +bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h +bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h +bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) +bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) +bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) +bam_aux.o: bam_aux.c $(bam_h) +bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) +bam_color.o: bam_color.c $(bam_h) +bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) +bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h +bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) +bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) +bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) +bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) +bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) +bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h +bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) +bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) +bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) +bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) +bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h +bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) +bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) +bam_tview_html.o: bam_tview_html.c $(bam_tview_h) +bam_flags.o: bam_flags.c $(htslib_sam_h) +bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) +bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h +bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) +bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) +cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) +dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) +errmod.o: errmod.c errmod.h $(htslib_ksort_h) +kprobaln.o: kprobaln.c kprobaln.h +padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) +phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) +sam.o: sam.c $(htslib_faidx_h) $(sam_h) +sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) +sam_opts.o: sam_opts.c $(sam_opts_h) +sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) +sample.o: sample.c $(sample_h) $(htslib_khash_h) +stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) +stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) + + +# test programs + +# For tests that might use it, set $REF_PATH explicitly to use only reference +# areas within the test suite (or set it to ':' to use no reference areas). +# (regression.sh sets $REF_PATH to a subdirectory itself.) +check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) + REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_rtrans_build + test/merge/test_trans_tbl_init + cd test/mpileup && ./regression.sh mpileup.reg + cd test/mpileup && ./regression.sh depth.reg + test/split/test_count_rg + test/split/test_expand_format_string + test/split/test_filter_header_rg + test/split/test_parse_args + + +test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) + +test_test_h = test/test.h $(htslib_sam_h) + +test/merge/test_bam_translate.o: test/merge/test_bam_translate.c bam_sort.o $(test_test_h) +test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c bam_sort.o +test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c bam_sort.o +test/split/test_count_rg.o: test/split/test_count_rg.c bam_split.o $(test_test_h) +test/split/test_expand_format_string.o: test/split/test_expand_format_string.c bam_split.o $(test_test_h) +test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c bam_split.o $(test_test_h) +test/split/test_parse_args.o: test/split/test_parse_args.c bam_split.o $(test_test_h) +test/test.o: test/test.c $(htslib_sam_h) $(test_test_h) +test/vcf-miniview.o: test/vcf-miniview.c $(htslib_vcf_h) + + +# misc programs + +misc/ace2sam: misc/ace2sam.o + $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) + +misc/maq2sam-short: misc/maq2sam-short.o + $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) + +misc/maq2sam-long: misc/maq2sam-long.o + $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) + +misc/md5fa: misc/md5fa.o $(HTSLIB) + $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) + +misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) + $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) + +misc/wgsim: misc/wgsim.o + $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) + +misc/ace2sam.o: misc/ace2sam.c $(htslib_kstring_h) $(htslib_kseq_h) +misc/md5fa.o: misc/md5fa.c $(htslib_kseq_h) $(htslib_hts_h) +misc/md5sum-lite.o: misc/md5sum-lite.c $(htslib_hts_h) +misc/wgsim.o: misc/wgsim.c $(htslib_kseq_h) + +misc/maq2sam-short.o: misc/maq2sam.c + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c + +misc/maq2sam-long.o: misc/maq2sam.c + $(CC) $(CFLAGS) -DMAQ_LONGREADS $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c + + +install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) + $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) + $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) + + +testclean: + -rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* + -cd test/dat && rm -f test_input_*.bam.bai + -cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam* + +mostlyclean: testclean + -rm -f *.o misc/*.o test/*.o test/*/*.o version.h + +clean: mostlyclean + -rm -f $(PROGRAMS) libbam.a $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) + +distclean: clean + -rm -f config.cache config.h config.log config.mk config.status + -rm -f TAGS + +clean-all: clean clean-htslib + + +tags: + ctags -f TAGS *.[ch] misc/*.[ch] + + +force: + + +.PHONY: all check clean clean-all distclean force install +.PHONY: lib mostlyclean print-version tags test testclean diff --git a/easybuild/easyconfigs/r/RSEM/sam/diff b/easybuild/easyconfigs/r/RSEM/sam/diff new file mode 100644 index 0000000000..2469cafcc9 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/diff @@ -0,0 +1,23 @@ +--- Makefile.orig 2016-05-13 11:39:28.000000000 +0200 ++++ Makefile 2016-05-13 12:29:50.000000000 +0200 +@@ -21,9 +21,9 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++#CC = gcc + CPPFLAGS = +-CFLAGS = -g -Wall -O2 ++#CFLAGS = -g -Wall -O2 + LDFLAGS = + LIBS = + +@@ -83,7 +83,7 @@ + # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally + ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz -ldl $(LIBS) ++ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile new file mode 100644 index 0000000000..00c103599b --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile @@ -0,0 +1,426 @@ +# Makefile for htslib, a C library for high-throughput sequencing data formats. +# +# Copyright (C) 2013-2015 Genome Research Ltd. +# +# Author: John Marshall +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. + +#CC = gcc +AR = ar +RANLIB = ranlib + +CPPFLAGS = +# TODO: probably update cram code to make it compile cleanly with -Wc++-compat +#CFLAGS = -g -Wall -O2 +EXTRA_CFLAGS_PIC = -fpic +LDFLAGS = +LIBS = + +# For now these don't work too well as samtools also needs to know to +# add -lbz2 and -llzma if linking against the static libhts.a library. +# TODO This needs configury and adding to htslib.pc.in. +# +# # Bzip2 support; optionally used by CRAM. +# HAVE_LIBBZ2 := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes) +# ifeq "$(HAVE_LIBBZ2)" "yes" +# CPPFLAGS += -DHAVE_LIBBZ2 +# LIBS += -lbz2 +# endif +# +# # Lzma support; optionally used by CRAM. +# HAVE_LIBLZMA := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes) +# ifeq "$(HAVE_LIBLZMA)" "yes" +# CPPFLAGS += -DHAVE_LIBLZMA +# LIBS += -llzma +# endif + +prefix = /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin +includedir = $(prefix)/include +libdir = $(exec_prefix)/lib +libexecdir = $(exec_prefix)/libexec +datarootdir = $(prefix)/share +mandir = $(datarootdir)/man +man1dir = $(mandir)/man1 +man5dir = $(mandir)/man5 +pkgconfigdir= $(libdir)/pkgconfig + +MKDIR_P = mkdir -p +INSTALL = install -p +INSTALL_PROGRAM = $(INSTALL) +INSTALL_DATA = $(INSTALL) -m 644 +INSTALL_DIR = $(MKDIR_P) -m 755 + +# Set by config.mk if plugins are enabled +plugindir = + +BUILT_PROGRAMS = \ + bgzip \ + htsfile \ + tabix + +BUILT_TEST_PROGRAMS = \ + test/fieldarith \ + test/hfile \ + test/sam \ + test/test-regidx \ + test/test_view \ + test/test-vcf-api \ + test/test-vcf-sweep + +all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) + +HTSPREFIX = +include htslib_vars.mk + + +PACKAGE_VERSION = 1.3 +LIBHTS_SOVERSION = 1 + + +# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string +# even if this is a dirty or untagged Git working tree. +NUMERIC_VERSION = $(PACKAGE_VERSION) + +# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git +# description of the working tree: either a release tag with the same value +# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. +# Much of this is also GNU Make-specific. If you don't have GNU Make and/or +# are not building from a Git repository, comment out this conditional. +ifneq "$(wildcard .git)" "" +original_version := $(PACKAGE_VERSION) +PACKAGE_VERSION := $(shell git describe --always --dirty) + +# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag +# with a numeric name, revert $(NUMERIC_VERSION) to the original version number +# written above, but with the patchlevel field bumped to 255. +ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "." +empty := +NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255) +endif + +# Force version.h to be remade if $(PACKAGE_VERSION) has changed. +version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) +endif + +version.h: + echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@ + +print-version: + @echo $(PACKAGE_VERSION) + + +.SUFFIXES: .bundle .c .o .pico .so + +.c.o: + $(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $< + +.c.pico: + $(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< + + +LIBHTS_OBJS = \ + kfunc.o \ + knetfile.o \ + kstring.o \ + bgzf.o \ + faidx.o \ + hfile.o \ + hfile_net.o \ + hts.o \ + md5.o \ + regidx.o \ + sam.o \ + synced_bcf_reader.o \ + vcf_sweep.o \ + tbx.o \ + vcf.o \ + vcfutils.o \ + cram/cram_codecs.o \ + cram/cram_decode.o \ + cram/cram_encode.o \ + cram/cram_external.o \ + cram/cram_index.o \ + cram/cram_io.o \ + cram/cram_samtools.o \ + cram/cram_stats.o \ + cram/files.o \ + cram/mFILE.o \ + cram/open_trace_file.o \ + cram/pooled_alloc.o \ + cram/rANS_static.o \ + cram/sam_header.o \ + cram/string_alloc.o \ + cram/thread_pool.o \ + cram/vlen.o \ + cram/zfio.o + +PLUGIN_OBJS = + +cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h) +cram_io_h = cram/cram_io.h $(cram_misc_h) +cram_misc_h = cram/misc.h cram/os.h +cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) +cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h) +cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h) +cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h +hfile_internal_h = hfile_internal.h $(htslib_hfile_h) +hts_internal_h = hts_internal.h $(htslib_hts_h) + + +# To be effective, config.mk needs to appear after most Makefile variables are +# set but before most rules appear, so that it can both use previously-set +# variables in its own rules' prerequisites and also update variables for use +# in later rules' prerequisites. + +# If your make doesn't accept -include, change this to 'include' if you are +# using the configure script or just comment the line out if you are not. +-include config.mk + +# Usually config.h is generated by running configure or config.status, +# but if those aren't used create a default config.h here. +config.h: + echo '/* Empty config.h generated by Makefile */' > $@ + + +lib-static: libhts.a + +# $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have +# GNU Make, comment out the parts of this conditional that don't apply. +PLATFORM := $(shell uname -s) +ifeq "$(PLATFORM)" "Darwin" +SHLIB_FLAVOUR = dylib +lib-shared: libhts.dylib +BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle) +else +SHLIB_FLAVOUR = so +lib-shared: libhts.so +BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so) +endif + +plugins: $(BUILT_PLUGINS) + + +libhts.a: $(LIBHTS_OBJS) + @-rm -f $@ + $(AR) -rc $@ $(LIBHTS_OBJS) + -$(RANLIB) $@ + + +# The target here is libhts.so, as that is the built file that other rules +# depend upon and that is used when -lhts appears in other program's recipes. +# As a byproduct invisible to make, libhts.so.NN is also created, as it is the +# file used at runtime (when $LD_LIBRARY_PATH includes the build directory). + +libhts.so: $(LIBHTS_OBJS:.o=.pico) + $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS) + ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) + +# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs +# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH +# includes this project's build directory). + +libhts.dylib: $(LIBHTS_OBJS) + $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS) + ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib + + +.pico.so: + $(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS) + +.o.bundle: + $(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS) + + +bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h) +kstring.o kstring.pico: kstring.c $(htslib_kstring_h) +knetfile.o knetfile.pico: knetfile.c $(htslib_knetfile_h) +hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h) +hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) +hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) +hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h) +hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h) +vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) +sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) +tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h) +faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) +synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) +vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h) +vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h) +kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h) +regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) +md5.o md5.pico: md5.c config.h $(htslib_hts_h) +plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h) + +cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h) +cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) +cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) +cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h) +cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h) +cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) +cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h) +cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h +cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h) +cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h +cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h) +cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h +cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h +cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h +cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h +cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h +cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h +cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h + + +bgzip: bgzip.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS) + +htsfile: htsfile.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS) + +tabix: tabix.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS) + +bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) +htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) +tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) + + +# For tests that might use it, set $REF_PATH explicitly to use only reference +# areas within the test suite (or set it to ':' to use no reference areas). +check test: htsfile $(BUILT_TEST_PROGRAMS) + test/fieldarith test/fieldarith.sam + test/hfile + test/sam test/ce.fa test/faidx.fa + test/test-regidx + cd test && REF_PATH=: ./test_view.pl + cd test && REF_PATH=: ./test.pl + +test/fieldarith: test/fieldarith.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS) + +test/hfile: test/hfile.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS) + +test/sam: test/sam.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS) + +test/test-regidx: test/test-regidx.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS) + +test/test_view: test/test_view.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS) + +test/test-vcf-api: test/test-vcf-api.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS) + +test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS) + +test/fieldarith.o: test/fieldarith.c $(htslib_sam_h) +test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h) +test/sam.o: test/sam.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) +test/test-regidx.o: test/test-regidx.c $(htslib_regidx_h) +test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h) +test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h) +test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h) + + +install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig + $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir) + if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi + $(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib + $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a + $(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir) + $(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir) + +installdirs: + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir) + if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi + +# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, +# with symlinks libhts.so (used via -lhts during linking of client programs) +# and libhts.so.NN (used by client executables at runtime). + +install-so: libhts.so installdirs + $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) + ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so + ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) + +install-dylib: libhts.dylib installdirs + $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib + ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib + ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib + +# Substitute these pseudo-autoconf variables only at install time +# so that "make install prefix=/prefix/path" etc continue to work. +install-pkgconfig: installdirs + sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc + chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc + +# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides +# flags for building against the uninstalled library in this build directory. +htslib-uninstalled.pc: htslib.pc.in + sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@ + + +testclean: + -rm -f test/*.tmp test/*.tmp.* + +mostlyclean: testclean + -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h + +clean: mostlyclean clean-$(SHLIB_FLAVOUR) + -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) + +distclean maintainer-clean: clean + -rm -f config.cache config.h config.log config.mk config.status + -rm -f TAGS *-uninstalled.pc + +clean-so: + -rm -f libhts.so libhts.so.* + +clean-dylib: + -rm -f libhts.dylib libhts.*.dylib + + +tags TAGS: + ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h + +# We recommend libhts-using programs be built against a separate htslib +# installation. However if you feel that you must bundle htslib source +# code with your program, this hook enables Automake-style "make dist" +# for this subdirectory. If you do bundle an htslib snapshot, please +# add identifying information to $(PACKAGE_VERSION) as appropriate. +# (The wildcards attempt to omit non-exported files (.git*, README.md, +# etc) and other detritus that might be in the top-level directory.) +distdir: + tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x) + +cd $(distdir) && $(MAKE) distclean + +force: + + +.PHONY: all check clean distclean distdir force +.PHONY: install install-pkgconfig installdirs lib-shared lib-static +.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean +.PHONY: clean-so install-so +.PHONY: clean-dylib install-dylib diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig new file mode 100644 index 0000000000..be2405e71c --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig @@ -0,0 +1,426 @@ +# Makefile for htslib, a C library for high-throughput sequencing data formats. +# +# Copyright (C) 2013-2015 Genome Research Ltd. +# +# Author: John Marshall +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. + +CC = gcc +AR = ar +RANLIB = ranlib + +CPPFLAGS = +# TODO: probably update cram code to make it compile cleanly with -Wc++-compat +CFLAGS = -g -Wall -O2 +EXTRA_CFLAGS_PIC = -fpic +LDFLAGS = +LIBS = + +# For now these don't work too well as samtools also needs to know to +# add -lbz2 and -llzma if linking against the static libhts.a library. +# TODO This needs configury and adding to htslib.pc.in. +# +# # Bzip2 support; optionally used by CRAM. +# HAVE_LIBBZ2 := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes) +# ifeq "$(HAVE_LIBBZ2)" "yes" +# CPPFLAGS += -DHAVE_LIBBZ2 +# LIBS += -lbz2 +# endif +# +# # Lzma support; optionally used by CRAM. +# HAVE_LIBLZMA := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes) +# ifeq "$(HAVE_LIBLZMA)" "yes" +# CPPFLAGS += -DHAVE_LIBLZMA +# LIBS += -llzma +# endif + +prefix = /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin +includedir = $(prefix)/include +libdir = $(exec_prefix)/lib +libexecdir = $(exec_prefix)/libexec +datarootdir = $(prefix)/share +mandir = $(datarootdir)/man +man1dir = $(mandir)/man1 +man5dir = $(mandir)/man5 +pkgconfigdir= $(libdir)/pkgconfig + +MKDIR_P = mkdir -p +INSTALL = install -p +INSTALL_PROGRAM = $(INSTALL) +INSTALL_DATA = $(INSTALL) -m 644 +INSTALL_DIR = $(MKDIR_P) -m 755 + +# Set by config.mk if plugins are enabled +plugindir = + +BUILT_PROGRAMS = \ + bgzip \ + htsfile \ + tabix + +BUILT_TEST_PROGRAMS = \ + test/fieldarith \ + test/hfile \ + test/sam \ + test/test-regidx \ + test/test_view \ + test/test-vcf-api \ + test/test-vcf-sweep + +all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) + +HTSPREFIX = +include htslib_vars.mk + + +PACKAGE_VERSION = 1.3 +LIBHTS_SOVERSION = 1 + + +# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string +# even if this is a dirty or untagged Git working tree. +NUMERIC_VERSION = $(PACKAGE_VERSION) + +# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git +# description of the working tree: either a release tag with the same value +# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. +# Much of this is also GNU Make-specific. If you don't have GNU Make and/or +# are not building from a Git repository, comment out this conditional. +ifneq "$(wildcard .git)" "" +original_version := $(PACKAGE_VERSION) +PACKAGE_VERSION := $(shell git describe --always --dirty) + +# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag +# with a numeric name, revert $(NUMERIC_VERSION) to the original version number +# written above, but with the patchlevel field bumped to 255. +ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "." +empty := +NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255) +endif + +# Force version.h to be remade if $(PACKAGE_VERSION) has changed. +version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) +endif + +version.h: + echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@ + +print-version: + @echo $(PACKAGE_VERSION) + + +.SUFFIXES: .bundle .c .o .pico .so + +.c.o: + $(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $< + +.c.pico: + $(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< + + +LIBHTS_OBJS = \ + kfunc.o \ + knetfile.o \ + kstring.o \ + bgzf.o \ + faidx.o \ + hfile.o \ + hfile_net.o \ + hts.o \ + md5.o \ + regidx.o \ + sam.o \ + synced_bcf_reader.o \ + vcf_sweep.o \ + tbx.o \ + vcf.o \ + vcfutils.o \ + cram/cram_codecs.o \ + cram/cram_decode.o \ + cram/cram_encode.o \ + cram/cram_external.o \ + cram/cram_index.o \ + cram/cram_io.o \ + cram/cram_samtools.o \ + cram/cram_stats.o \ + cram/files.o \ + cram/mFILE.o \ + cram/open_trace_file.o \ + cram/pooled_alloc.o \ + cram/rANS_static.o \ + cram/sam_header.o \ + cram/string_alloc.o \ + cram/thread_pool.o \ + cram/vlen.o \ + cram/zfio.o + +PLUGIN_OBJS = + +cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h) +cram_io_h = cram/cram_io.h $(cram_misc_h) +cram_misc_h = cram/misc.h cram/os.h +cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) +cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h) +cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h) +cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h +hfile_internal_h = hfile_internal.h $(htslib_hfile_h) +hts_internal_h = hts_internal.h $(htslib_hts_h) + + +# To be effective, config.mk needs to appear after most Makefile variables are +# set but before most rules appear, so that it can both use previously-set +# variables in its own rules' prerequisites and also update variables for use +# in later rules' prerequisites. + +# If your make doesn't accept -include, change this to 'include' if you are +# using the configure script or just comment the line out if you are not. +-include config.mk + +# Usually config.h is generated by running configure or config.status, +# but if those aren't used create a default config.h here. +config.h: + echo '/* Empty config.h generated by Makefile */' > $@ + + +lib-static: libhts.a + +# $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have +# GNU Make, comment out the parts of this conditional that don't apply. +PLATFORM := $(shell uname -s) +ifeq "$(PLATFORM)" "Darwin" +SHLIB_FLAVOUR = dylib +lib-shared: libhts.dylib +BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle) +else +SHLIB_FLAVOUR = so +lib-shared: libhts.so +BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so) +endif + +plugins: $(BUILT_PLUGINS) + + +libhts.a: $(LIBHTS_OBJS) + @-rm -f $@ + $(AR) -rc $@ $(LIBHTS_OBJS) + -$(RANLIB) $@ + + +# The target here is libhts.so, as that is the built file that other rules +# depend upon and that is used when -lhts appears in other program's recipes. +# As a byproduct invisible to make, libhts.so.NN is also created, as it is the +# file used at runtime (when $LD_LIBRARY_PATH includes the build directory). + +libhts.so: $(LIBHTS_OBJS:.o=.pico) + $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS) + ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) + +# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs +# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH +# includes this project's build directory). + +libhts.dylib: $(LIBHTS_OBJS) + $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS) + ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib + + +.pico.so: + $(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS) + +.o.bundle: + $(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS) + + +bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h) +kstring.o kstring.pico: kstring.c $(htslib_kstring_h) +knetfile.o knetfile.pico: knetfile.c $(htslib_knetfile_h) +hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h) +hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) +hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) +hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h) +hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h) +vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) +sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) +tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h) +faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) +synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) +vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h) +vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h) +kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h) +regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) +md5.o md5.pico: md5.c config.h $(htslib_hts_h) +plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h) + +cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h) +cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) +cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) +cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h) +cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h) +cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) +cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h) +cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h +cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h) +cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h +cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h) +cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h +cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h +cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h +cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h +cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h +cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h +cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h + + +bgzip: bgzip.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS) + +htsfile: htsfile.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS) + +tabix: tabix.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS) + +bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) +htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) +tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) + + +# For tests that might use it, set $REF_PATH explicitly to use only reference +# areas within the test suite (or set it to ':' to use no reference areas). +check test: htsfile $(BUILT_TEST_PROGRAMS) + test/fieldarith test/fieldarith.sam + test/hfile + test/sam test/ce.fa test/faidx.fa + test/test-regidx + cd test && REF_PATH=: ./test_view.pl + cd test && REF_PATH=: ./test.pl + +test/fieldarith: test/fieldarith.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS) + +test/hfile: test/hfile.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS) + +test/sam: test/sam.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS) + +test/test-regidx: test/test-regidx.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS) + +test/test_view: test/test_view.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS) + +test/test-vcf-api: test/test-vcf-api.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS) + +test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS) + +test/fieldarith.o: test/fieldarith.c $(htslib_sam_h) +test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h) +test/sam.o: test/sam.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) +test/test-regidx.o: test/test-regidx.c $(htslib_regidx_h) +test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h) +test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h) +test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h) + + +install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig + $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir) + if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi + $(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib + $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a + $(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir) + $(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir) + +installdirs: + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir) + if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi + +# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, +# with symlinks libhts.so (used via -lhts during linking of client programs) +# and libhts.so.NN (used by client executables at runtime). + +install-so: libhts.so installdirs + $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) + ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so + ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) + +install-dylib: libhts.dylib installdirs + $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib + ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib + ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib + +# Substitute these pseudo-autoconf variables only at install time +# so that "make install prefix=/prefix/path" etc continue to work. +install-pkgconfig: installdirs + sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc + chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc + +# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides +# flags for building against the uninstalled library in this build directory. +htslib-uninstalled.pc: htslib.pc.in + sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@ + + +testclean: + -rm -f test/*.tmp test/*.tmp.* + +mostlyclean: testclean + -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h + +clean: mostlyclean clean-$(SHLIB_FLAVOUR) + -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) + +distclean maintainer-clean: clean + -rm -f config.cache config.h config.log config.mk config.status + -rm -f TAGS *-uninstalled.pc + +clean-so: + -rm -f libhts.so libhts.so.* + +clean-dylib: + -rm -f libhts.dylib libhts.*.dylib + + +tags TAGS: + ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h + +# We recommend libhts-using programs be built against a separate htslib +# installation. However if you feel that you must bundle htslib source +# code with your program, this hook enables Automake-style "make dist" +# for this subdirectory. If you do bundle an htslib snapshot, please +# add identifying information to $(PACKAGE_VERSION) as appropriate. +# (The wildcards attempt to omit non-exported files (.git*, README.md, +# etc) and other detritus that might be in the top-level directory.) +distdir: + tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x) + +cd $(distdir) && $(MAKE) distclean + +force: + + +.PHONY: all check clean distclean distdir force +.PHONY: install install-pkgconfig installdirs lib-shared lib-static +.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean +.PHONY: clean-so install-so +.PHONY: clean-dylib install-dylib diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/diff b/easybuild/easyconfigs/r/RSEM/sam/hts/diff new file mode 100644 index 0000000000..97af9b3e44 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/hts/diff @@ -0,0 +1,18 @@ +--- Makefile.orig 2016-05-13 12:08:45.000000000 +0200 ++++ Makefile 2016-05-13 12:10:21.000000000 +0200 +@@ -22,13 +22,13 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++#CC = gcc + AR = ar + RANLIB = ranlib + + CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat +-CFLAGS = -g -Wall -O2 ++#CFLAGS = -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic + LDFLAGS = + LIBS = -- GitLab From 703061c2172a007d4150587ff2caaa4d4d315237 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 14:11:34 +0200 Subject: [PATCH 1666/2133] add easyconfig tvb-data-20160209-intel-2016a-Python-2.7.11.eb, add easyconfig tvb-framework-20160329-intel-2016a-Python-2.7.11.eb, add easyconfig tvb-library-20160416-intel-2016a-Python-2.7.11.eb, add easyconfig psutil-4.1.0-intel-2016a-Python-2.7.11.eb --- .../psutil-4.1.0-intel-2016a-Python-2.7.11.eb | 25 +++++++++++ ...data-20160209-intel-2016a-Python-2.7.11.eb | 40 +++++++++++++++++ ...work-20160329-intel-2016a-Python-2.7.11.eb | 43 +++++++++++++++++++ ...rary-20160416-intel-2016a-Python-2.7.11.eb | 40 +++++++++++++++++ 4 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/p/psutil/psutil-4.1.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/tvb-data/tvb-data-20160209-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/tvb-library/tvb-library-20160416-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/psutil/psutil-4.1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/psutil/psutil-4.1.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..add4ca70ed --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-4.1.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'psutil' +version = '4.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/psutil' +description = """psutil is a cross-platform library for retrieving information onrunning processes and + system utilization (CPU, memory, disks, network)in Python.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tvb-data/tvb-data-20160209-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-data/tvb-data-20160209-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..313af45870 --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-data/tvb-data-20160209-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'tvb-data' +version = '20160209' +commit = '8f46bd7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + Various demonstration data for use with TVB.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-data/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('Python', '2.7.11'), # provides numpy, Cython + ('networkx', '1.11', versionsuffix), + ('numexpr', '2.5.2', versionsuffix), + ('gdist', '1.0.3', versionsuffix), + ('NiBabel', '2.0.2', versionsuffix), + ('scikit-learn', '0.17.1', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix), + ('lxml', '3.5.0', versionsuffix), + ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.16'), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb_data'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1a013dadc1 --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'tvb-framework' +version = '20160329' +commit = '7e6c51a977136a7ca44988f24914bff700168013' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + TVB Scientific Library is the most important scientific contribution of TVB Project.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-framework/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = ['tvb-framework-%(version)s_no-fixed-matplotlib.patch'] + +dependencies = [ + ('Python', '2.7.11'), # provides numpy, Cython + ('networkx', '1.11', versionsuffix), + ('numexpr', '2.5.2', versionsuffix), + ('gdist', '1.0.3', versionsuffix), + ('NiBabel', '2.0.2', versionsuffix), + ('scikit-learn', '0.17.1', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix), + ('lxml', '3.5.0', versionsuffix), + ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.16'), + ('psutil', '4.1.0', versionsuffix), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb.core'} + +sanity_check_paths = { + 'files': ['tvb-framework-%s/tvb/config/logger/logger_config.conf' % commit], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tvb-library/tvb-library-20160416-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-library/tvb-library-20160416-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f3c72162a8 --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-library/tvb-library-20160416-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'tvb-library' +version = '20160416' +commit = '20172bc' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + TVB Scientific Library is the most important scientific contribution of TVB Project.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-library/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('Python', '2.7.11'), # provides numpy, Cython + ('networkx', '1.11', versionsuffix), + ('numexpr', '2.5.2', versionsuffix), + ('gdist', '1.0.3', versionsuffix), + ('NiBabel', '2.0.2', versionsuffix), + ('scikit-learn', '0.17.1', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix), + ('lxml', '3.5.0', versionsuffix), + ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.16'), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb.simulator'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 509a51519bd4e1bcd63fdca1a7e20aff7606391e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 14:13:02 +0200 Subject: [PATCH 1667/2133] add patch file for tvb-framework --- ...vb-framework-20160329_no-fixed-matplotlib.patch | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329_no-fixed-matplotlib.patch diff --git a/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329_no-fixed-matplotlib.patch b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329_no-fixed-matplotlib.patch new file mode 100644 index 0000000000..8983c5f8ea --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329_no-fixed-matplotlib.patch @@ -0,0 +1,14 @@ +--- setup.py.orig 2016-03-29 08:34:20.000000000 +0200 ++++ setup.py 2016-04-28 15:27:35.764121169 +0200 +@@ -47,9 +47,9 @@ + TVB_TEAM += "Stuart Knock, Marmaduke Woodman, Paula Sansz Leon, " + + TVB_INSTALL_REQUIREMENTS = ["apscheduler", "beautifulsoup", "cherrypy", "genshi", "cfflib", "formencode==1.3.0a1", +- "h5py==2.3.0", "lxml", "minixsv", "mod_pywebsocket", "networkx", "nibabel", "numpy", ++ "h5py", "lxml", "minixsv", "mod_pywebsocket", "networkx", "nibabel", "numpy", + "numexpr", "psutil", "scikit-learn", "scipy", "simplejson", "Pillow", +- "sqlalchemy==0.7.8", "sqlalchemy-migrate==0.7.2", "matplotlib==1.2.1"] ++ "sqlalchemy==0.7.8", "sqlalchemy-migrate==0.7.2", "matplotlib"] + + EXCLUDE_INTROSPECT_FOLDERS = [folder for folder in os.listdir(".") + if os.path.isdir(os.path.join(".", folder)) and folder != "tvb"] -- GitLab From e628bb6ac7329c3cca02d1b31e3e1799fedf8a20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 14:22:50 +0200 Subject: [PATCH 1668/2133] add easyconfig networkx-1.11-intel-2016a-Python-2.7.11.eb --- ...networkx-1.11-intel-2016a-Python-2.7.11.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..43100d8ffb --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'tools' -- GitLab From a5f6b02a3abef0ce392d411fb4ad70a220b74bac Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 13 May 2016 09:36:24 -0400 Subject: [PATCH 1669/2133] use %(pyshortver)s rather than hardcoding 2.7 --- .../m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb | 2 +- .../easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb index 6bb8c242f7..cc883fdc72 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb @@ -19,7 +19,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/python2.7/site-packages/minieigen.%s' % SHLIB_EXT], + 'files': ['lib/python%%(pyshortver)s/site-packages/minieigen.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb index e96c03e7a3..139241b97c 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb @@ -32,7 +32,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -- GitLab From 74c659030a52fb2edba7a07203ece1637ad96c42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 17:15:57 +0200 Subject: [PATCH 1670/2133] add easyconfig TVB-20160416-intel-2016a-Python-2.7.11.eb --- .../TVB-20160416-intel-2016a-Python-2.7.11.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/t/TVB/TVB-20160416-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/t/TVB/TVB-20160416-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/TVB/TVB-20160416-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..5a7b80d98f --- /dev/null +++ b/easybuild/easyconfigs/t/TVB/TVB-20160416-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,20 @@ +easyblock = 'Bundle' + +name = 'TVB' +version = '20160416' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://thevirtualbrain.org' +description = """The Virtual Brain will deliver the first open simulation of the human brain + based on individual large-scale connectivity.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('tvb-data', '20160209', versionsuffix), + ('tvb-framework', '20160329', versionsuffix), + ('tvb-library', version, versionsuffix), +] +hiddendependencies = dependencies[:] + +moduleclass = 'bio' -- GitLab From b5e99de36919a3cef7f6ecaf4eb437dc0c9ea0c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 19:29:55 +0200 Subject: [PATCH 1671/2133] include numactl as an explicit dependency in hwloc easyconfigs using PGI toolchain --- .../h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb | 5 ++++- .../h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb index 54ea46766a..7ea9401fcd 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb @@ -16,7 +16,10 @@ toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] -# numactl is a direct dependency of PGI +dependencies = [ + ('numactl', '2.0.11', '', ('GCCcore', '4.9.3')), +] + configopts = "--enable-libnuma=$EBROOTNUMACTL" moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb index 1b876ae44f..e7bd276c18 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb @@ -16,7 +16,10 @@ toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] -# numactl is a direct dependency of PGI +dependencies = [ + ('numactl', '2.0.11', '', ('GCCcore', '5.3.0')), +] + configopts = "--enable-libnuma=$EBROOTNUMACTL" moduleclass = 'system' -- GitLab From 37195fcce4756ed239ace629e7e566e896098825 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 19:41:33 +0200 Subject: [PATCH 1672/2133] break up long lines --- easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb | 3 ++- easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb index 18ef21e40a..02a330d8d9 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb @@ -2,7 +2,8 @@ name = 'SuperLU' version = '5.1.1' homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb index 411ef70cfb..533110bf6f 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb @@ -2,7 +2,8 @@ name = 'SuperLU' version = '5.1.1' homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" toolchain = {'name': 'ictce', 'version': '7.3.5'} toolchainopts = {'opt': True, 'pic': True} -- GitLab From a875c3f2016b1847c5f948bbc31826e582b655d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 10:05:16 +0200 Subject: [PATCH 1673/2133] correct install location of OpenCV Python bindings --- .../o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 4 ++-- .../o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb | 18 ++++++------------ .../o/OpenCV/OpenCV-2.4.9-intel-2014b.eb | 18 ++++++------------ 3 files changed, 14 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb index 89e2746bd8..00815da8bc 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -39,7 +39,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' -configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%(pyshortver)s/site-packages ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' @@ -56,7 +56,7 @@ configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/cv2.so'] + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb index 96d8323ca5..4231bf81f8 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -23,22 +23,16 @@ builddependencies = [ ('CMake', '3.0.0'), ] -python = 'Python' -pythonver = '2.7.8' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -java = 'Java' -javaver = '1.7.0_79' - dependencies = [ - (python, pythonver), + ('Python', '2.7.8'), ('zlib', '1.2.8'), ('FFmpeg', '2.4'), ('libjpeg-turbo', '1.3.1'), ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - (java, javaver, '', True), - ('ant', '1.9.3', '-%s-%s' % (java, javaver), True), + ('Java', '1.7.0_79', '', True), + ('ant', '1.9.3', '-Java-%(javaver)s', True), ('GLib', '2.40.0') ] @@ -46,7 +40,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' -configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%s/site-packages ' % pythonshortver +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' @@ -63,13 +57,13 @@ configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/cv2.so'] + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], 'dirs': ['include'] } modextrapaths = { - 'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver, + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'CLASSPATH': 'share/OpenCV/java', } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb index 776b0d7db5..bf5ac8dc56 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb @@ -23,22 +23,16 @@ builddependencies = [ ('CMake', '3.0.0'), ] -python = 'Python' -pythonver = '2.7.8' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -java = 'Java' -javaver = '1.7.0_60' - dependencies = [ - (python, pythonver), + ('Python', '2.7.8'), ('zlib', '1.2.8'), ('FFmpeg', '2.4'), ('libjpeg-turbo', '1.3.1'), ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - (java, javaver, '', True), - ('ant', '1.9.3', '-%s-%s' % (java, javaver), True), + ('Java', '1.7.0_60', '', True), + ('ant', '1.9.3', '-Java-%(javaver)s', True), ('GLib', '2.40.0') ] @@ -46,7 +40,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' -configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%s/site-packages ' % pythonshortver +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' @@ -63,13 +57,13 @@ configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/cv2.so'] + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], 'dirs': ['include'] } modextrapaths = { - 'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver, + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'CLASSPATH': 'share/OpenCV/java', } -- GitLab From f4cb5ad5f931bd3aa471efece5a65b73093ec3be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 12:24:22 +0200 Subject: [PATCH 1674/2133] add comment + author in patch for Score-P 2.0.1 --- .../s/Score-P/Score-P-2.0.1_fix_score_configure.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch index c387be0132..53c43dee48 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch @@ -1,3 +1,5 @@ +prevent build-score/configure from picking up $CFLAGS etc., backported from Score-P 2.0.2 +author: Markus Geimer (JSC) --- build-score/configure.orig 2016-05-11 09:21:03.716441529 +0200 +++ build-score/configure 2016-05-11 09:38:14.651525955 +0200 @@ -735,6 +735,7 @@ afs_srcdir -- GitLab From 666589950123850517c4a0ef406a349fe131aca7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 12:26:11 +0200 Subject: [PATCH 1675/2133] include XZ as dependency for libunwind --- .../easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index 9583401685..ac65492ae4 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -19,6 +19,12 @@ checksums = [ 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz ] +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] -- GitLab From 3c768a72fc16a6857a8610314ba3dd430e54280f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 14:38:44 +0200 Subject: [PATCH 1676/2133] include XZ as dependency for libunwind --- .../l/libunwind/libunwind-1.1-foss-2015a.eb | 10 ++++++++++ .../l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 10 ++++++++++ .../l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 10 ++++++++++ 3 files changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb index 74be1e3d78..15053fb3db 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb @@ -15,6 +15,16 @@ toolchain = {'version': '2015a', 'name': 'foss'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index 957e854ad9..6d87f10400 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -15,6 +15,16 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index 5059851443..6e07f18865 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -15,6 +15,16 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] -- GitLab From bcd1bb2e559a20366e4a21b88288c527c0be982b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 14:47:15 +0200 Subject: [PATCH 1677/2133] add easyconfigs for XZ dependencies --- .../a/Automake/Automake-1.15-ictce-5.3.0.eb | 33 +++++++++++++++++++ .../Autotools-20150215-ictce-5.3.0.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-ictce-5.3.0.eb | 17 ++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb | 30 +++++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb | 30 +++++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb | 30 +++++++++++++++++ 6 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb new file mode 100644 index 0000000000..cc76e86a61 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb new file mode 100644 index 0000000000..36c5a28f14 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.3.0.eb new file mode 100644 index 0000000000..1b3599b1ed --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.16')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb new file mode 100644 index 0000000000..049e77b657 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('gettext', '0.19.4'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..f9a06be732 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215', '', ('GCC', '4.7.2')), +] + +dependencies = [ + ('gettext', '0.18.2'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..96fe0ea8c8 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('gettext', '0.18.2'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 725123396f9aa06459af3c612f72f54387af45e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 15:38:26 +0200 Subject: [PATCH 1678/2133] define with_shared_libs by comparing OS_TYPE with 'Linux' --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb index 460cd7abe7..46b2debed4 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.bzip.org/%(version)s/'] buildopts = "CC=gcc CFLAGS='-Wall -Winline -O3 -fPIC -g $(BIGFILES)'" -# disable building of shared libraries, doesn't work everywhere (e.g. on OS X, where 'gcc' is actually Clang...) -with_shared_libs = False +# building of shared libraries doesn't work on OS X (where 'gcc' is actually Clang...) +with_shared_libs = OS_TYPE == 'Linux' moduleclass = 'tools' -- GitLab From 3abec3c98df891559a3bc73262ab41a7a9464cd7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 15:47:25 +0200 Subject: [PATCH 1679/2133] remove duplicate non-version patch for DIAL --- easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch b/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch deleted file mode 100644 index d5a95a417e..0000000000 --- a/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- DIAL/src/Makefile.in 2015-02-10 14:10:33.143293723 +0100 -+++ DIAL/src/Makefile.in 2015-02-10 14:10:39.462384572 +0100 -@@ -246,7 +246,7 @@ - @DEBUG_FALSE@@PROFILE_FALSE@@TESTING_TRUE@OPTIMIZATIONS = -ggdb - @DEBUG_FALSE@@PROFILE_TRUE@OPTIMIZATIONS = -ggdb -pg -DNDEBUG -O2 -funroll-all-loops $(ARCH) - @DEBUG_TRUE@OPTIMIZATIONS = -ggdb -DDEBUG --AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall -Werror \ -+AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall \ - -Wunused-variable -Wunused-parameter -Wreturn-type -Wswitch \ - -Wcast-align -Winline -Wnested-externs -Wextra $(OPTIMIZATIONS) \ - -std=c99 -- GitLab From 218e9baa654a501e04a87d6b2d9172183cae1435 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 15:48:23 +0200 Subject: [PATCH 1680/2133] fix typo in DIAL easyconfig --- easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb index 9f8127a929..0edd0228ed 100644 --- a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -26,7 +26,7 @@ binaries = [ 'assemble', 'assemble1', 'assemble_illumina', 'build_sff_index', 'c 'update_status',] sanity_check_paths = { - 'files': ['bin/%s' % bin for binfile in binaries], + 'files': ['bin/%s' % binfile for binfile in binaries], 'dirs': ['bin'] } -- GitLab From 65f54a4918f04358a8bdd4499180b8def5499dbb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 14 May 2016 21:28:22 +0100 Subject: [PATCH 1681/2133] Add comment explaining use of upstream unconventional versioning --- .../a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index af32067597..110e6af4ca 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -5,6 +5,7 @@ easyblock = 'Tarball' name = 'annovar' +# Unconventional version is taken from the upstream site version = '2016Feb01' versionsuffix = '-Perl-%(perlver)s' -- GitLab From 4c77a1e79fcbea5cca7ead451a94d31e12c5b832 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 14 May 2016 21:32:45 +0100 Subject: [PATCH 1682/2133] Add comment explaining use of upstream unconventional versioning --- .../a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index eacaffe6ed..14f3ea6b69 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -5,6 +5,7 @@ easyblock = 'Tarball' name = 'annovar' +# UNconventional versioning is taken from upstream version = '2016Feb01' versionsuffix = '-Perl-%(perlver)s' -- GitLab From e8b33b6a01ce3b1d8cf8020162a6fe08250e0346 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 May 2016 11:48:39 +0200 Subject: [PATCH 1683/2133] add patch to fix broken OpenSSL tests due to expired certificates --- .../o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb | 2 + .../OpenSSL-1.0.0-goalf-1.1.0-no-OFED.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.0-goolf-1.4.10.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1f-GCC-4.8.2.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1f-cgmpolf-1.1.6.eb | 2 + .../OpenSSL-1.0.1f-cgmvolf-1.1.12rc1.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.2.7.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1f-cgoolf-1.1.7.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12.eb | 2 + .../OpenSSL-1.0.1f-gmvolf-1.7.12rc1.eb | 2 + .../OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb | 5 +- .../OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb | 5 +- .../OpenSSL/OpenSSL-1.0.1f-ictce-3.2.2.u3.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb | 8 +- .../o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1f-ictce-5.4.0.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1f-iqacml-3.7.3.eb | 5 + .../o/OpenSSL/OpenSSL-1.0.1i-intel-2014b.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1k-GCC-4.9.2.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.14.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb | 2 +- .../o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1q-foss-2015b.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1q-intel-2015b.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb | 5 +- .../OpenSSL-1.0.x_fix-tests-certs.patch | 579 ++++++++++++++++++ 37 files changed, 669 insertions(+), 15 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.x_fix-tests-certs.patch diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb index 11891cf96a..31798451a4 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] # makefile is not suitable for parallel build diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goalf-1.1.0-no-OFED.eb index b20db23b0a..d8b87dfdff 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goalf-1.1.0-no-OFED.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] # makefile is not suitable for parallel build diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goolf-1.4.10.eb index db9d43d1ce..fbc79c380f 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goolf-1.4.10.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] # makefile is not suitable for parallel build diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-GCC-4.8.2.eb index 413c8374f6..4654b89426 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-GCC-4.8.2.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f-fix_pod_syntax-1.patch'] +patches = [ + 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmpolf-1.1.6.eb index ad1d42662f..b65d36ca86 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmpolf-1.1.6.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.1.12rc1.eb index 533a7cef1c..bbd1b1d7f0 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.1.12rc1.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.2.7.eb index 0a8200f83c..df0e78c6e2 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.2.7.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgoolf-1.1.7.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgoolf-1.1.7.eb index 973932317d..1da82cfc0b 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgoolf-1.1.7.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12.eb index 707bd90aa3..35f8ec876d 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12rc1.eb index 9b0c99840e..18a5bc06b4 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12rc1.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb index 1f693bfc6b..090668fbfb 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f-fix_pod_syntax-1.patch'] +patches = [ + 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb index 0b7691ae3d..edb92686ac 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f-fix_pod_syntax-1.patch'] +patches = [ + 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb index 4edbca03d8..ef533a11f5 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f-fix_pod_syntax-1.patch'] +patches = [ + 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-3.2.2.u3.eb index 908a928059..1609277d54 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-3.2.2.u3.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f_icc-fixes.patch'] +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb index 7029f97900..62338512e9 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb @@ -12,9 +12,11 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f-fix_pod_syntax-1.patch'] - -patches = ['OpenSSL-1.0.1f_icc-fixes.patch'] +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb index 4c9a5a74b5..bf52ea9bcc 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb index a9093ec8b3..a0eb2be098 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.4.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.4.0.eb index 4050211bd7..055777f95e 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.4.0.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb index 14f3a0762b..b401f764ea 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-iqacml-3.7.3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-iqacml-3.7.3.eb index 5cfad5f0b3..ca90aecbb3 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-iqacml-3.7.3.eb @@ -12,6 +12,11 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1i-intel-2014b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1i-intel-2014b.eb index d31ac88a20..aec4b94ad1 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1i-intel-2014b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1i-intel-2014b.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-GCC-4.9.2.eb index 39a21a3a41..e10bf5f0ac 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-GCC-4.9.2.eb @@ -14,6 +14,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.14.eb index 7815b2d7b3..20662edace 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.14.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb index 895b5bd87b..668e579ba1 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb index 3ffb667048..91cb41c8eb 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb @@ -13,8 +13,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] patches = [ - 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb index a127a7e7bb..307f185342 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-%(version)s_icc-fixes.patch', 'OpenSSL-%(version)s_fix-parallel.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb index 6800732437..c4f94fabf9 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-%(version)s_icc-fixes.patch'] +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb index a6496a921f..108fade18d 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.8')] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb index 733ddd9ac4..8c74a57361 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.8')] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb index 9e06d07cee..4d4f0712ca 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-%(version)s_icc-fixes.patch'] +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb index a34f9121d1..654b06cdb8 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-%(version)s_icc-fixes.patch'] +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-foss-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-foss-2015b.eb index 17db49d12f..470877ecda 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-foss-2015b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-foss-2015b.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.8')] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-intel-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-intel-2015b.eb index 3a69395fe3..1c6c615bff 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-intel-2015b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-intel-2015b.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-%(version)s_icc-fixes.patch'] +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb index 9c3838a1b7..df437ed5a6 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.8')] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb index a5aab91ad9..5cf77af391 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1q_icc-fixes.patch'] +patches = [ + 'OpenSSL-1.0.1q_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb index 976aa24ab2..517a86ba16 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1q_icc-fixes.patch'] +patches = [ + 'OpenSSL-1.0.1q_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.x_fix-tests-certs.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.x_fix-tests-certs.patch new file mode 100644 index 0000000000..9bc7df2d14 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.x_fix-tests-certs.patch @@ -0,0 +1,579 @@ +fix broken tests by updating S/MIME certificates +https://github.com/openssl/openssl/commit/24762dee178bace3c3 +diff --git a/test/smime-certs/smdsa1.pem b/test/smime-certs/smdsa1.pem +index d5677db..b424f67 100644 +--- a/test/smime-certs/smdsa1.pem ++++ b/test/smime-certs/smdsa1.pem +@@ -1,34 +1,47 @@ +------BEGIN DSA PRIVATE KEY----- +-MIIBuwIBAAKBgQDFJfsIPOIawMO5biw+AoYUhNVxReBOLQosU3Qv4B8krac0BNr3 +-OjSGLh1wZxHqhlAE0QmasTaKojuk20nNWeFnczSz6vDl0IVJEhS8VYor5kt9gLqt +-GcoAgsf4gRDIutJyQDaNn3IVY89uXUVIoexvQeLQDBCgQPC5O8rJdqBwtwIVAK2J +-jt+dqk07eQUE59koYUEKyNorAoGBAI4IEpusf8G14kCHmRtnHXM2tG5EWJDmW6Qt +-wjqvWp1GKUx5WFy1tVWR9nl5rL0Di+kNdENo+SkKj7h3uDulGOI6T0mQYbV2h1IK +-+FMOGnOqvZ8eNTE2n4PGTo5puZ63LBm+QYrQsrNiUY4vakLFQ2rEK/SLwdsDFK4Z +-SJCBQw5zAoGATQlPPF+OeU8nu3rsdXGDiZdJzOkuCce3KQfTABA9C+Dk4CVcvBdd +-YRLGpnykumkNTO1sTO+4/Gphsuje1ujK9td4UEhdYqylCe5QjEMrszDlJtelDQF9 +-C0yhdjKGTP0kxofLhsGckcuQvcKEKffT2pDDKJIy4vWQO0UyJl1vjLcCFG2uiGGx +-9fMUZq1v0ePD4Wo0Xkxo +------END DSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIICZQIBADCCAjkGByqGSM44BAEwggIsAoIBAQCQfLlNdehPnTrGIMhw4rk0uua6 ++k1nCG3zcyfXli17BdB2k0HBPaTA3a3ZHfOt1Awy0Uu0wZ3gdPr9z0I64hnJXIGou ++zIanZ7nYRImHtX5JMFbXeyxo1Owd2Zs3oEk9nQUoUsMxvmYC/ghPL5Zx1pPxcHCO ++wzWxoG4yZMjimXOc1/W7zvK/4/g/Cz9fItD3zdcydfgM/hK0/CeYQ21xfhqf4mjK ++v9plnCcWgToGI+7H8VK80MFbkO2QKRz3vP1/TjK6PRm9sEeB5b10+SvGv2j2w+CC ++0fXL4s6n7PtBlm/bww8xL1/Az8kwejUcII1Dc8uNwwISwGbwaGBvl7IHpm21AiEA ++rodZi+nCKZdTL8IgCjX3n0DuhPRkVQPjz/B6VweLW9MCggEAfimkUNwnsGFp7mKM ++zJKhHoQkMB1qJzyIHjDzQ/J1xjfoF6i27afw1/WKboND5eseZhlhA2TO5ZJB6nGx ++DOE9lVQxYVml++cQj6foHh1TVJAgGl4mWuveW/Rz+NEhpK4zVeEsfMrbkBypPByy ++xzF1Z49t568xdIo+e8jLI8FjEdXOIUg4ehB3NY6SL8r4oJ49j/sJWfHcDoWH/LK9 ++ZaBF8NpflJe3F40S8RDvM8j2HC+y2Q4QyKk1DXGiH+7yQLGWzr3M73kC3UBnnH0h ++Hxb7ISDCT7dCw/lH1nCbVFBOM0ASI26SSsFSXQrvD2kryRcTZ0KkyyhhoPODWpU+ ++TQMsxQQjAiEAkolGvb/76X3vm5Ov09ezqyBYt9cdj/FLH7DyMkxO7X0= ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIIDpDCCAw2gAwIBAgIJAMtotfHYdEsWMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDlaFw0xNjA1MTAxMzUzMDlaMEUx ++MIIFkDCCBHigAwIBAgIJANk5lu6mSyBDMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzFaFw0yMzA1MjYxNzI4MzFaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBEU0EgIzEwggG3MIIBLAYHKoZIzjgEATCCAR8CgYEAxSX7 +-CDziGsDDuW4sPgKGFITVcUXgTi0KLFN0L+AfJK2nNATa9zo0hi4dcGcR6oZQBNEJ +-mrE2iqI7pNtJzVnhZ3M0s+rw5dCFSRIUvFWKK+ZLfYC6rRnKAILH+IEQyLrSckA2 +-jZ9yFWPPbl1FSKHsb0Hi0AwQoEDwuTvKyXagcLcCFQCtiY7fnapNO3kFBOfZKGFB +-CsjaKwKBgQCOCBKbrH/BteJAh5kbZx1zNrRuRFiQ5lukLcI6r1qdRilMeVhctbVV +-kfZ5eay9A4vpDXRDaPkpCo+4d7g7pRjiOk9JkGG1dodSCvhTDhpzqr2fHjUxNp+D +-xk6OabmetywZvkGK0LKzYlGOL2pCxUNqxCv0i8HbAxSuGUiQgUMOcwOBhAACgYBN +-CU88X455Tye7eux1cYOJl0nM6S4Jx7cpB9MAED0L4OTgJVy8F11hEsamfKS6aQ1M +-7WxM77j8amGy6N7W6Mr213hQSF1irKUJ7lCMQyuzMOUm16UNAX0LTKF2MoZM/STG +-h8uGwZyRy5C9woQp99PakMMokjLi9ZA7RTImXW+Mt6OBgzCBgDAdBgNVHQ4EFgQU +-4Qfbhpi5yqXaXuCLXj427mR25MkwHwYDVR0jBBgwFoAUE89Lp7uJLrM4Vxd2xput +-aFvl7RcwDAYDVR0TAQH/BAIwADAOBgNVHQ8BAf8EBAMCBsAwIAYDVR0RBBkwF4EV +-c21pbWVkc2ExQG9wZW5zc2wub3JnMA0GCSqGSIb3DQEBBQUAA4GBAFrdUzKK1pWO +-kd02S423KUBc4GWWyiGlVoEO7WxVhHLJ8sm67X7OtJOwe0UGt+Nc5qLtyJYSirw8 +-phjiTdNpQCTJ8+Kc56tWkJ6H7NAI4vTJtPL5BM/EmeYrVSU9JI9xhqpyKw9IBD+n +-hRJ79W9FaiJRvaAOX+TkyTukJrxAWRyv ++ZXN0IFMvTUlNRSBFRSBEU0EgIzEwggNGMIICOQYHKoZIzjgEATCCAiwCggEBAJB8 ++uU116E+dOsYgyHDiuTS65rqTWcIbfNzJ9eWLXsF0HaTQcE9pMDdrdkd863UDDLRS ++7TBneB0+v3PQjriGclcgai7MhqdnudhEiYe1fkkwVtd7LGjU7B3ZmzegST2dBShS ++wzG+ZgL+CE8vlnHWk/FwcI7DNbGgbjJkyOKZc5zX9bvO8r/j+D8LP18i0PfN1zJ1 +++Az+ErT8J5hDbXF+Gp/iaMq/2mWcJxaBOgYj7sfxUrzQwVuQ7ZApHPe8/X9OMro9 ++Gb2wR4HlvXT5K8a/aPbD4ILR9cvizqfs+0GWb9vDDzEvX8DPyTB6NRwgjUNzy43D ++AhLAZvBoYG+XsgembbUCIQCuh1mL6cIpl1MvwiAKNfefQO6E9GRVA+PP8HpXB4tb ++0wKCAQB+KaRQ3CewYWnuYozMkqEehCQwHWonPIgeMPND8nXGN+gXqLbtp/DX9Ypu ++g0Pl6x5mGWEDZM7lkkHqcbEM4T2VVDFhWaX75xCPp+geHVNUkCAaXiZa695b9HP4 ++0SGkrjNV4Sx8ytuQHKk8HLLHMXVnj23nrzF0ij57yMsjwWMR1c4hSDh6EHc1jpIv ++yvignj2P+wlZ8dwOhYf8sr1loEXw2l+Ul7cXjRLxEO8zyPYcL7LZDhDIqTUNcaIf ++7vJAsZbOvczveQLdQGecfSEfFvshIMJPt0LD+UfWcJtUUE4zQBIjbpJKwVJdCu8P ++aSvJFxNnQqTLKGGg84NalT5NAyzFA4IBBQACggEAGXSQADbuRIZBjiQ6NikwZl+x ++EDEffIE0RWbvwf1tfWxw4ZvanO/djyz5FePO0AIJDBCLUjr9D32nkmIG1Hu3dWgV ++86knQsM6uFiMSzY9nkJGZOlH3w4NHLE78pk75xR1sg1MEZr4x/t+a/ea9Y4AXklE ++DCcaHtpMGeAx3ZAqSKec+zQOOA73JWP1/gYHGdYyTQpQtwRTsh0Gi5mOOdpoJ0vp ++O83xYbFCZ+ZZKX1RWOjJe2OQBRtw739q1nRga1VMLAT/LFSQsSE3IOp8hiWbjnit ++1SE6q3II2a/aHZH/x4OzszfmtQfmerty3eQSq3bgajfxCsccnRjSbLeNiazRSKNg ++MF4wDAYDVR0TAQH/BAIwADAOBgNVHQ8BAf8EBAMCBeAwHQYDVR0OBBYEFNHQYTOO ++xaZ/N68OpxqjHKuatw6sMB8GA1UdIwQYMBaAFMmRUwpjexZbi71E8HaIqSTm5bZs ++MA0GCSqGSIb3DQEBBQUAA4IBAQAAiLociMMXcLkO/uKjAjCIQMrsghrOrxn4ZGBx ++d/mCTeqPxhcrX2UorwxVCKI2+Dmz5dTC2xKprtvkiIadJamJmxYYzeF1pgRriFN3 ++MkmMMkTbe/ekSvSeMtHQ2nHDCAJIaA/k9akWfA0+26Ec25/JKMrl3LttllsJMK1z ++Xj7TcQpAIWORKWSNxY/ezM34+9ABHDZB2waubFqS+irlZsn38aZRuUI0K67fuuIt ++17vMUBqQpe2hfNAjpZ8dIpEdAGjQ6izV2uwP1lXbiaK9U4dvUqmwyCIPniX7Hpaf ++0VnX0mEViXMT6vWZTjLBUv0oKmO7xBkWHIaaX6oyF32pK5AO + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smdsa2.pem b/test/smime-certs/smdsa2.pem +index ef86c11..648447f 100644 +--- a/test/smime-certs/smdsa2.pem ++++ b/test/smime-certs/smdsa2.pem +@@ -1,34 +1,47 @@ +------BEGIN DSA PRIVATE KEY----- +-MIIBvAIBAAKBgQDFJfsIPOIawMO5biw+AoYUhNVxReBOLQosU3Qv4B8krac0BNr3 +-OjSGLh1wZxHqhlAE0QmasTaKojuk20nNWeFnczSz6vDl0IVJEhS8VYor5kt9gLqt +-GcoAgsf4gRDIutJyQDaNn3IVY89uXUVIoexvQeLQDBCgQPC5O8rJdqBwtwIVAK2J +-jt+dqk07eQUE59koYUEKyNorAoGBAI4IEpusf8G14kCHmRtnHXM2tG5EWJDmW6Qt +-wjqvWp1GKUx5WFy1tVWR9nl5rL0Di+kNdENo+SkKj7h3uDulGOI6T0mQYbV2h1IK +-+FMOGnOqvZ8eNTE2n4PGTo5puZ63LBm+QYrQsrNiUY4vakLFQ2rEK/SLwdsDFK4Z +-SJCBQw5zAoGBAIPmO8BtJ+Yac58trrPwq9b/6VW3jQTWzTLWSH84/QQdqQa+Pz3v +-It/+hHM0daNF5uls8ICsPL1aLXmRx0pHvIyb0aAzYae4T4Jv/COPDMTdKbA1uitJ +-VbkGZrm+LIrs7I9lOkb4T0vI6kL/XdOCXY1469zsqCgJ/O2ibn6mq0nWAhR716o2 +-Nf8SimTZYB0/CKje6M5ufA== +------END DSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIICZAIBADCCAjkGByqGSM44BAEwggIsAoIBAQCQfLlNdehPnTrGIMhw4rk0uua6 ++k1nCG3zcyfXli17BdB2k0HBPaTA3a3ZHfOt1Awy0Uu0wZ3gdPr9z0I64hnJXIGou ++zIanZ7nYRImHtX5JMFbXeyxo1Owd2Zs3oEk9nQUoUsMxvmYC/ghPL5Zx1pPxcHCO ++wzWxoG4yZMjimXOc1/W7zvK/4/g/Cz9fItD3zdcydfgM/hK0/CeYQ21xfhqf4mjK ++v9plnCcWgToGI+7H8VK80MFbkO2QKRz3vP1/TjK6PRm9sEeB5b10+SvGv2j2w+CC ++0fXL4s6n7PtBlm/bww8xL1/Az8kwejUcII1Dc8uNwwISwGbwaGBvl7IHpm21AiEA ++rodZi+nCKZdTL8IgCjX3n0DuhPRkVQPjz/B6VweLW9MCggEAfimkUNwnsGFp7mKM ++zJKhHoQkMB1qJzyIHjDzQ/J1xjfoF6i27afw1/WKboND5eseZhlhA2TO5ZJB6nGx ++DOE9lVQxYVml++cQj6foHh1TVJAgGl4mWuveW/Rz+NEhpK4zVeEsfMrbkBypPByy ++xzF1Z49t568xdIo+e8jLI8FjEdXOIUg4ehB3NY6SL8r4oJ49j/sJWfHcDoWH/LK9 ++ZaBF8NpflJe3F40S8RDvM8j2HC+y2Q4QyKk1DXGiH+7yQLGWzr3M73kC3UBnnH0h ++Hxb7ISDCT7dCw/lH1nCbVFBOM0ASI26SSsFSXQrvD2kryRcTZ0KkyyhhoPODWpU+ ++TQMsxQQiAiAdCUJ5n2Q9hIynN8BMpnRcdfH696BKejGx+2Mr2kfnnA== ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIIDpTCCAw6gAwIBAgIJAMtotfHYdEsXMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDlaFw0xNjA1MTAxMzUzMDlaMEUx ++MIIFkDCCBHigAwIBAgIJANk5lu6mSyBEMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzFaFw0yMzA1MjYxNzI4MzFaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBEU0EgIzIwggG4MIIBLAYHKoZIzjgEATCCAR8CgYEAxSX7 +-CDziGsDDuW4sPgKGFITVcUXgTi0KLFN0L+AfJK2nNATa9zo0hi4dcGcR6oZQBNEJ +-mrE2iqI7pNtJzVnhZ3M0s+rw5dCFSRIUvFWKK+ZLfYC6rRnKAILH+IEQyLrSckA2 +-jZ9yFWPPbl1FSKHsb0Hi0AwQoEDwuTvKyXagcLcCFQCtiY7fnapNO3kFBOfZKGFB +-CsjaKwKBgQCOCBKbrH/BteJAh5kbZx1zNrRuRFiQ5lukLcI6r1qdRilMeVhctbVV +-kfZ5eay9A4vpDXRDaPkpCo+4d7g7pRjiOk9JkGG1dodSCvhTDhpzqr2fHjUxNp+D +-xk6OabmetywZvkGK0LKzYlGOL2pCxUNqxCv0i8HbAxSuGUiQgUMOcwOBhQACgYEA +-g+Y7wG0n5hpzny2us/Cr1v/pVbeNBNbNMtZIfzj9BB2pBr4/Pe8i3/6EczR1o0Xm +-6WzwgKw8vVoteZHHSke8jJvRoDNhp7hPgm/8I48MxN0psDW6K0lVuQZmub4siuzs +-j2U6RvhPS8jqQv9d04JdjXjr3OyoKAn87aJufqarSdajgYMwgYAwHQYDVR0OBBYE +-FHsAGNfVltSYUq4hC+YVYwsYtA+dMB8GA1UdIwQYMBaAFBPPS6e7iS6zOFcXdsab +-rWhb5e0XMAwGA1UdEwEB/wQCMAAwDgYDVR0PAQH/BAQDAgbAMCAGA1UdEQQZMBeB +-FXNtaW1lZHNhMkBvcGVuc3NsLm9yZzANBgkqhkiG9w0BAQUFAAOBgQCx9BtCbaYF +-FXjLClkuKXbESaDZA1biPgY25i00FsUzARuhCpqD2v+0tu5c33ZzIhL6xlvBRU5l +-6Atw/xpZhae+hdBEtxPJoGekLLrHOau7Md3XwDjV4lFgcEJkWZoaSOOIK+4D5jF0 +-jZWtHjnwEzuLYlo7ScHSsbcQfjH0M1TP5A== ++ZXN0IFMvTUlNRSBFRSBEU0EgIzIwggNGMIICOQYHKoZIzjgEATCCAiwCggEBAJB8 ++uU116E+dOsYgyHDiuTS65rqTWcIbfNzJ9eWLXsF0HaTQcE9pMDdrdkd863UDDLRS ++7TBneB0+v3PQjriGclcgai7MhqdnudhEiYe1fkkwVtd7LGjU7B3ZmzegST2dBShS ++wzG+ZgL+CE8vlnHWk/FwcI7DNbGgbjJkyOKZc5zX9bvO8r/j+D8LP18i0PfN1zJ1 +++Az+ErT8J5hDbXF+Gp/iaMq/2mWcJxaBOgYj7sfxUrzQwVuQ7ZApHPe8/X9OMro9 ++Gb2wR4HlvXT5K8a/aPbD4ILR9cvizqfs+0GWb9vDDzEvX8DPyTB6NRwgjUNzy43D ++AhLAZvBoYG+XsgembbUCIQCuh1mL6cIpl1MvwiAKNfefQO6E9GRVA+PP8HpXB4tb ++0wKCAQB+KaRQ3CewYWnuYozMkqEehCQwHWonPIgeMPND8nXGN+gXqLbtp/DX9Ypu ++g0Pl6x5mGWEDZM7lkkHqcbEM4T2VVDFhWaX75xCPp+geHVNUkCAaXiZa695b9HP4 ++0SGkrjNV4Sx8ytuQHKk8HLLHMXVnj23nrzF0ij57yMsjwWMR1c4hSDh6EHc1jpIv ++yvignj2P+wlZ8dwOhYf8sr1loEXw2l+Ul7cXjRLxEO8zyPYcL7LZDhDIqTUNcaIf ++7vJAsZbOvczveQLdQGecfSEfFvshIMJPt0LD+UfWcJtUUE4zQBIjbpJKwVJdCu8P ++aSvJFxNnQqTLKGGg84NalT5NAyzFA4IBBQACggEAItQlFu0t7Mw1HHROuuwKLS+E ++h2WNNZP96MLQTygOVlqgaJY+1mJLzvl/51LLH6YezX0t89Z2Dm/3SOJEdNrdbIEt ++tbu5rzymXxFhc8uaIYZFhST38oQwJOjM8wFitAQESe6/9HZjkexMqSqx/r5aEKTa ++LBinqA1BJRI72So1/1dv8P99FavPADdj8V7fAccReKEQKnfnwA7mrnD+OlIqFKFn ++3wCGk8Sw7tSJ9g6jgCI+zFwrKn2w+w+iot/Ogxl9yMAtKmAd689IAZr5GPPvV2y0 ++KOogCiUYgSTSawZhr+rjyFavfI5dBWzMq4tKx/zAi6MJ+6hGJjJ8jHoT9JAPmaNg ++MF4wDAYDVR0TAQH/BAIwADAOBgNVHQ8BAf8EBAMCBeAwHQYDVR0OBBYEFGaxw04k ++qpufeGZC+TTBq8oMnXyrMB8GA1UdIwQYMBaAFMmRUwpjexZbi71E8HaIqSTm5bZs ++MA0GCSqGSIb3DQEBBQUAA4IBAQCk2Xob1ICsdHYx/YsBzY6E1eEwcI4RZbZ3hEXp ++VA72/Mbz60gjv1OwE5Ay4j+xG7IpTio6y2A9ZNepGpzidYcsL/Lx9Sv1LlN0Ukzb ++uk6Czd2sZJp+PFMTTrgCd5rXKnZs/0D84Vci611vGMA1hnUnbAnBBmgLXe9pDNRV ++6mhmCLLjJ4GOr5Wxt/hhknr7V2e1VMx3Q47GZhc0o/gExfhxXA8+gicM0nEYNakD ++2A1F0qDhQGakjuofANHhjdUDqKJ1sxurAy80fqb0ddzJt2el89iXKN+aXx/zEX96 ++GI5ON7z/bkVwIi549lUOpWb2Mved61NBzCLKVP7HSuEIsC/I + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smdsa3.pem b/test/smime-certs/smdsa3.pem +index eeb848d..77acc5e 100644 +--- a/test/smime-certs/smdsa3.pem ++++ b/test/smime-certs/smdsa3.pem +@@ -1,34 +1,47 @@ +------BEGIN DSA PRIVATE KEY----- +-MIIBvAIBAAKBgQDFJfsIPOIawMO5biw+AoYUhNVxReBOLQosU3Qv4B8krac0BNr3 +-OjSGLh1wZxHqhlAE0QmasTaKojuk20nNWeFnczSz6vDl0IVJEhS8VYor5kt9gLqt +-GcoAgsf4gRDIutJyQDaNn3IVY89uXUVIoexvQeLQDBCgQPC5O8rJdqBwtwIVAK2J +-jt+dqk07eQUE59koYUEKyNorAoGBAI4IEpusf8G14kCHmRtnHXM2tG5EWJDmW6Qt +-wjqvWp1GKUx5WFy1tVWR9nl5rL0Di+kNdENo+SkKj7h3uDulGOI6T0mQYbV2h1IK +-+FMOGnOqvZ8eNTE2n4PGTo5puZ63LBm+QYrQsrNiUY4vakLFQ2rEK/SLwdsDFK4Z +-SJCBQw5zAoGAYzOpPmh8Je1IDauEXhgaLz14wqYUHHcrj2VWVJ6fRm8GhdQFJSI7 +-GUk08pgKZSKic2lNqxuzW7/vFxKQ/nvzfytY16b+2i+BR4Q6yvMzCebE1hHVg0Ju +-TwfUMwoFEOhYP6ZwHSUiQl9IBMH9TNJCMwYMxfY+VOrURFsjGTRUgpwCFQCIGt5g +-Y+XZd0Sv69CatDIRYWvaIA== +------END DSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIICZQIBADCCAjkGByqGSM44BAEwggIsAoIBAQCQfLlNdehPnTrGIMhw4rk0uua6 ++k1nCG3zcyfXli17BdB2k0HBPaTA3a3ZHfOt1Awy0Uu0wZ3gdPr9z0I64hnJXIGou ++zIanZ7nYRImHtX5JMFbXeyxo1Owd2Zs3oEk9nQUoUsMxvmYC/ghPL5Zx1pPxcHCO ++wzWxoG4yZMjimXOc1/W7zvK/4/g/Cz9fItD3zdcydfgM/hK0/CeYQ21xfhqf4mjK ++v9plnCcWgToGI+7H8VK80MFbkO2QKRz3vP1/TjK6PRm9sEeB5b10+SvGv2j2w+CC ++0fXL4s6n7PtBlm/bww8xL1/Az8kwejUcII1Dc8uNwwISwGbwaGBvl7IHpm21AiEA ++rodZi+nCKZdTL8IgCjX3n0DuhPRkVQPjz/B6VweLW9MCggEAfimkUNwnsGFp7mKM ++zJKhHoQkMB1qJzyIHjDzQ/J1xjfoF6i27afw1/WKboND5eseZhlhA2TO5ZJB6nGx ++DOE9lVQxYVml++cQj6foHh1TVJAgGl4mWuveW/Rz+NEhpK4zVeEsfMrbkBypPByy ++xzF1Z49t568xdIo+e8jLI8FjEdXOIUg4ehB3NY6SL8r4oJ49j/sJWfHcDoWH/LK9 ++ZaBF8NpflJe3F40S8RDvM8j2HC+y2Q4QyKk1DXGiH+7yQLGWzr3M73kC3UBnnH0h ++Hxb7ISDCT7dCw/lH1nCbVFBOM0ASI26SSsFSXQrvD2kryRcTZ0KkyyhhoPODWpU+ ++TQMsxQQjAiEArJr6p2zTbhRppQurHGTdmdYHqrDdZH4MCsD9tQCw1xY= ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIIDpDCCAw2gAwIBAgIJAMtotfHYdEsYMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDlaFw0xNjA1MTAxMzUzMDlaMEUx ++MIIFkDCCBHigAwIBAgIJANk5lu6mSyBFMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzFaFw0yMzA1MjYxNzI4MzFaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBEU0EgIzMwggG3MIIBLAYHKoZIzjgEATCCAR8CgYEAxSX7 +-CDziGsDDuW4sPgKGFITVcUXgTi0KLFN0L+AfJK2nNATa9zo0hi4dcGcR6oZQBNEJ +-mrE2iqI7pNtJzVnhZ3M0s+rw5dCFSRIUvFWKK+ZLfYC6rRnKAILH+IEQyLrSckA2 +-jZ9yFWPPbl1FSKHsb0Hi0AwQoEDwuTvKyXagcLcCFQCtiY7fnapNO3kFBOfZKGFB +-CsjaKwKBgQCOCBKbrH/BteJAh5kbZx1zNrRuRFiQ5lukLcI6r1qdRilMeVhctbVV +-kfZ5eay9A4vpDXRDaPkpCo+4d7g7pRjiOk9JkGG1dodSCvhTDhpzqr2fHjUxNp+D +-xk6OabmetywZvkGK0LKzYlGOL2pCxUNqxCv0i8HbAxSuGUiQgUMOcwOBhAACgYBj +-M6k+aHwl7UgNq4ReGBovPXjCphQcdyuPZVZUnp9GbwaF1AUlIjsZSTTymAplIqJz +-aU2rG7Nbv+8XEpD+e/N/K1jXpv7aL4FHhDrK8zMJ5sTWEdWDQm5PB9QzCgUQ6Fg/ +-pnAdJSJCX0gEwf1M0kIzBgzF9j5U6tREWyMZNFSCnKOBgzCBgDAdBgNVHQ4EFgQU +-VhpVXqQ/EzUMdxLvP7o9EhJ8h70wHwYDVR0jBBgwFoAUE89Lp7uJLrM4Vxd2xput +-aFvl7RcwDAYDVR0TAQH/BAIwADAOBgNVHQ8BAf8EBAMCBsAwIAYDVR0RBBkwF4EV +-c21pbWVkc2EzQG9wZW5zc2wub3JnMA0GCSqGSIb3DQEBBQUAA4GBACM9e75EQa8m +-k/AZkH/tROqf3yeqijULl9x8FjFatqoY+29OM6oMGM425IqSkKd2ipz7OxO0SShu +-rE0O3edS7DvYBwvhWPviRaYBMyZ4iFJVup+fOzoYK/j/bASxS3BHQBwb2r4rhe25 +-OlTyyFEk7DJyW18YFOG97S1P52oQ5f5x ++ZXN0IFMvTUlNRSBFRSBEU0EgIzMwggNGMIICOQYHKoZIzjgEATCCAiwCggEBAJB8 ++uU116E+dOsYgyHDiuTS65rqTWcIbfNzJ9eWLXsF0HaTQcE9pMDdrdkd863UDDLRS ++7TBneB0+v3PQjriGclcgai7MhqdnudhEiYe1fkkwVtd7LGjU7B3ZmzegST2dBShS ++wzG+ZgL+CE8vlnHWk/FwcI7DNbGgbjJkyOKZc5zX9bvO8r/j+D8LP18i0PfN1zJ1 +++Az+ErT8J5hDbXF+Gp/iaMq/2mWcJxaBOgYj7sfxUrzQwVuQ7ZApHPe8/X9OMro9 ++Gb2wR4HlvXT5K8a/aPbD4ILR9cvizqfs+0GWb9vDDzEvX8DPyTB6NRwgjUNzy43D ++AhLAZvBoYG+XsgembbUCIQCuh1mL6cIpl1MvwiAKNfefQO6E9GRVA+PP8HpXB4tb ++0wKCAQB+KaRQ3CewYWnuYozMkqEehCQwHWonPIgeMPND8nXGN+gXqLbtp/DX9Ypu ++g0Pl6x5mGWEDZM7lkkHqcbEM4T2VVDFhWaX75xCPp+geHVNUkCAaXiZa695b9HP4 ++0SGkrjNV4Sx8ytuQHKk8HLLHMXVnj23nrzF0ij57yMsjwWMR1c4hSDh6EHc1jpIv ++yvignj2P+wlZ8dwOhYf8sr1loEXw2l+Ul7cXjRLxEO8zyPYcL7LZDhDIqTUNcaIf ++7vJAsZbOvczveQLdQGecfSEfFvshIMJPt0LD+UfWcJtUUE4zQBIjbpJKwVJdCu8P ++aSvJFxNnQqTLKGGg84NalT5NAyzFA4IBBQACggEAcXvtfiJfIZ0wgGpN72ZeGrJ9 ++msUXOxow7w3fDbP8r8nfVkBNbfha8rx0eY6fURFVZzIOd8EHGKypcH1gS6eZNucf ++zgsH1g5r5cRahMZmgGXBEBsWrh2IaDG7VSKt+9ghz27EKgjAQCzyHQL5FCJgR2p7 ++cv0V4SRqgiAGYlJ191k2WtLOsVd8kX//jj1l8TUgE7TqpuSEpaSyQ4nzJROpZWZp ++N1RwFmCURReykABU/Nzin/+rZnvZrp8WoXSXEqxeB4mShRSaH57xFnJCpRwKJ4qS ++2uhATzJaKH7vu63k3DjftbSBVh+32YXwtHc+BGjs8S2aDtCW3FtDA7Z6J8BIxaNg ++MF4wDAYDVR0TAQH/BAIwADAOBgNVHQ8BAf8EBAMCBeAwHQYDVR0OBBYEFMJxatDE ++FCEFGl4uoiQQ1050Ju9RMB8GA1UdIwQYMBaAFMmRUwpjexZbi71E8HaIqSTm5bZs ++MA0GCSqGSIb3DQEBBQUAA4IBAQBGZD1JnMep39KMOhD0iBTmyjhtcnRemckvRask ++pS/CqPwo+M+lPNdxpLU2w9b0QhPnj0yAS/BS1yBjsLGY4DP156k4Q3QOhwsrTmrK ++YOxg0w7DOpkv5g11YLJpHsjSOwg5uIMoefL8mjQK6XOFOmQXHJrUtGulu+fs6FlM ++khGJcW4xYVPK0x/mHvTT8tQaTTkgTdVHObHF5Dyx/F9NMpB3RFguQPk2kT4lJc4i ++Up8T9mLzaxz6xc4wwh8h70Zw81lkGYhX+LRk3sfd/REq9x4QXQNP9t9qU1CgrBzv ++4orzt9cda4r+rleSg2XjWnXzMydE6DuwPVPZlqnLbSYUy660 + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smroot.pem b/test/smime-certs/smroot.pem +index a59eb26..d1a253f 100644 +--- a/test/smime-certs/smroot.pem ++++ b/test/smime-certs/smroot.pem +@@ -1,30 +1,49 @@ +------BEGIN RSA PRIVATE KEY----- +-MIICXAIBAAKBgQDBV1Z/Q5gPF7lojc8pKUdyz5+Jf2B3vs4he6egekugWnoJduki +-9Lnae/JchB/soIX0co3nLc11NuFFlnAWJNMDJr08l5AHAJLYNHevF5l/f9oDQwvZ +-speKh1xpIAJNqCTzVeQ/ZLx6/GccIXV/xDuKIiovqJTPgR5WPkYKaw++lQIDAQAB +-AoGALXnUj5SflJU4+B2652ydMKUjWl0KnL/VjkyejgGV/j6py8Ybaixz9q8Gv7oY +-JDlRqMC1HfZJCFQDQrHy5VJ+CywA/H9WrqKo/Ch9U4tJAZtkig1Cmay/BAYixVu0 +-xBeim10aKF6hxHH4Chg9We+OCuzWBWJhqveNjuDedL/i7JUCQQDlejovcwBUCbhJ +-U12qKOwlaboolWbl7yF3XdckTJZg7+1UqQHZH5jYZlLZyZxiaC92SNV0SyTLJZnS +-Jh5CO+VDAkEA16/pPcuVtMMz/R6SSPpRSIAa1stLs0mFSs3NpR4pdm0n42mu05pO +-1tJEt3a1g7zkreQBf53+Dwb+lA841EkjRwJBAIFmt0DifKDnCkBu/jZh9SfzwsH3 +-3Zpzik+hXxxdA7+ODCrdUul449vDd5zQD5t+XKU61QNLDGhxv5e9XvrCg7kCQH/a +-3ldsVF0oDaxxL+QkxoREtCQ5tLEd1u7F2q6Tl56FDE0pe6Ih6bQ8RtG+g9EI60IN +-U7oTrOO5kLWx5E0q4ccCQAZVgoenn9MhRU1agKOCuM6LT2DxReTu4XztJzynej+8 +-0J93n3ebanB1MlRpn1XJwhQ7gAC8ImaQKLJK5jdJzFc= +------END RSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIIEvQIBADANBgkqhkiG9w0BAQEFAASCBKcwggSjAgEAAoIBAQCyyQXED5HyVWwq ++nXyzmY317yMUJrIfsKvREG2C691dJNHgNg+oq5sjt/fzkyS84AvdOiicAsao4cYL ++DulthaLpbC7msEBhvwAil0FNb5g3ERupe1KuTdUV1UuD/i6S2VoaNXUBBn1rD9Wc ++BBc0lnx/4Wt92eQTI6925pt7ZHPQw2Olp7TQDElyi5qPxCem4uT0g3zbZsWqmmsI ++MXbu+K3dEprzqA1ucKXbxUmZNkMwVs2XCmlLxrRUj8C3/zENtH17HWCznhR/IVcV ++kgIuklkeiDsEhbWvUQumVXR7oPh/CPZAbjGqq5mVueHSHrp7brBVZKHZvoUka28Q ++LWitq1W5AgMBAAECggEASkRnOMKfBeOmQy2Yl6K57eeg0sYgSDnDpd0FINWJ5x9c ++b58FcjOXBodtYKlHIY6QXx3BsM0WaSEge4d+QBi7S+u8r+eXVwNYswXSArDQsk9R ++Bl5MQkvisGciL3pvLmFLpIeASyS/BLJXMbAhU58PqK+jT2wr6idwxBuXivJ3ichu ++ISdT1s2aMmnD86ulCD2DruZ4g0mmk5ffV+Cdj+WWkyvEaJW2GRYov2qdaqwSOxV4 ++Yve9qStvEIWAf2cISQjbnw2Ww6Z5ebrqlOz9etkmwIly6DTbrIneBnoqJlFFWGlF ++ghuzc5RE2w1GbcKSOt0qXH44MTf/j0r86dlu7UIxgQKBgQDq0pEaiZuXHi9OQAOp ++PsDEIznCU1bcTDJewANHag5DPEnMKLltTNyLaBRulMypI+CrDbou0nDr29VOzfXx ++mNvi/c7RttOBOx7kXKvu0JUFKe2oIWRsg0KsyMX7UFMVaHFgrW+8DhQc7HK7URiw ++nitOnA7YwIHRF9BMmcWcLFEYBQKBgQDC6LPbXV8COKO0YCfGXPnE7EZGD/p0Q92Z ++8CoSefphEScSdO1IpxFXG7fOZ4x2GQb9q7D3IvaeKAqNjUjkuyxdB30lIWDBwSWw ++fFgsa2SZwD5P60G/ar50YJr6LiF333aUMDVmC9swFfZERAEmGUz2NTrPWQdIx/lu ++PyDtUR75JQKBgHaoCCJ8vl5SJl1IA5GV4Bo8IoeLTSzsY9d09zMy6BoZcMD1Ix2T ++5S2cXhayoegl9PT6bsYSGHVWFCdJ86ktMI826TcXRzDaCvYhzc9THroJQcnfdbtP ++aHWezkv7fsAmkoPjn75K7ubeo+r7Q5qbkg6a1PW58N8TRXIvkackzaVxAoGBALAq ++qh3U+AHG9dgbrPeyo6KkuCOtX39ks8/mbfCDRZYkbb9V5f5r2tVz3R93IlK/7jyr ++yWimtmde46Lrl33922w+T5OW5qBZllo9GWkUrDn3s5qClcuQjJIdmxYTSfbSCJiK ++NkmE39lHkG5FVRB9f71tgTlWS6ox7TYDYxx83NTtAoGAUJPAkGt4yGAN4Pdebv53 ++bSEpAAULBHntiqDEOu3lVColHuZIucml/gbTpQDruE4ww4wE7dOhY8Q4wEBVYbRI ++vHkSiWpJUvZCuKG8Foh5pm9hU0qb+rbQV7NhLJ02qn1AMGO3F/WKrHPPY8/b9YhQ ++KfvPCYimQwBjVrEnSntLPR0= ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIICaTCCAdKgAwIBAgIJAP6VN47boiXRMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDdaFw0xNjA1MTExMzUzMDdaMEQx +-CzAJBgNVBAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRU +-ZXN0IFMvTUlNRSBSU0EgUm9vdDCBnzANBgkqhkiG9w0BAQEFAAOBjQAwgYkCgYEA +-wVdWf0OYDxe5aI3PKSlHcs+fiX9gd77OIXunoHpLoFp6CXbpIvS52nvyXIQf7KCF +-9HKN5y3NdTbhRZZwFiTTAya9PJeQBwCS2DR3rxeZf3/aA0ML2bKXiodcaSACTagk +-81XkP2S8evxnHCF1f8Q7iiIqL6iUz4EeVj5GCmsPvpUCAwEAAaNjMGEwHQYDVR0O +-BBYEFBPPS6e7iS6zOFcXdsabrWhb5e0XMB8GA1UdIwQYMBaAFBPPS6e7iS6zOFcX +-dsabrWhb5e0XMA8GA1UdEwEB/wQFMAMBAf8wDgYDVR0PAQH/BAQDAgEGMA0GCSqG +-SIb3DQEBBQUAA4GBAIECprq5viDvnDbkyOaiSr9ubMUmWqvycfAJMdPZRKcOZczS +-l+L9R9lF3JSqbt3knOe9u6bGDBOTY2285PdCCuHRVMk2Af1f6El1fqAlRUwNqipp +-r68sWFuRqrcRNtk6QQvXfkOhrqQBuDa7te/OVQLa2lGN9Dr2mQsD8ijctatG ++MIIDbjCCAlagAwIBAgIJAMc+8VKBJ/S9MA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MjlaFw0yMzA3MTUxNzI4MjlaMEQx ++CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRU ++ZXN0IFMvTUlNRSBSU0EgUm9vdDCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoC ++ggEBALLJBcQPkfJVbCqdfLOZjfXvIxQmsh+wq9EQbYLr3V0k0eA2D6irmyO39/OT ++JLzgC906KJwCxqjhxgsO6W2FoulsLuawQGG/ACKXQU1vmDcRG6l7Uq5N1RXVS4P+ ++LpLZWho1dQEGfWsP1ZwEFzSWfH/ha33Z5BMjr3bmm3tkc9DDY6WntNAMSXKLmo/E ++J6bi5PSDfNtmxaqaawgxdu74rd0SmvOoDW5wpdvFSZk2QzBWzZcKaUvGtFSPwLf/ ++MQ20fXsdYLOeFH8hVxWSAi6SWR6IOwSFta9RC6ZVdHug+H8I9kBuMaqrmZW54dIe ++untusFVkodm+hSRrbxAtaK2rVbkCAwEAAaNjMGEwHQYDVR0OBBYEFMmRUwpjexZb ++i71E8HaIqSTm5bZsMB8GA1UdIwQYMBaAFMmRUwpjexZbi71E8HaIqSTm5bZsMA8G ++A1UdEwEB/wQFMAMBAf8wDgYDVR0PAQH/BAQDAgEGMA0GCSqGSIb3DQEBBQUAA4IB ++AQAwpIVWQey2u/XoQSMSu0jd0EZvU+lhLaFrDy/AHQeG3yX1+SAOM6f6w+efPvyb ++Op1NPI9UkMPb4PCg9YC7jgYokBkvAcI7J4FcuDKMVhyCD3cljp0ouuKruvEf4FBl ++zyQ9pLqA97TuG8g1hLTl8G90NzTRcmKpmhs18BmCxiqHcTfoIpb3QvPkDX8R7LVt ++9BUGgPY+8ELCgw868TuHh/Cnc67gBtRjBp0sCYVzGZmKsO5f1XdHrAZKYN5mEp0C ++7/OqcDoFqORTquLeycg1At/9GqhDEgxNrqA+YEsPbLGAfsNuXUsXs2ubpGsOZxKt ++Emsny2ah6fU2z7PztrUy/A80 + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smrsa1.pem b/test/smime-certs/smrsa1.pem +index 2cf3148..d0d0b9e 100644 +--- a/test/smime-certs/smrsa1.pem ++++ b/test/smime-certs/smrsa1.pem +@@ -1,31 +1,49 @@ +------BEGIN RSA PRIVATE KEY----- +-MIICXgIBAAKBgQC6A978j4pmPgUtUQqF+bjh6vdhwGOGZSD7xXgFTMjm88twfv+E +-ixkq2KXSDjD0ZXoQbdOaSbvGRQrIJpG2NGiKAFdYNrP025kCCdh5wF/aEI7KLEm7 +-JlHwXpQsuj4wkMgmkFjL3Ty4Z55aNH+2pPQIa0k+ENJXm2gDuhqgBmduAwIDAQAB +-AoGBAJMuYu51aO2THyeHGwt81uOytcCbqGP7eoib62ZOJhxPRGYjpmuqX+R9/V5i +-KiwGavm63JYUx0WO9YP+uIZxm1BUATzkgkS74u5LP6ajhkZh6/Bck1oIYYkbVOXl +-JVrdENuH6U7nupznsyYgONByo+ykFPVUGmutgiaC7NMVo/MxAkEA6KLejWXdCIEn +-xr7hGph9NlvY9xuRIMexRV/WrddcFfCdjI1PciIupgrIkR65M9yr7atm1iU6/aRf +-KOr8rLZsSQJBAMyyXN71NsDNx4BP6rtJ/LJMP0BylznWkA7zWfGCbAYn9VhZVlSY +-Eu9Gyr7quD1ix7G3kInKVYOEEOpockBLz+sCQQCedyMmKjcQLfpMVYW8uhbAynvW +-h36qV5yXZxszO7nMcCTBsxhk5IfmLv5EbCs3+p9avCDGyoGOeUMg+kC33WORAkAg +-oUIarH4o5+SoeJTTfCzTA0KF9H5U0vYt2+73h7HOnWoHxl3zqDZEfEVvf50U8/0f +-QELDJETTbScBJtsnkq43AkEA38etvoZ2i4FJvvo7R/9gWBHVEcrGzcsCBYrNnIR1 +-SZLRwHEGaiOK1wxMsWzqp7PJwL9z/M8A8DyOFBx3GPOniA== +------END RSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIIEvAIBADANBgkqhkiG9w0BAQEFAASCBKYwggSiAgEAAoIBAQDXr9uzB/20QXKC ++xhkfNnJvl2xl1hzdOcrQmAqo+AAAcA/D49ImuJDVQRaK2bcj54XB26i1kXuOrxID ++3/etUb8yudfx8OAVwh8G0xVA4zhr8uXW85W2tBr4v0Lt+W6lSd6Hmfrk4GmE9LTU ++/vzl9HUPW6SZShN1G0nY6oeUXvLi0vasEUKv3a51T6JFYg4c7qt5RCk/w8kwrQ0D ++orQwCdkOPEIiC4b+nPStF12SVm5bx8rbYzioxuY/PdSebvt0APeqgRxSpCxqYnHs ++CoNeHzSrGXcP0COzFeUOz2tdrhmH09JLbGZs4nbojPxMkjpJSv3/ekDG2CHYxXSH ++XxpJstxZAgMBAAECggEASY4xsJaTEPwY3zxLqPdag2/yibBBW7ivz/9p80HQTlXp ++KnbxXj8nNXLjCytAZ8A3P2t316PrrTdLP4ML5lGwkM4MNPhek00GY79syhozTa0i ++cPHVJt+5Kwee/aVI9JmCiGAczh0yHyOM3+6ttIZvvXMVaSl4BUHvJ0ikQBc5YdzL ++s6VM2gCOR6K6n+39QHDI/T7WwO9FFSNnpWFOCHwAWtyBMlleVj+xeZX8OZ/aT+35 ++27yjsGNBftWKku29VDineiQC+o+fZGJs6w4JZHoBSP8TfxP8fRCFVNA281G78Xak ++cEnKXwZ54bpoSa3ThKl+56J6NHkkfRGb8Rgt/ipJYQKBgQD5DKb82mLw85iReqsT ++8bkp408nPOBGz7KYnQsZqAVNGfehM02+dcN5z+w0jOj6GMPLPg5whlEo/O+rt9ze ++j6c2+8/+B4Bt5oqCKoOCIndH68jl65+oUxFkcHYxa3zYKGC9Uvb+x2BtBmYgvDRG ++ew6I2Q3Zyd2ThZhJygUZpsjsbQKBgQDdtNiGTkgWOm+WuqBI1LT5cQfoPfgI7/da ++ZA+37NBUQRe0cM7ddEcNqx7E3uUa1JJOoOYv65VyGI33Ul+evI8h5WE5bupcCEFk ++LolzbMc4YQUlsySY9eUXM8jQtfVtaWhuQaABt97l+9oADkrhA+YNdEu2yiz3T6W+ ++msI5AnvkHQKBgDEjuPMdF/aY6dqSjJzjzfgg3KZOUaZHJuML4XvPdjRPUlfhKo7Q ++55/qUZ3Qy8tFBaTderXjGrJurc+A+LiFOaYUq2ZhDosguOWUA9yydjyfnkUXZ6or ++sbvSoM+BeOGhnezdKNT+e90nLRF6cQoTD7war6vwM6L+8hxlGvqDuRNFAoGAD4K8 ++d0D4yB1Uez4ZQp8m/iCLRhM3zCBFtNw1QU/fD1Xye5w8zL96zRkAsRNLAgKHLdsR ++355iuTXAkOIBcJCOjveGQsdgvAmT0Zdz5FBi663V91o+IDlryqDD1t40CnCKbtRG ++hng/ruVczg4x7OYh7SUKuwIP/UlkNh6LogNreX0CgYBQF9troLex6X94VTi1V5hu ++iCwzDT6AJj63cS3VRO2ait3ZiLdpKdSNNW2WrlZs8FZr/mVutGEcWho8BugGMWST ++1iZkYwly9Xfjnpd0I00ZIlr2/B3+ZsK8w5cOW5Lpb7frol6+BkDnBjbNZI5kQndn ++zQpuMJliRlrq/5JkIbH6SA== ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIICizCCAfSgAwIBAgIJAMtotfHYdEsTMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDhaFw0xNjA1MTAxMzUzMDhaMEUx ++MIIDbDCCAlSgAwIBAgIJANk5lu6mSyBAMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzBaFw0yMzA1MjYxNzI4MzBaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBSU0EgIzEwgZ8wDQYJKoZIhvcNAQEBBQADgY0AMIGJAoGB +-ALoD3vyPimY+BS1RCoX5uOHq92HAY4ZlIPvFeAVMyObzy3B+/4SLGSrYpdIOMPRl +-ehBt05pJu8ZFCsgmkbY0aIoAV1g2s/TbmQIJ2HnAX9oQjsosSbsmUfBelCy6PjCQ +-yCaQWMvdPLhnnlo0f7ak9AhrST4Q0lebaAO6GqAGZ24DAgMBAAGjgYMwgYAwHQYD +-VR0OBBYEFE2vMvKz5jrC7Lbdg68XwZ95iL/QMB8GA1UdIwQYMBaAFBPPS6e7iS6z +-OFcXdsabrWhb5e0XMAwGA1UdEwEB/wQCMAAwDgYDVR0PAQH/BAQDAgXgMCAGA1Ud +-EQQZMBeBFXNtaW1lcnNhMUBvcGVuc3NsLm9yZzANBgkqhkiG9w0BAQUFAAOBgQAi +-O3GOkUl646oLnOimc36i9wxZ1tejsqs8vMjJ0Pym6Uq9FE2JoGzJ6OhB1GOsEVmj +-9cQ5UNQcRYL3cqOFtl6f4Dpu/lhzfbaqgmLjv29G1mS0uuTZrixhlyCXjwcbOkNC +-I/+wvHHENYIK5+T/79M9LaZ2Qk4F9MNE1VMljdz9Qw== ++ZXN0IFMvTUlNRSBFRSBSU0EgIzEwggEiMA0GCSqGSIb3DQEBAQUAA4IBDwAwggEK ++AoIBAQDXr9uzB/20QXKCxhkfNnJvl2xl1hzdOcrQmAqo+AAAcA/D49ImuJDVQRaK ++2bcj54XB26i1kXuOrxID3/etUb8yudfx8OAVwh8G0xVA4zhr8uXW85W2tBr4v0Lt +++W6lSd6Hmfrk4GmE9LTU/vzl9HUPW6SZShN1G0nY6oeUXvLi0vasEUKv3a51T6JF ++Yg4c7qt5RCk/w8kwrQ0DorQwCdkOPEIiC4b+nPStF12SVm5bx8rbYzioxuY/PdSe ++bvt0APeqgRxSpCxqYnHsCoNeHzSrGXcP0COzFeUOz2tdrhmH09JLbGZs4nbojPxM ++kjpJSv3/ekDG2CHYxXSHXxpJstxZAgMBAAGjYDBeMAwGA1UdEwEB/wQCMAAwDgYD ++VR0PAQH/BAQDAgXgMB0GA1UdDgQWBBTmjc+lrTQuYx/VBOBGjMvufajvhDAfBgNV ++HSMEGDAWgBTJkVMKY3sWW4u9RPB2iKkk5uW2bDANBgkqhkiG9w0BAQUFAAOCAQEA ++dr2IRXcFtlF16kKWs1VTaFIHHNQrfSVHBkhKblPX3f/0s/i3eXgwKUu7Hnb6T3/o ++E8L+e4ioQNhahTLt9ruJNHWA/QDwOfkqM3tshCs2xOD1Cpy7Bd3Dn0YBrHKyNXRK ++WelGp+HetSXJGW4IZJP7iES7Um0DGktLabhZbe25EnthRDBjNnaAmcofHECWESZp ++lEHczGZfS9tRbzOCofxvgLbF64H7wYSyjAe6R8aain0VRbIusiD4tCHX/lOMh9xT ++GNBW8zTL+tV9H1unjPMORLnT0YQ3oAyEND0jCu0ACA1qGl+rzxhF6bQcTUNEbRMu ++9Hjq6s316fk4Ne0EUF3PbA== + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smrsa2.pem b/test/smime-certs/smrsa2.pem +index d41f69c..2f17cb2 100644 +--- a/test/smime-certs/smrsa2.pem ++++ b/test/smime-certs/smrsa2.pem +@@ -1,31 +1,49 @@ +------BEGIN RSA PRIVATE KEY----- +-MIICWwIBAAKBgQCwBfryW4Vu5U9wNIDKspJO/N9YF4CcTlrCUyzVlKgb+8urHlSe +-59i5verR9IOCCXkemjOzZ/3nALTGqYZlnEvHp0Rjk+KdKXnKBIB+SRPpeu3LcXMT +-WPgsThPa0UQxedNKG0g6aG+kLhsDlFBCoxd09jJtSpb9jmroJOq0ZYEHLwIDAQAB +-AoGAKa/w4677Je1W5+r3SYoLDnvi5TkDs4D3C6ipKJgBTEdQz+DqB4w/DpZE4551 +-+rkFn1LDxcxuHGRVa+tAMhZW97fwq9YUbjVZEyOz79qrX+BMyl/NbHkf1lIKDo3q +-dWalzQvop7nbzeLC+VmmviwZfLQUbA61AQl3jm4dswT4XykCQQDloDadEv/28NTx +-bvvywvyGuvJkCkEIycm4JrIInvwsd76h/chZ3oymrqzc7hkEtK6kThqlS5y+WXl6 +-QzPruTKTAkEAxD2ro/VUoN+scIVaLmn0RBmZ67+9Pdn6pNSfjlK3s0T0EM6/iUWS +-M06l6L9wFS3/ceu1tIifsh9BeqOGTa+udQJARIFnybTBaIqw/NZ/lA1YCVn8tpvY +-iyaoZ6gjtS65TQrsdKeh/i3HCHNUXxUpoZ3F/H7QtD+6o49ODou+EbVOwQJAVmex +-A2gp8wuJKaINqxIL81AybZLnCCzKJ3lXJ5tUNyLNM/lUbGStktm2Q1zHRQwTxV07 +-jFn7trn8YrtNjzcjYQJAUKIJRt38A8Jw3HoPT+D0WS2IgxjVL0eYGsZX1lyeammG +-6rfnQ3u5uP7mEK2EH2o8mDUpAE0gclWBU9UkKxJsGA== +------END RSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIIEvgIBADANBgkqhkiG9w0BAQEFAASCBKgwggSkAgEAAoIBAQDcYC4tS2Uvn1Z2 ++iDgtfkJA5tAqgbN6X4yK02RtVH5xekV9+6+eTt/9S+iFAzAnwqR/UB1R67ETrsWq ++V8u9xLg5fHIwIkmu9/6P31UU9cghO7J1lcrhHvooHaFpcXepPWQacpuBq2VvcKRD ++lDfVmdM5z6eS3dSZPTOMMP/xk4nhZB8mcw27qiccPieS0PZ9EZB63T1gmwaK1Rd5 ++U94Pl0+zpDqhViuXmBfiIDWjjz0BzHnHSz5Rg4S3oXF1NcojhptIWyI0r7dgn5J3 ++NxC4kgKdjzysxo6iWd0nLgz7h0jUdj79EOis4fg9G4f0EFWyQf7iDxGaA93Y9ePB ++Jv5iFZVZAgMBAAECggEBAILIPX856EHb0KclbhlpfY4grFcdg9LS04grrcTISQW1 ++J3p9nBpZ+snKe6I8Yx6lf5PiipPsSLlCliHiWpIzJZVQCkAQiSPiHttpEYgP2IYI ++dH8dtznkdVbLRthZs0bnnPmpHCpW+iqpcYJ9eqkz0cvUNUGOjjWmwWmoRqwp/8CW ++3S1qbkQiCh0Mk2fQeGar76R06kXQ9MKDEj14zyS3rJX+cokjEoMSlH8Sbmdh2mJz ++XlNZcvqmeGJZwQWgbVVHOMUuZaKJiFa+lqvOdppbqSx0AsCRq6vjmjEYQEoOefYK ++3IJM9IvqW5UNx0Cy4kQdjhZFFwMO/ALD3QyF21iP4gECgYEA+isQiaWdaY4UYxwK ++Dg+pnSCKD7UGZUaCUIv9ds3CbntMOONFe0FxPsgcc4jRYQYj1rpQiFB8F11+qXGa ++P/IHcnjr2+mTrNY4I9Bt1Lg+pHSS8QCgzeueFybYMLaSsXUo7tGwpvw6UUb6/YWI ++LNCzZbrCLg1KZjGODhhxtvN45ZkCgYEA4YNSe+GMZlxgsvxbLs86WOm6DzJUPvxN ++bWmni0+Oe0cbevgGEUjDVc895uMFnpvlgO49/C0AYJ+VVbStjIMgAeMnWj6OZoSX ++q49rI8KmKUxKgORZiiaMqGWQ7Rxv68+4S8WANsjFxoUrE6dNV3uYDIUsiSLbZeI8 ++38KVTcLohcECgYEAiOdyWHGq0G4xl/9rPUCzCMsa4velNV09yYiiwBZgVgfhsawm ++hQpOSBZJA60XMGqkyEkT81VgY4UF4QLLcD0qeCnWoXWVHFvrQyY4RNZDacpl87/t ++QGO2E2NtolL3umesa+2TJ/8Whw46Iu2llSjtVDm9NGiPk5eA7xPPf1iEi9kCgYAb ++0EmVE91wJoaarLtGS7LDkpgrFacEWbPnAbfzW62UENIX2Y1OBm5pH/Vfi7J+vHWS ++8E9e0eIRCL2vY2hgQy/oa67H151SkZnvQ/IP6Ar8Xvd1bDSK8HQ6tMQqKm63Y9g0 ++KDjHCP4znOsSMnk8h/bZ3HcAtvbeWwftBR/LBnYNQQKBgA1leIXLLHRoX0VtS/7e ++y7Xmn7gepj+gDbSuCs5wGtgw0RB/1z/S3QoS2TCbZzKPBo20+ivoRP7gcuFhduFR ++hT8V87esr/QzLVpjLedQDW8Xb7GiO3BsU/gVC9VcngenbL7JObl3NgvdreIYo6+n ++yrLyf+8hjm6H6zkjqiOkHAl+ ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIICizCCAfSgAwIBAgIJAMtotfHYdEsUMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDhaFw0xNjA1MTAxMzUzMDhaMEUx ++MIIDbDCCAlSgAwIBAgIJANk5lu6mSyBBMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzBaFw0yMzA1MjYxNzI4MzBaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBSU0EgIzIwgZ8wDQYJKoZIhvcNAQEBBQADgY0AMIGJAoGB +-ALAF+vJbhW7lT3A0gMqykk7831gXgJxOWsJTLNWUqBv7y6seVJ7n2Lm96tH0g4IJ +-eR6aM7Nn/ecAtMaphmWcS8enRGOT4p0pecoEgH5JE+l67ctxcxNY+CxOE9rRRDF5 +-00obSDpob6QuGwOUUEKjF3T2Mm1Klv2Oaugk6rRlgQcvAgMBAAGjgYMwgYAwHQYD +-VR0OBBYEFIL/u+mEvaw7RuKLRuElfVkxSQjYMB8GA1UdIwQYMBaAFBPPS6e7iS6z +-OFcXdsabrWhb5e0XMAwGA1UdEwEB/wQCMAAwDgYDVR0PAQH/BAQDAgXgMCAGA1Ud +-EQQZMBeBFXNtaW1lcnNhMkBvcGVuc3NsLm9yZzANBgkqhkiG9w0BAQUFAAOBgQC2 +-rXR5bm/9RtOMQPleNpd3y6uUX3oy+0CafK5Yl3PMnItjjnKJ0l1/DbLbDj2twehe +-ewaB8CROcBCA3AMLSmGvPKgUCFMGtWam3328M4fBHzon5ka7qDXzM+imkAly/Yx2 +-YNdR/aNOug+5sXygHmTSKqiCpQjOIClzXoPVVeEVHw== ++ZXN0IFMvTUlNRSBFRSBSU0EgIzIwggEiMA0GCSqGSIb3DQEBAQUAA4IBDwAwggEK ++AoIBAQDcYC4tS2Uvn1Z2iDgtfkJA5tAqgbN6X4yK02RtVH5xekV9+6+eTt/9S+iF ++AzAnwqR/UB1R67ETrsWqV8u9xLg5fHIwIkmu9/6P31UU9cghO7J1lcrhHvooHaFp ++cXepPWQacpuBq2VvcKRDlDfVmdM5z6eS3dSZPTOMMP/xk4nhZB8mcw27qiccPieS ++0PZ9EZB63T1gmwaK1Rd5U94Pl0+zpDqhViuXmBfiIDWjjz0BzHnHSz5Rg4S3oXF1 ++NcojhptIWyI0r7dgn5J3NxC4kgKdjzysxo6iWd0nLgz7h0jUdj79EOis4fg9G4f0 ++EFWyQf7iDxGaA93Y9ePBJv5iFZVZAgMBAAGjYDBeMAwGA1UdEwEB/wQCMAAwDgYD ++VR0PAQH/BAQDAgXgMB0GA1UdDgQWBBT0arpyYMHXDPVL7MvzE+lx71L7sjAfBgNV ++HSMEGDAWgBTJkVMKY3sWW4u9RPB2iKkk5uW2bDANBgkqhkiG9w0BAQUFAAOCAQEA ++I8nM42am3aImkZyrw8iGkaGhKyi/dfajSWx6B9izBUh+3FleBnUxxOA+mn7M8C47 ++Ne18iaaWK8vEux9KYTIY8BzXQZL1AuZ896cXEc6bGKsME37JSsocfuB5BIGWlYLv ++/ON5/SJ0iVFj4fAp8z7Vn5qxRJj9BhZDxaO1Raa6cz6pm0imJy9v8y01TI6HsK8c ++XJQLs7/U4Qb91K+IDNX/lgW3hzWjifNpIpT5JyY3DUgbkD595LFV5DDMZd0UOqcv ++6cyN42zkX8a0TWr3i5wu7pw4k1oD19RbUyljyleEp0DBauIct4GARdBGgi5y1H2i ++NzYzLAPBkHCMY0Is3KKIBw== + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smrsa3.pem b/test/smime-certs/smrsa3.pem +index c8cbe55..14c27f6 100644 +--- a/test/smime-certs/smrsa3.pem ++++ b/test/smime-certs/smrsa3.pem +@@ -1,31 +1,49 @@ +------BEGIN RSA PRIVATE KEY----- +-MIICXAIBAAKBgQC6syTZtZNe1hRScFc4PUVyVLsr7+C1HDIZnOHmwFoLayX6RHwy +-ep/TkdwiPHnemVLuwvpSjLMLZkXy/J764kSHJrNeVl3UvmCVCOm40hAtK1+F39pM +-h8phkbPPD7i+hwq4/Vs79o46nzwbVKmzgoZBJhZ+codujUSYM3LjJ4aq+wIDAQAB +-AoGAE1Zixrnr3bLGwBMqtYSDIOhtyos59whImCaLr17U9MHQWS+mvYO98if1aQZi +-iQ/QazJ+wvYXxWJ+dEB+JvYwqrGeuAU6He/rAb4OShG4FPVU2D19gzRnaButWMeT +-/1lgXV08hegGBL7RQNaN7b0viFYMcKnSghleMP0/q+Y/oaECQQDkXEwDYJW13X9p +-ijS20ykWdY5lLknjkHRhhOYux0rlhOqsyMZjoUmwI2m0qj9yrIysKhrk4MZaM/uC +-hy0xp3hdAkEA0Uv/UY0Kwsgc+W6YxeypECtg1qCE6FBib8n4iFy/6VcWqhvE5xrs +-OdhKv9/p6aLjLneGd1sU+F8eS9LGyKIbNwJBAJPgbNzXA7uUZriqZb5qeTXxBDfj +-RLfXSHYKAKEULxz3+JvRHB9SR4yHMiFrCdExiZrHXUkPgYLSHLGG5a4824UCQD6T +-9XvhquUARkGCAuWy0/3Eqoihp/t6BWSdQ9Upviu7YUhtUxsyXo0REZB7F4pGrJx5 +-GlhXgFaewgUzuUHFzlMCQCzJMMWslWpoLntnR6sMhBMhBFHSw+Y5CbxBmFrdtSkd +-VdtNO1VuDCTxjjW7W3Khj7LX4KZ1ye/5jfAgnnnXisc= +------END RSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIIEvgIBADANBgkqhkiG9w0BAQEFAASCBKgwggSkAgEAAoIBAQCyK+BTAOJKJjji ++OhY60NeZjzGGZxEBfCm62n0mwkzusW/V/e63uwj6uOVCFoVBz5doMf3M6QIS2jL3 ++Aw6Qs5+vcuLA0gHrqIwjYQz1UZ5ETLKLKbQw6YOIVfsFSTxytUVpfcByrubWiLKX ++63theG1/IVokDK/9/k52Kyt+wcCjuRb7AJQFj2OLDRuWm/gavozkK103gQ+dUq4H ++XamZMtTq1EhQOfc0IUeCOEL6xz4jzlHHfzLdkvb7Enhav2sXDfOmZp/DYf9IqS7l ++vFkkINPVbYFBTexaPZlFwmpGRjkmoyH/w+Jlcpzs+w6p1diWRpaSn62bbkRN49j6 ++L2dVb+DfAgMBAAECggEAciwDl6zdVT6g/PbT/+SMA+7qgYHSN+1koEQaJpgjzGEP ++lUUfj8TewCtzXaIoyj9IepBuXryBg6snNXpT/w3bqgYon/7zFBvxkUpDj4A5tvKf ++BuY2fZFlpBvUu1Ju1eKrFCptBBBoA9mc+BUB/ze4ktrAdJFcxZoMlVScjqGB3GdR ++OHw2x9BdWGCJBhiu9VHhAAb/LVWi6xgDumYSWZwN2yovg+7J91t5bsENeBRHycK+ ++i5dNFh1umIK9N0SH6bpHPnLHrCRchrQ6ZRRxL4ZBKA9jFRDeI7OOsJuCvhGyJ1se ++snsLjr/Ahg00aiHCcC1SPQ6pmXAVBCG7hf4AX82V4QKBgQDaFDE+Fcpv84mFo4s9 ++wn4CZ8ymoNIaf5zPl/gpH7MGots4NT5+Ns+6zzJQ6TEpDjTPx+vDaabP7QGXwVZn ++8NAHYvCQK37b+u9HrOt256YYRDOmnJFSbsJdmqzMEzpTNmQ8GuI37cZCS9CmSMv+ ++ab/plcwuv0cJRSC83NN2AFyu1QKBgQDRJzKIBQlpprF9rA0D5ZjLVW4OH18A0Mmm ++oanw7qVutBaM4taFN4M851WnNIROyYIlkk2fNgW57Y4M8LER4zLrjU5HY4lB0BMX ++LQWDbyz4Y7L4lVnnEKfQxWFt9avNZwiCxCxEKy/n/icmVCzc91j9uwKcupdzrN6E ++yzPd1s5y4wKBgQCkJvzmAdsOp9/Fg1RFWcgmIWHvrzBXl+U+ceLveZf1j9K5nYJ7 ++2OBGer4iH1XM1I+2M4No5XcWHg3L4FEdDixY0wXHT6Y/CcThS+015Kqmq3fBmyrc ++RNjzQoF9X5/QkSmkAIx1kvpgXtcgw70htRIrToGSUpKzDKDW6NYXhbA+PQKBgDJK ++KH5IJ8E9kYPUMLT1Kc4KVpISvPcnPLVSPdhuqVx69MkfadFSTb4BKbkwiXegQCjk ++isFzbeEM25EE9q6EYKP+sAm+RyyJ6W0zKBY4TynSXyAiWSGUAaXTL+AOqCaVVZiL ++rtEdSUGQ/LzclIT0/HLV2oTw4KWxtTdc3LXEhpNdAoGBAM3LckiHENqtoeK2gVNw ++IPeEuruEqoN4n+XltbEEv6Ymhxrs6T6HSKsEsLhqsUiIvIzH43KMm45SNYTn5eZh ++yzYMXLmervN7c1jJe2Y2MYv6hE+Ypj1xGW4w7s8WNKmVzLv97beisD9AZrS7sXfF ++RvOAi5wVkYylDxV4238MAZIq ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIICizCCAfSgAwIBAgIJAMtotfHYdEsVMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDlaFw0xNjA1MTAxMzUzMDlaMEUx ++MIIDbDCCAlSgAwIBAgIJANk5lu6mSyBCMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzBaFw0yMzA1MjYxNzI4MzBaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBSU0EgIzMwgZ8wDQYJKoZIhvcNAQEBBQADgY0AMIGJAoGB +-ALqzJNm1k17WFFJwVzg9RXJUuyvv4LUcMhmc4ebAWgtrJfpEfDJ6n9OR3CI8ed6Z +-Uu7C+lKMswtmRfL8nvriRIcms15WXdS+YJUI6bjSEC0rX4Xf2kyHymGRs88PuL6H +-Crj9Wzv2jjqfPBtUqbOChkEmFn5yh26NRJgzcuMnhqr7AgMBAAGjgYMwgYAwHQYD +-VR0OBBYEFDsSFjNtYZzd0tTHafNS7tneQQj6MB8GA1UdIwQYMBaAFBPPS6e7iS6z +-OFcXdsabrWhb5e0XMAwGA1UdEwEB/wQCMAAwDgYDVR0PAQH/BAQDAgXgMCAGA1Ud +-EQQZMBeBFXNtaW1lcnNhM0BvcGVuc3NsLm9yZzANBgkqhkiG9w0BAQUFAAOBgQBE +-tUDB+1Dqigu4p1xtdq7JRK6S+gfA7RWmhz0j2scb2zhpS12h37JLHsidGeKAzZYq +-jUjOrH/j3xcV5AnuJoqImJaN23nzzxtR4qGGX2mrq6EtObzdEGgCUaizsGM+0slJ +-PYxcy8KeY/63B1BpYhj2RjGkL6HrvuAaxVORa3acoA== ++ZXN0IFMvTUlNRSBFRSBSU0EgIzMwggEiMA0GCSqGSIb3DQEBAQUAA4IBDwAwggEK ++AoIBAQCyK+BTAOJKJjjiOhY60NeZjzGGZxEBfCm62n0mwkzusW/V/e63uwj6uOVC ++FoVBz5doMf3M6QIS2jL3Aw6Qs5+vcuLA0gHrqIwjYQz1UZ5ETLKLKbQw6YOIVfsF ++STxytUVpfcByrubWiLKX63theG1/IVokDK/9/k52Kyt+wcCjuRb7AJQFj2OLDRuW ++m/gavozkK103gQ+dUq4HXamZMtTq1EhQOfc0IUeCOEL6xz4jzlHHfzLdkvb7Enha ++v2sXDfOmZp/DYf9IqS7lvFkkINPVbYFBTexaPZlFwmpGRjkmoyH/w+Jlcpzs+w6p ++1diWRpaSn62bbkRN49j6L2dVb+DfAgMBAAGjYDBeMAwGA1UdEwEB/wQCMAAwDgYD ++VR0PAQH/BAQDAgXgMB0GA1UdDgQWBBQ6CkW5sa6HrBsWvuPOvMjyL5AnsDAfBgNV ++HSMEGDAWgBTJkVMKY3sWW4u9RPB2iKkk5uW2bDANBgkqhkiG9w0BAQUFAAOCAQEA ++JhcrD7AKafVzlncA3cZ6epAruj1xwcfiE+EbuAaeWEGjoSltmevcjgoIxvijRVcp ++sCbNmHJZ/siQlqzWjjf3yoERvLDqngJZZpQeocMIbLRQf4wgLAuiBcvT52wTE+sa ++VexeETDy5J1OW3wE4A3rkdBp6hLaymlijFNnd5z/bP6w3AcIMWm45yPm0skM8RVr ++O3UstEFYD/iy+p+Y/YZDoxYQSW5Vl+NkpGmc5bzet8gQz4JeXtH3z5zUGoDM4XK7 ++tXP3yUi2eecCbyjh/wgaQiVdylr1Kv3mxXcTl+cFO22asDkh0R/y72nTCu5fSILY ++CscFo2Z2pYROGtZDmYqhRw== + -----END CERTIFICATE----- -- GitLab From 73fdfc638a0da3bea0ac53e15f29b480f2138b15 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Sun, 15 May 2016 16:41:57 +0200 Subject: [PATCH 1684/2133] Fix checksum after updating patch --- easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index c013f5f3e6..5df9e5efff 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -32,7 +32,7 @@ patches = [ checksums = [ '031a82fa26e2c9412e55d964f92fc9e9', # scorep-2.0.1.tar.gz - 'e5bfc115b9013b87a294a3bd84db02ed', # Score-P-2.0.1_fix_score_configure.patch + '557b3a292591740271be7f336d5b7473', # Score-P-2.0.1_fix_score_configure.patch ] dependencies = [ -- GitLab From 83129f4445b05f5dbc7a4d20468b63f9512ab4b0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 15 May 2016 22:03:37 +0100 Subject: [PATCH 1685/2133] Update sympy to 1.0 and add patch to fix Unicode-related test failure --- .../mpmath-0.19-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ .../sympy-1.0-foss-2016a-Python-2.7.11.eb | 33 ++++++++++++++++++ .../s/sympy/sympy-1.0_tests-unicode.patch | 19 +++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..6602e3fb19 --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '0.19' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/fredrik-johansson/mpmath/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Python', '2.7.11')] + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpmath'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..4c408ec5d7 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +#Patch to fix tests +patches = ['sympy-1.0_tests-unicode.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('mpmath', '0.19', '-Python-%(pyver)s'), +] + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)-py%(pyshortver)s.egg/%(name)s'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch new file mode 100644 index 0000000000..a17da8977f --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch @@ -0,0 +1,19 @@ +Fix for Unicode error that causes one of the tests to fail + +For reference, see +http://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte +and http://nedbatchelder.com/text/unipain/unipain.html + + +diff -ur sympy-sympy-1.0/sympy/utilities/autowrap.py sympy-sympy-1.0.new/sympy/utilities/autowrap.py +--- sympy-sympy-1.0/sympy/utilities/autowrap.py 2016-03-08 18:35:33.000000000 +0000 ++++ sympy-sympy-1.0.new/sympy/utilities/autowrap.py 2016-05-15 10:54:52.870235379 +0100 +@@ -164,7 +164,7 @@ + except CalledProcessError as e: + raise CodeWrapError( + "Error while executing command: %s. Command output is:\n%s" % ( +- " ".join(command), e.output.decode())) ++ " ".join(command), e.output.decode('ascii', 'ignore'))) + if not self.quiet: + print(retoutput) + -- GitLab From a7995c806ecdb67cbbe8041d8cc571bdfe8f6202 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 May 2016 10:37:37 +0800 Subject: [PATCH 1686/2133] drop unnecessary comments --- .../a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index 049507e41f..d13b10cfef 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -20,9 +20,6 @@ configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' configopts += '--with-fft-flavor=fftw3-mkl ' configopts += '--with-fft-libs="$LIBFFT"' -# there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? -# eb --try-amend can be used to install those variants from the same easyconfig file... - sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], -- GitLab From 5fdcf6ce002aa13e8815c42b46820dd8d6356035 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 May 2016 10:39:38 +0800 Subject: [PATCH 1687/2133] rename variant --- ....9_libxc.eb => ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/ABINIT/{ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb => ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb} (97%) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb similarity index 97% rename from easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb rename to easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb index 113a1ca853..cfbc03496c 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'ABINIT' version = "7.10.5" -versionsuffix = "_libxc" +versionsuffix = "-libxc" homepage = 'http://www.abinit.org/' description = """ABINIT is a package whose main program allows one to find the total energy, -- GitLab From a36025898df5b11b7838e507cc0b105d5fcb5cc5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 May 2016 12:16:43 +0800 Subject: [PATCH 1688/2133] remove unnecessary comments --- .../a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb index cfbc03496c..9651451f5d 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb @@ -21,9 +21,6 @@ configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' configopts += '--with-fft-flavor=fftw3-mkl ' configopts += '--with-fft-libs="$LIBFFT" ' -# there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? -# eb --try-amend can be used to install those variants from the same easyconfig file... - # libxc variant configopts += '--with-dft-flavor=libxc ' -- GitLab From 57d47457ef583e6ad0755d3a66a3f9cf65bcdff0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 16 May 2016 06:00:04 +0100 Subject: [PATCH 1689/2133] Fix typo in sanity check macros --- .../easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb index 4c408ec5d7..6ab91f87e3 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb @@ -27,7 +27,7 @@ runtest = 'python setup.py test' sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)-py%(pyshortver)s.egg/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg/%(name)s'], } moduleclass = 'math' -- GitLab From 7a6a7ba89c52be30e19e5546fafb96bbaf8975d2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 16 May 2016 10:05:45 +0100 Subject: [PATCH 1690/2133] Add authorship info to the patch for unicode --- easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch index a17da8977f..87e12a3b40 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch @@ -4,6 +4,10 @@ For reference, see http://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte and http://nedbatchelder.com/text/unipain/unipain.html +Patch created by: + +Adam Huffman +The Francis Crick Institute diff -ur sympy-sympy-1.0/sympy/utilities/autowrap.py sympy-sympy-1.0.new/sympy/utilities/autowrap.py --- sympy-sympy-1.0/sympy/utilities/autowrap.py 2016-03-08 18:35:33.000000000 +0000 -- GitLab From 225b21792ef7ff57a6e5ad60686d569277128ca1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 16 May 2016 10:10:26 +0100 Subject: [PATCH 1691/2133] Add link for upstream versioning --- .../a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index 110e6af4ca..b0297d5d90 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -6,6 +6,7 @@ easyblock = 'Tarball' name = 'annovar' # Unconventional version is taken from the upstream site +# http://annovar.openbioinformatics.org/en/latest/user-guide/download/ version = '2016Feb01' versionsuffix = '-Perl-%(perlver)s' -- GitLab From 207aaede2ddbdade821faaf9b554a34644dc2013 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 16 May 2016 10:19:38 +0100 Subject: [PATCH 1692/2133] Fix merge conflict from annovar --- .../a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index 2ab347b203..e14e022891 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -19,13 +19,9 @@ toolchain = {'name': 'foss', 'version': '2016a'} # Registration required for download # http://www.openbioinformatics.org/annovar/annovar_download_form.php -<<<<<<< HEAD # rename after download to %(name)s-%(version)s.tar.gz sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['2b26e514c54a847bfdcf4ce57e43f95c'] -======= -sources = ['%(name)s.latest.tar.gz'] ->>>>>>> annovar dependencies = [('Perl', '5.22.1')] -- GitLab From 3b931d441a287ca1d2be5b399c87ce6bcc344fc6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 May 2016 12:26:15 +0200 Subject: [PATCH 1693/2133] add back patch in OpenSSL easyconfig --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb index 91cb41c8eb..4428c9a63c 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb @@ -13,6 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', 'OpenSSL-1.0.x_fix-tests-certs.patch', ] -- GitLab From 922ad368943477ba75a831f18969b85f49fc7bcf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 May 2016 12:27:10 +0200 Subject: [PATCH 1694/2133] remove unneeded patch in OpenSSL easyconfig --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb index c4f94fabf9..85aca68623 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb @@ -12,10 +12,7 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = [ - 'OpenSSL-%(version)s_icc-fixes.patch', - 'OpenSSL-1.0.x_fix-tests-certs.patch', -] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] dependencies = [('zlib', '1.2.8')] -- GitLab From e73986eef546f8d93b0d26664c74db6bab061803 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 May 2016 10:25:48 +0200 Subject: [PATCH 1695/2133] bump version to 2.8.0 and update release notes --- RELEASE_NOTES | 71 +++++++++++++++++++++++++++++++++++++++++++++++++-- setup.py | 2 +- 2 files changed, 70 insertions(+), 3 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b5c225454e..cb97cc538e 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,75 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 5,580 easyconfig files, for 862 different software packages, -34 different (compiler) toolchains, 12 software bundles and 1 meta-package. +The latest version of easybuild-easyconfig provides 6,063 easyconfig files, for 931 different software packages, +36 different (compiler) toolchains, 12 software bundles and 1 meta-package. + + +v2.8.0 (May 18th 2016) +---------------------- + +feature + bugfix release +- added example easyconfig files for 69 new software packages: + ALPS (#2888), annovar (#3010), BayeScEnv (#2765), BayesAss (#2870), BerkeleyGW (#2925), Blitz++ (#2784, #3004), + bam-readcount (#2850), Commet (#2938), CrossTalkZ (#2939), cuDNN (#2882), DBus (#2855), DFT-D3 (#2107), + DIAL (#3056), dask (#2885), dbus-glib (#2855), FFLAS-FFPACK (#2793), FLAC (#2824), FLANN (#3015, #3029), + FLEUR (#3043), GConf (#2855), GROMOS++ (#1297), GST-plugins-base (#2855), GStreamer (#2855), GTOOL (#2805), + Givaro (#2793), gdist (#2935), gromosXX (#1297), HISAT2 (#2809), i-PI (#2940), Kraken (#3037, #3041), LAME (#2823), + LASTZ (#3002), LinBox (#2793), Loki (#2839), libQGLViewer (#2923, #3008), libXxf86vm (#2855), + MDSplus (#2787, #2838, #3027), MRIcron (#2831), Mawk (#2732), minieigen (#2839), mpmath (#3058), NBO (#3047, 3048), + NGS (#2803), NGS-Python (#2810), ncbi-vdb (#2808), OptiX (#2795), PCL (#3024), PEAR (#2731), PLplot (#2990), + Postgres-XL (#2891), PyGTS (#2969), RSeQC (#2788), Rust (#2920, #2943), rainbow (#2730), SHAPEIT (#2806), + SIONlib (#2908), Saxon-HE (#2773), Singularity (#2901), SoX (#2825), Subread (#2790), SuperLU (#2665), + travis (#2953), VASP (#2950), Wannier90 (#2906, #3042), wget (#3041), wxPython (#2855), xf86vidmodeproto (#2855), + Yade (#2839), Yambo (#2932) +- add test configuration for Travis (#2942, #2944, #2954) +- added easyconfigs for new PGI-based toolchains: pomkl/2016.03 (#2899, #2900, #3046), pomkl/2016.04 (#3044) +- added new easyconfigs for existing toolchains: + foss/2016.04 (#3013), intel/2016.02-GCC-5.3 (#2523), intel/2016.03-GCC-5.3 (#3009) +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + incl. CGAL 4.8, Clang 3.8.0, icc/ifort 2016.2.181 & 2016.3.210, imkl 11.3.2.181 & 11.3.3.210, impi 5.1.3.181, + LLVM 3.8.0, OpenCV 2.4.12, pandas 0.18.0, Qt 5.6.0, Scalasca 2.3, Score-P 2.0.1, SuiteSparse 4.5.2, WRF 3.8 +- various other enhancements, including: + - enhance ORCA easyconfig for compatibility with SLURM (#1819) + - enable -fPIC in GraphicsMagick easyconfig, required by Octave (#2764) + - clean up binutils easyconfigs to use binutils easyblock (#3006) + - add include/GraphicsMagick to CPATH in GraphicsMagick easyconfigs (#3034) + - update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (#3050) +- various bug fixes, including: + - fix perl extensions download urls (#2738) + - add Autconf as build dep for GCCcore (#2772) + - fix versions of extensions in Bioconductor 3.2 bundles (#2769) + - fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender (#2785, #2874) + - use 'env' wherever preconfig/build/installopts is used to set environmental variables (#2807, #2811, #2812) + - add zlib as explicit dep in Tk easyconfigs (#2815) + - consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#2774, #2779, #2816) + - fix homepage and description in Pygments easyconfigs (#2822) + - include pkg-config as build dependencies for libXau, libXdmcp, libxcb (#2827) + - consistently use XORG_*_SOURCE constants (#2829, #2830) + - update source URLs in ScientificPython easyconfig files (#2847) + - use XORG_LIB_SOURCE in libICE/libSM easyconfigs (#2848) + - add checksums in SuiteSparse easyconfigs (#2849) + - fix build deps for GObject-Introspection (#2852) + - correctly specify Perl location in git easyconfig (#2866) + - fix bitstring 3.1.3 download URL in Python easyconfigs, source tarball on PyPI disappeared (#2880) + - fix Perl dependency in worker, it required non-standard Perl modules (#2884) + - add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma (#2887) + - fix download URL for packmol (#2902) + - drop usempi toolchain in numexpr easyconfigs, not needed (#2937) + - fix use of resolve_dependencies in tests according to changes in framework (#2952) + - add dependency extensions for MarkupSafe and jsonscheme in IPython 3.2.3 easyconfigs (#2967) + - add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being used (#2971) + - add xproto build dependency for makedepend v1.0.5 (#2982) + - disable parallel build for Doxygen (#2986) + - fix source URLs for FreezeThaw and Tie::Function extensions for Perl v5.22.1 (#2988) + - add sed command in worker easyconfig files to fix module_path in conf/worker.conf (#2997, #3000) + - drop toolchainopts from Eigen easyconfigs, since it is headers-only (#3025) + - clean up dummy bzip2 easyconfig, define buildopts rather than defining $CC and $CFLAGS via os.environ (#3036) + - use %(pyshortver)s template rather than hardcoding 2.7 in VTK easyconfigs (#3052) + - correct install location of OpenCV Python bindings (#3054) + - include XZ as dependency for libunwind (#3055) + - add patch to fix broken OpenSSL tests due to expired certificates (#3057) + v2.7.0 (March 20th 2016) ------------------------ diff --git a/setup.py b/setup.py index cf1d254d29..d2fef70086 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.8.0.dev0' +VERSION = '2.8.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 1e705738e9567b5237324ca729f7646b1aedbadd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 May 2016 14:06:18 +0200 Subject: [PATCH 1696/2133] fix build status badges in README, use the ones from Travis --- README.rst | 22 ++++++---------------- 1 file changed, 6 insertions(+), 16 deletions(-) diff --git a/README.rst b/README.rst index becdc63ccb..b6fcf302e9 100644 --- a/README.rst +++ b/README.rst @@ -34,22 +34,12 @@ Related Python packages: *Build status overview:* -* **master** branch *(Python 2.4, Python 2.6, Python 2.7)* +* **master** branch: - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python24/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python24/ + .. image:: https://travis-ci.org/hpcugent/easybuild-easyconfigs.svg?branch=master + :target: https://travis-ci.org/hpcugent/easybuild-easyconfigs/branches - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master/ +* **develop** branch: - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python27/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python27/ - -* **develop** branch *(Python 2.4, Python 2.6, Python 2.7)* - - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python24/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python24/ - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop/ - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python27/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python27/ + .. image:: https://travis-ci.org/hpcugent/easybuild-easyconfigs.svg?branch=develop + :target: https://travis-ci.org/hpcugent/easybuild-easyconfigs/branches -- GitLab From 98ab18eb46e99ecef1396cfa001cfbb94a1c7859 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 May 2016 18:02:56 +0200 Subject: [PATCH 1697/2133] fix broken link to VSC website --- setup.py | 2 +- test/__init__.py | 2 +- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/suite.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/setup.py b/setup.py index cf1d254d29..6315d80947 100644 --- a/setup.py +++ b/setup.py @@ -4,7 +4,7 @@ # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # diff --git a/test/__init__.py b/test/__init__.py index 856f7e4178..e44e0c6e58 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -4,7 +4,7 @@ # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2d23e93e64..c92b7c5d93 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -4,7 +4,7 @@ # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 79a1fb0d08..18f087e264 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -5,7 +5,7 @@ # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # -- GitLab From c2c6064c86b5a9c18bc8eaf6db4bffc0981b2996 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 May 2016 18:40:55 +0200 Subject: [PATCH 1698/2133] include #2927,#3061,#3062 in release notes --- RELEASE_NOTES | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index cb97cc538e..55f4ecd971 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,8 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,063 easyconfig files, for 931 different software packages, -36 different (compiler) toolchains, 12 software bundles and 1 meta-package. +The latest version of easybuild-easyconfig provides 6,064 easyconfig files, for 931 different software packages, +37 different (compiler) toolchains, 12 software bundles and 1 meta-package. v2.8.0 (May 18th 2016) @@ -24,8 +24,9 @@ feature + bugfix release SIONlib (#2908), Saxon-HE (#2773), Singularity (#2901), SoX (#2825), Subread (#2790), SuperLU (#2665), travis (#2953), VASP (#2950), Wannier90 (#2906, #3042), wget (#3041), wxPython (#2855), xf86vidmodeproto (#2855), Yade (#2839), Yambo (#2932) -- add test configuration for Travis (#2942, #2944, #2954) -- added easyconfigs for new PGI-based toolchains: pomkl/2016.03 (#2899, #2900, #3046), pomkl/2016.04 (#3044) +- add test configuration for Travis (#2942, #2944, #2954, #3061) +- added easyconfigs for new PGI-based toolchains + - pomkl/2016.03 (#2899, #2900, #3046), pomkl/2016.04 (#3044), CrayPGI/2016.04 (#2927) - added new easyconfigs for existing toolchains: foss/2016.04 (#3013), intel/2016.02-GCC-5.3 (#2523), intel/2016.03-GCC-5.3 (#3009) - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... @@ -71,6 +72,7 @@ feature + bugfix release - correct install location of OpenCV Python bindings (#3054) - include XZ as dependency for libunwind (#3055) - add patch to fix broken OpenSSL tests due to expired certificates (#3057) + - fix broken link to VSC website in license headers (#3062) v2.7.0 (March 20th 2016) -- GitLab From bc0544e7432494b9fd1d575f235fb60ecc473528 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 May 2016 19:26:21 +0200 Subject: [PATCH 1699/2133] fix typo --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 55f4ecd971..295e4c0820 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -40,7 +40,7 @@ feature + bugfix release - update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (#3050) - various bug fixes, including: - fix perl extensions download urls (#2738) - - add Autconf as build dep for GCCcore (#2772) + - add Autoconf as build dep for GCCcore (#2772) - fix versions of extensions in Bioconductor 3.2 bundles (#2769) - fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender (#2785, #2874) - use 'env' wherever preconfig/build/installopts is used to set environmental variables (#2807, #2811, #2812) -- GitLab From d6e1b94b159fa6e0412e1c8d31f7d1254324e4b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 May 2016 07:11:37 +0200 Subject: [PATCH 1700/2133] fix minor style issue in v2.8.0 release notes --- RELEASE_NOTES | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 295e4c0820..bcf497ffd9 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -36,10 +36,10 @@ feature + bugfix release - enhance ORCA easyconfig for compatibility with SLURM (#1819) - enable -fPIC in GraphicsMagick easyconfig, required by Octave (#2764) - clean up binutils easyconfigs to use binutils easyblock (#3006) - - add include/GraphicsMagick to CPATH in GraphicsMagick easyconfigs (#3034) + - add include/GraphicsMagick to $CPATH in GraphicsMagick easyconfigs (#3034) - update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (#3050) - various bug fixes, including: - - fix perl extensions download urls (#2738) + - fix Perl extensions download urls (#2738) - add Autoconf as build dep for GCCcore (#2772) - fix versions of extensions in Bioconductor 3.2 bundles (#2769) - fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender (#2785, #2874) @@ -48,14 +48,13 @@ feature + bugfix release - consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#2774, #2779, #2816) - fix homepage and description in Pygments easyconfigs (#2822) - include pkg-config as build dependencies for libXau, libXdmcp, libxcb (#2827) - - consistently use XORG_*_SOURCE constants (#2829, #2830) + - consistently use XORG_*_SOURCE constants (#2829, #2830, #2848) - update source URLs in ScientificPython easyconfig files (#2847) - - use XORG_LIB_SOURCE in libICE/libSM easyconfigs (#2848) - add checksums in SuiteSparse easyconfigs (#2849) - fix build deps for GObject-Introspection (#2852) - correctly specify Perl location in git easyconfig (#2866) - fix bitstring 3.1.3 download URL in Python easyconfigs, source tarball on PyPI disappeared (#2880) - - fix Perl dependency in worker, it required non-standard Perl modules (#2884) + - fix Perl dependency in worker easyconfig, it requires non-standard Perl modules (#2884) - add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma (#2887) - fix download URL for packmol (#2902) - drop usempi toolchain in numexpr easyconfigs, not needed (#2937) -- GitLab From 7bca09efb06814a305de6ff5b41c1fedfd89ff22 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 18 May 2016 09:46:28 +0200 Subject: [PATCH 1701/2133] fixed patch --- .../r/RSEM/RSEM-1.2.30-foss-2016a.eb | 47 +- .../r/RSEM/RSEM-1.2.30_boost.patch | 23 - .../r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch | 162 ------- .../r/RSEM/RSEM-1.2.30_makefiles.patch | 59 +++ easybuild/easyconfigs/r/RSEM/sam/Makefile | 314 ------------- .../easyconfigs/r/RSEM/sam/Makefile.orig | 314 ------------- easybuild/easyconfigs/r/RSEM/sam/diff | 23 - easybuild/easyconfigs/r/RSEM/sam/hts/Makefile | 426 ------------------ .../easyconfigs/r/RSEM/sam/hts/Makefile.orig | 426 ------------------ easybuild/easyconfigs/r/RSEM/sam/hts/diff | 18 - 10 files changed, 69 insertions(+), 1743 deletions(-) delete mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch delete mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/Makefile delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/Makefile.orig delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/diff delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/Makefile delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/diff diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb index 0daeb572d1..9b54daaecd 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'RSEM' version = '1.2.30' @@ -11,47 +11,20 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/deweylab/RSEM/archive/'] sources = ['v%(version)s.tar.gz'] -#patches = ['RSEM-%(version)s_boost.patch'] +#patches = ['RSEM-%(version)s_zlib.patch'] +patches = ['RSEM-%(version)s_makefiles.patch'] -dependencies = [ - ('ncurses', '6.0'), -] +skipsteps = ['configure'] +installopts = "prefix=%(installdir)s" -list_of_executables = [ - "rsem_perl_utils.pm", - "rsem-bam2readdepth", - "rsem-bam2wig", - "rsem-build-read-index", - "rsem-calculate-credibility-intervals", - "rsem-calculate-expression", - "rsem-control-fdr", - "rsem-extract-reference-transcripts", - "rsem-generate-data-matrix", - "rsem-generate-ngvector", - "rsem-gen-transcript-plots", - "rsem-get-unique", - "rsem-gff3-to-gtf", - "rsem-parse-alignments", - "rsem-plot-model", - "rsem-plot-transcript-wiggles", - "rsem-prepare-reference", - "rsem-preref", - "rsem-refseq-extract-primary-assembly", - "rsem-run-ebseq", - "rsem-run-em", - "rsem-run-gibbs", - "rsem-sam-validator", - "rsem-scan-for-paired-end-reads", - "rsem-simulate-reads", - "rsem-synthesis-reference-transcripts", - "rsem-tbam2gbam", +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), ] -files_to_copy = [(list_of_executables, "bin"), "WHAT_IS_NEW"] - sanity_check_paths = { - 'files': ['''"bin/%s" % x for x in list_of_executables'''], - 'dirs': [], + 'files': [], + 'dirs': ['bin/samtools-1.3'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch deleted file mode 100644 index 5782cb6a2d..0000000000 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch +++ /dev/null @@ -1,23 +0,0 @@ ---- samtools-1.3/Makefile.orig 2016-05-13 11:39:28.000000000 +0200 -+++ samtools-1.3/Makefile 2016-05-13 11:42:52.000000000 +0200 -@@ -21,9 +21,9 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc -+#CC = gcc - CPPFLAGS = --CFLAGS = -g -Wall -O2 -+#CFLAGS = -g -Wall -O2 - LDFLAGS = - LIBS = - -@@ -83,7 +83,7 @@ - # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally - ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) - ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz -ldl $(LIBS) -+ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch deleted file mode 100644 index 206ac1fda2..0000000000 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch +++ /dev/null @@ -1,162 +0,0 @@ -#Use EB provided libz and use EB provided CXX and CXXFLAGS -# January 11, 2016 by B. Hajgato (Vrije Ubiversiteit Brussel) ---- Makefile.orig 2016-01-08 02:23:01.000000000 +0100 -+++ Makefile 2016-01-18 12:02:56.406105229 +0100 -@@ -1,6 +1,6 @@ --CC = g++ --CFLAGS = -Wall -c -I. --COFLAGS = -Wall -O3 -ffast-math -c -I. -+#CC = g++ -+#CFLAGS = -Wall -c -I. -+COFLAGS = ${CXXFLAGS} -Wall -c -I. - PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads - - .PHONY : all ebseq clean -@@ -8,6 +8,8 @@ - all : $(PROGRAMS) - - sam/libbam.a : -+ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i sam/Makefile -+ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i sam/bcftools/Makefile - cd sam ; ${MAKE} all - - Transcript.h : utils.h -@@ -15,10 +17,10 @@ - Transcripts.h : utils.h my_assert.h Transcript.h - - rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp -- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts -+ $(CXX) -Wall ${CXXFLAGS} extractRef.cpp -o rsem-extract-reference-transcripts - - rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp -- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts -+ $(CXX) -Wall ${CXXFLAGS} synthesisRef.cpp -o rsem-synthesis-reference-transcripts - - BowtieRefSeqPolicy.h : RefSeqPolicy.h - -@@ -28,10 +30,10 @@ - - - rsem-preref : preRef.o -- $(CC) preRef.o -o rsem-preref -+ $(CXX) preRef.o -o rsem-preref - - preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp -- $(CC) $(COFLAGS) preRef.cpp -+ $(CXX) $(COFLAGS) preRef.cpp - - - SingleRead.h : Read.h -@@ -52,14 +54,14 @@ - - - rsem-parse-alignments : parseIt.o sam/libbam.a -- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread -+ $(CXX) -o rsem-parse-alignments parseIt.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread - - parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp -- $(CC) -Wall -O2 -c -I. parseIt.cpp -+ $(CXX) $(COFLAGS) parseIt.cpp - - - rsem-build-read-index : utils.h buildReadIndex.cpp -- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index -+ $(CXX) ${CXXFLAGS} buildReadIndex.cpp -o rsem-build-read-index - - - simul.h : boost/random.hpp -@@ -87,57 +89,57 @@ - WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h - - rsem-run-em : EM.o sam/libbam.a -- $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread -+ $(CXX) -o rsem-run-em EM.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread - - EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp -- $(CC) $(COFLAGS) EM.cpp -+ $(CXX) $(COFLAGS) EM.cpp - - bc_aux.h : sam/bam.h - - BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h - - rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a -- $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall tbam2gbam.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp -- $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall bam2wig.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp -- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h -- $(CC) $(COFLAGS) wiggle.cpp -+ $(CXX) $(COFLAGS) wiggle.cpp - - rsem-simulate-reads : simulation.o -- $(CC) -o rsem-simulate-reads simulation.o -+ $(CXX) -o rsem-simulate-reads simulation.o - - simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp -- $(CC) $(COFLAGS) simulation.cpp -+ $(CXX) $(COFLAGS) simulation.cpp - - rsem-run-gibbs : Gibbs.o -- $(CC) -o rsem-run-gibbs Gibbs.o -lpthread -+ $(CXX) -o rsem-run-gibbs Gibbs.o -lpthread - - #some header files are omitted - Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp -- $(CC) $(COFLAGS) Gibbs.cpp -+ $(CXX) $(COFLAGS) Gibbs.cpp - - Buffer.h : my_assert.h - - rsem-calculate-credibility-intervals : calcCI.o -- $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread -+ $(CXX) -o rsem-calculate-credibility-intervals calcCI.o -lpthread - - #some header files are omitted - calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp -- $(CC) $(COFLAGS) calcCI.cpp -+ $(CXX) $(COFLAGS) calcCI.cpp - - rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a -- $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall getUnique.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a -- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall samValidator.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a -- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall scanForPairedEndReads.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - ebseq : - cd EBSeq ; ${MAKE} all ---- sam/Makefile.orig 2016-01-08 02:23:01.000000000 +0100 -+++ sam/Makefile 2016-01-18 12:08:43.769066188 +0100 -@@ -1,7 +1,7 @@ --CC= gcc -+#CC= gcc - CFLAGS_EXTRA= - #CFLAGS_EXTRA= -L/usr/include/ncurses --CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) -+#CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) - #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib - DFLAGS_EXTRA= - #DFLAGS_EXTRA= -Dexpl=exp -Dlogl=log ---- sam/bcftools/Makefile.orig 2016-01-08 02:23:01.000000000 +0100 -+++ sam/bcftools/Makefile 2016-01-18 12:09:10.076063429 +0100 -@@ -1,5 +1,5 @@ --CC= gcc --CFLAGS= -g -Wall -O2 #-m64 #-arch ppc -+#CC= gcc -+#CFLAGS= -g -Wall -O2 #-m64 #-arch ppc - DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE - LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o - OMISC= .. \ No newline at end of file diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch new file mode 100644 index 0000000000..483f79b1f2 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch @@ -0,0 +1,59 @@ +--- RSEM-1.2.30/Makefile 2016-04-20 23:59:26.000000000 +0200 ++++ RSEM-1.2.30.new/Makefile 2016-05-13 16:25:04.000000000 +0200 +@@ -11,12 +11,12 @@ + BOOST = . + + # Compilation variables +-CXX = g++ +-CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) +-CPPFLAGS = ++#CXX = g++ ++CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) ++#CPPFLAGS = + +-LDFLAGS = +-LDLIBS = ++#LDFLAGS = ++#LDLIBS = + + # Installation variables + INSTALL = install +--- RSEM-1.2.30/samtools-1.3/Makefile 2016-04-20 23:59:26.000000000 +0200 ++++ RSEM-1.2.30.new/samtools-1.3/Makefile 2016-05-13 16:25:42.000000000 +0200 +@@ -21,10 +21,10 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-CPPFLAGS = +-CFLAGS = -g -Wall -O2 +-LDFLAGS = ++#CC = gcc ++#CPPFLAGS = ++#CFLAGS = -g -Wall -O2 ++#LDFLAGS = + LIBS = + + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE +--- RSEM-1.2.30/samtools-1.3/htslib-1.3/Makefile 2016-04-20 23:59:26.000000000 +0200 ++++ RSEM-1.2.30.new/samtools-1.3/htslib-1.3/Makefile 2016-05-13 16:26:24.000000000 +0200 +@@ -22,15 +22,15 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++#CC = gcc + AR = ar + RANLIB = ranlib + +-CPPFLAGS = ++#CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat +-CFLAGS = -g -Wall -O2 ++#CFLAGS = -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic +-LDFLAGS = ++#LDFLAGS = + LIBS = + + # For now these don't work too well as samtools also needs to know to diff --git a/easybuild/easyconfigs/r/RSEM/sam/Makefile b/easybuild/easyconfigs/r/RSEM/sam/Makefile deleted file mode 100644 index c7e392d67c..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/Makefile +++ /dev/null @@ -1,314 +0,0 @@ -# Makefile for samtools, utilities for the Sequence Alignment/Map format. -# -# Copyright (C) 2008-2015 Genome Research Ltd. -# Portions copyright (C) 2010-2012 Broad Institute. -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -# DEALINGS IN THE SOFTWARE. - -#CC = gcc -CPPFLAGS = -#CFLAGS = -g -Wall -O2 -LDFLAGS = -LIBS = - -DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o -AOBJS= bam_index.o bam_plcmd.o sam_view.o \ - bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o \ - bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ - bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o \ - cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ - faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \ - bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ - bam_quickcheck.o bam_addrprg.o - -prefix = /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin -datarootdir = $(prefix)/share -mandir = $(datarootdir)/man -man1dir = $(mandir)/man1 - -MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_PROGRAM = $(INSTALL) -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 - - -PROGRAMS = samtools - -BUILT_MISC_PROGRAMS = \ - misc/ace2sam misc/maq2sam-long misc/maq2sam-short \ - misc/md5fa misc/md5sum-lite misc/wgsim - -MISC_PROGRAMS = \ - $(BUILT_MISC_PROGRAMS) \ - misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ - misc/interpolate_sam.pl misc/novo2sam.pl \ - misc/plot-bamstats misc/psl2sam.pl \ - misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \ - misc/soap2sam.pl \ - misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl - -BUILT_TEST_PROGRAMS = \ - test/merge/test_bam_translate \ - test/merge/test_rtrans_build \ - test/merge/test_trans_tbl_init \ - test/split/test_count_rg \ - test/split/test_expand_format_string \ - test/split/test_filter_header_rg \ - test/split/test_parse_args \ - test/vcf-miniview - -all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) - -# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally -ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) -ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) -ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) - -# Usually config.mk and config.h are generated by running configure -# or config.status, but if those aren't used create defaults here. - -config.mk: - @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ - -config.h: - echo '/* Basic config.h generated by Makefile */' > $@ - echo '#define HAVE_CURSES' >> $@ - echo '#define HAVE_CURSES_H' >> $@ - -include config.mk - - -PACKAGE_VERSION = 1.3 - -# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git -# description of the working tree: either a release tag with the same value -# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. -# $(shell), :=, etc are GNU Make-specific. If you don't have GNU Make, -# comment out this conditional. -ifneq "$(wildcard .git)" "" -PACKAGE_VERSION := $(shell git describe --always --dirty) - -# Force version.h to be remade if $(PACKAGE_VERSION) has changed. -version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) -endif - -# If you don't have GNU Make but are building from a Git repository, you may -# wish to replace this with a rule that always rebuilds version.h: -# version.h: force -# echo '#define SAMTOOLS_VERSION "`git describe --always --dirty`"' > $@ -version.h: - echo '#define SAMTOOLS_VERSION "$(PACKAGE_VERSION)"' > $@ - -print-version: - @echo $(PACKAGE_VERSION) - - -.SUFFIXES: .c .o - -.c.o: - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< - - -lib:libbam.a - -libbam.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - -samtools: $(AOBJS) libbam.a $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) - -bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) -bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h -bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) -bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) -bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) -sam_h = sam.h $(htslib_sam_h) $(bam_h) -sam_opts_h = sam_opts.h $(htslib_hts_h) -sample_h = sample.h $(htslib_kstring_h) - -bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h -bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h -bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) -bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) -bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) -bam_aux.o: bam_aux.c $(bam_h) -bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) -bam_color.o: bam_color.c $(bam_h) -bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) -bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h -bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) -bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) -bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) -bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) -bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) -bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) -bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h -bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) -bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) -bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) -bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) -bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h -bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) -bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) -bam_tview_html.o: bam_tview_html.c $(bam_tview_h) -bam_flags.o: bam_flags.c $(htslib_sam_h) -bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) -bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h -bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) -bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) -cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) -dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) -errmod.o: errmod.c errmod.h $(htslib_ksort_h) -kprobaln.o: kprobaln.c kprobaln.h -padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) -phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) -sam.o: sam.c $(htslib_faidx_h) $(sam_h) -sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) -sam_opts.o: sam_opts.c $(sam_opts_h) -sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) -sample.o: sample.c $(sample_h) $(htslib_khash_h) -stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) -stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) - - -# test programs - -# For tests that might use it, set $REF_PATH explicitly to use only reference -# areas within the test suite (or set it to ':' to use no reference areas). -# (regression.sh sets $REF_PATH to a subdirectory itself.) -check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) - REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) - test/merge/test_bam_translate test/merge/test_bam_translate.tmp - test/merge/test_rtrans_build - test/merge/test_trans_tbl_init - cd test/mpileup && ./regression.sh mpileup.reg - cd test/mpileup && ./regression.sh depth.reg - test/split/test_count_rg - test/split/test_expand_format_string - test/split/test_filter_header_rg - test/split/test_parse_args - - -test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) - -test_test_h = test/test.h $(htslib_sam_h) - -test/merge/test_bam_translate.o: test/merge/test_bam_translate.c bam_sort.o $(test_test_h) -test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c bam_sort.o -test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c bam_sort.o -test/split/test_count_rg.o: test/split/test_count_rg.c bam_split.o $(test_test_h) -test/split/test_expand_format_string.o: test/split/test_expand_format_string.c bam_split.o $(test_test_h) -test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c bam_split.o $(test_test_h) -test/split/test_parse_args.o: test/split/test_parse_args.c bam_split.o $(test_test_h) -test/test.o: test/test.c $(htslib_sam_h) $(test_test_h) -test/vcf-miniview.o: test/vcf-miniview.c $(htslib_vcf_h) - - -# misc programs - -misc/ace2sam: misc/ace2sam.o - $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) - -misc/maq2sam-short: misc/maq2sam-short.o - $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) - -misc/maq2sam-long: misc/maq2sam-long.o - $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) - -misc/md5fa: misc/md5fa.o $(HTSLIB) - $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) - -misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) - $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) - -misc/wgsim: misc/wgsim.o - $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) - -misc/ace2sam.o: misc/ace2sam.c $(htslib_kstring_h) $(htslib_kseq_h) -misc/md5fa.o: misc/md5fa.c $(htslib_kseq_h) $(htslib_hts_h) -misc/md5sum-lite.o: misc/md5sum-lite.c $(htslib_hts_h) -misc/wgsim.o: misc/wgsim.c $(htslib_kseq_h) - -misc/maq2sam-short.o: misc/maq2sam.c - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c - -misc/maq2sam-long.o: misc/maq2sam.c - $(CC) $(CFLAGS) -DMAQ_LONGREADS $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c - - -install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) - $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) - $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) - - -testclean: - -rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* - -cd test/dat && rm -f test_input_*.bam.bai - -cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam* - -mostlyclean: testclean - -rm -f *.o misc/*.o test/*.o test/*/*.o version.h - -clean: mostlyclean - -rm -f $(PROGRAMS) libbam.a $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) - -distclean: clean - -rm -f config.cache config.h config.log config.mk config.status - -rm -f TAGS - -clean-all: clean clean-htslib - - -tags: - ctags -f TAGS *.[ch] misc/*.[ch] - - -force: - - -.PHONY: all check clean clean-all distclean force install -.PHONY: lib mostlyclean print-version tags test testclean diff --git a/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig b/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig deleted file mode 100644 index 525288c2c8..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig +++ /dev/null @@ -1,314 +0,0 @@ -# Makefile for samtools, utilities for the Sequence Alignment/Map format. -# -# Copyright (C) 2008-2015 Genome Research Ltd. -# Portions copyright (C) 2010-2012 Broad Institute. -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -# DEALINGS IN THE SOFTWARE. - -CC = gcc -CPPFLAGS = -CFLAGS = -g -Wall -O2 -LDFLAGS = -LIBS = - -DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o -AOBJS= bam_index.o bam_plcmd.o sam_view.o \ - bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o \ - bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ - bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o \ - cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ - faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \ - bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ - bam_quickcheck.o bam_addrprg.o - -prefix = /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin -datarootdir = $(prefix)/share -mandir = $(datarootdir)/man -man1dir = $(mandir)/man1 - -MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_PROGRAM = $(INSTALL) -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 - - -PROGRAMS = samtools - -BUILT_MISC_PROGRAMS = \ - misc/ace2sam misc/maq2sam-long misc/maq2sam-short \ - misc/md5fa misc/md5sum-lite misc/wgsim - -MISC_PROGRAMS = \ - $(BUILT_MISC_PROGRAMS) \ - misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ - misc/interpolate_sam.pl misc/novo2sam.pl \ - misc/plot-bamstats misc/psl2sam.pl \ - misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \ - misc/soap2sam.pl \ - misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl - -BUILT_TEST_PROGRAMS = \ - test/merge/test_bam_translate \ - test/merge/test_rtrans_build \ - test/merge/test_trans_tbl_init \ - test/split/test_count_rg \ - test/split/test_expand_format_string \ - test/split/test_filter_header_rg \ - test/split/test_parse_args \ - test/vcf-miniview - -all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) - -# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally -ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) -ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) -ALL_LIBS = -lz -ldl $(LIBS) - -# Usually config.mk and config.h are generated by running configure -# or config.status, but if those aren't used create defaults here. - -config.mk: - @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ - -config.h: - echo '/* Basic config.h generated by Makefile */' > $@ - echo '#define HAVE_CURSES' >> $@ - echo '#define HAVE_CURSES_H' >> $@ - -include config.mk - - -PACKAGE_VERSION = 1.3 - -# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git -# description of the working tree: either a release tag with the same value -# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. -# $(shell), :=, etc are GNU Make-specific. If you don't have GNU Make, -# comment out this conditional. -ifneq "$(wildcard .git)" "" -PACKAGE_VERSION := $(shell git describe --always --dirty) - -# Force version.h to be remade if $(PACKAGE_VERSION) has changed. -version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) -endif - -# If you don't have GNU Make but are building from a Git repository, you may -# wish to replace this with a rule that always rebuilds version.h: -# version.h: force -# echo '#define SAMTOOLS_VERSION "`git describe --always --dirty`"' > $@ -version.h: - echo '#define SAMTOOLS_VERSION "$(PACKAGE_VERSION)"' > $@ - -print-version: - @echo $(PACKAGE_VERSION) - - -.SUFFIXES: .c .o - -.c.o: - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< - - -lib:libbam.a - -libbam.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - -samtools: $(AOBJS) libbam.a $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) - -bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) -bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h -bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) -bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) -bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) -sam_h = sam.h $(htslib_sam_h) $(bam_h) -sam_opts_h = sam_opts.h $(htslib_hts_h) -sample_h = sample.h $(htslib_kstring_h) - -bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h -bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h -bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) -bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) -bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) -bam_aux.o: bam_aux.c $(bam_h) -bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) -bam_color.o: bam_color.c $(bam_h) -bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) -bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h -bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) -bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) -bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) -bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) -bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) -bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) -bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h -bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) -bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) -bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) -bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) -bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h -bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) -bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) -bam_tview_html.o: bam_tview_html.c $(bam_tview_h) -bam_flags.o: bam_flags.c $(htslib_sam_h) -bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) -bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h -bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) -bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) -cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) -dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) -errmod.o: errmod.c errmod.h $(htslib_ksort_h) -kprobaln.o: kprobaln.c kprobaln.h -padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) -phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) -sam.o: sam.c $(htslib_faidx_h) $(sam_h) -sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) -sam_opts.o: sam_opts.c $(sam_opts_h) -sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) -sample.o: sample.c $(sample_h) $(htslib_khash_h) -stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) -stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) - - -# test programs - -# For tests that might use it, set $REF_PATH explicitly to use only reference -# areas within the test suite (or set it to ':' to use no reference areas). -# (regression.sh sets $REF_PATH to a subdirectory itself.) -check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) - REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) - test/merge/test_bam_translate test/merge/test_bam_translate.tmp - test/merge/test_rtrans_build - test/merge/test_trans_tbl_init - cd test/mpileup && ./regression.sh mpileup.reg - cd test/mpileup && ./regression.sh depth.reg - test/split/test_count_rg - test/split/test_expand_format_string - test/split/test_filter_header_rg - test/split/test_parse_args - - -test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) - -test_test_h = test/test.h $(htslib_sam_h) - -test/merge/test_bam_translate.o: test/merge/test_bam_translate.c bam_sort.o $(test_test_h) -test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c bam_sort.o -test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c bam_sort.o -test/split/test_count_rg.o: test/split/test_count_rg.c bam_split.o $(test_test_h) -test/split/test_expand_format_string.o: test/split/test_expand_format_string.c bam_split.o $(test_test_h) -test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c bam_split.o $(test_test_h) -test/split/test_parse_args.o: test/split/test_parse_args.c bam_split.o $(test_test_h) -test/test.o: test/test.c $(htslib_sam_h) $(test_test_h) -test/vcf-miniview.o: test/vcf-miniview.c $(htslib_vcf_h) - - -# misc programs - -misc/ace2sam: misc/ace2sam.o - $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) - -misc/maq2sam-short: misc/maq2sam-short.o - $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) - -misc/maq2sam-long: misc/maq2sam-long.o - $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) - -misc/md5fa: misc/md5fa.o $(HTSLIB) - $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) - -misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) - $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) - -misc/wgsim: misc/wgsim.o - $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) - -misc/ace2sam.o: misc/ace2sam.c $(htslib_kstring_h) $(htslib_kseq_h) -misc/md5fa.o: misc/md5fa.c $(htslib_kseq_h) $(htslib_hts_h) -misc/md5sum-lite.o: misc/md5sum-lite.c $(htslib_hts_h) -misc/wgsim.o: misc/wgsim.c $(htslib_kseq_h) - -misc/maq2sam-short.o: misc/maq2sam.c - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c - -misc/maq2sam-long.o: misc/maq2sam.c - $(CC) $(CFLAGS) -DMAQ_LONGREADS $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c - - -install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) - $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) - $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) - - -testclean: - -rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* - -cd test/dat && rm -f test_input_*.bam.bai - -cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam* - -mostlyclean: testclean - -rm -f *.o misc/*.o test/*.o test/*/*.o version.h - -clean: mostlyclean - -rm -f $(PROGRAMS) libbam.a $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) - -distclean: clean - -rm -f config.cache config.h config.log config.mk config.status - -rm -f TAGS - -clean-all: clean clean-htslib - - -tags: - ctags -f TAGS *.[ch] misc/*.[ch] - - -force: - - -.PHONY: all check clean clean-all distclean force install -.PHONY: lib mostlyclean print-version tags test testclean diff --git a/easybuild/easyconfigs/r/RSEM/sam/diff b/easybuild/easyconfigs/r/RSEM/sam/diff deleted file mode 100644 index 2469cafcc9..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/diff +++ /dev/null @@ -1,23 +0,0 @@ ---- Makefile.orig 2016-05-13 11:39:28.000000000 +0200 -+++ Makefile 2016-05-13 12:29:50.000000000 +0200 -@@ -21,9 +21,9 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc -+#CC = gcc - CPPFLAGS = --CFLAGS = -g -Wall -O2 -+#CFLAGS = -g -Wall -O2 - LDFLAGS = - LIBS = - -@@ -83,7 +83,7 @@ - # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally - ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) - ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz -ldl $(LIBS) -+ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile deleted file mode 100644 index 00c103599b..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile +++ /dev/null @@ -1,426 +0,0 @@ -# Makefile for htslib, a C library for high-throughput sequencing data formats. -# -# Copyright (C) 2013-2015 Genome Research Ltd. -# -# Author: John Marshall -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -# DEALINGS IN THE SOFTWARE. - -#CC = gcc -AR = ar -RANLIB = ranlib - -CPPFLAGS = -# TODO: probably update cram code to make it compile cleanly with -Wc++-compat -#CFLAGS = -g -Wall -O2 -EXTRA_CFLAGS_PIC = -fpic -LDFLAGS = -LIBS = - -# For now these don't work too well as samtools also needs to know to -# add -lbz2 and -llzma if linking against the static libhts.a library. -# TODO This needs configury and adding to htslib.pc.in. -# -# # Bzip2 support; optionally used by CRAM. -# HAVE_LIBBZ2 := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes) -# ifeq "$(HAVE_LIBBZ2)" "yes" -# CPPFLAGS += -DHAVE_LIBBZ2 -# LIBS += -lbz2 -# endif -# -# # Lzma support; optionally used by CRAM. -# HAVE_LIBLZMA := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes) -# ifeq "$(HAVE_LIBLZMA)" "yes" -# CPPFLAGS += -DHAVE_LIBLZMA -# LIBS += -llzma -# endif - -prefix = /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin -includedir = $(prefix)/include -libdir = $(exec_prefix)/lib -libexecdir = $(exec_prefix)/libexec -datarootdir = $(prefix)/share -mandir = $(datarootdir)/man -man1dir = $(mandir)/man1 -man5dir = $(mandir)/man5 -pkgconfigdir= $(libdir)/pkgconfig - -MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_PROGRAM = $(INSTALL) -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 - -# Set by config.mk if plugins are enabled -plugindir = - -BUILT_PROGRAMS = \ - bgzip \ - htsfile \ - tabix - -BUILT_TEST_PROGRAMS = \ - test/fieldarith \ - test/hfile \ - test/sam \ - test/test-regidx \ - test/test_view \ - test/test-vcf-api \ - test/test-vcf-sweep - -all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) - -HTSPREFIX = -include htslib_vars.mk - - -PACKAGE_VERSION = 1.3 -LIBHTS_SOVERSION = 1 - - -# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string -# even if this is a dirty or untagged Git working tree. -NUMERIC_VERSION = $(PACKAGE_VERSION) - -# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git -# description of the working tree: either a release tag with the same value -# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. -# Much of this is also GNU Make-specific. If you don't have GNU Make and/or -# are not building from a Git repository, comment out this conditional. -ifneq "$(wildcard .git)" "" -original_version := $(PACKAGE_VERSION) -PACKAGE_VERSION := $(shell git describe --always --dirty) - -# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag -# with a numeric name, revert $(NUMERIC_VERSION) to the original version number -# written above, but with the patchlevel field bumped to 255. -ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "." -empty := -NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255) -endif - -# Force version.h to be remade if $(PACKAGE_VERSION) has changed. -version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) -endif - -version.h: - echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@ - -print-version: - @echo $(PACKAGE_VERSION) - - -.SUFFIXES: .bundle .c .o .pico .so - -.c.o: - $(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $< - -.c.pico: - $(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< - - -LIBHTS_OBJS = \ - kfunc.o \ - knetfile.o \ - kstring.o \ - bgzf.o \ - faidx.o \ - hfile.o \ - hfile_net.o \ - hts.o \ - md5.o \ - regidx.o \ - sam.o \ - synced_bcf_reader.o \ - vcf_sweep.o \ - tbx.o \ - vcf.o \ - vcfutils.o \ - cram/cram_codecs.o \ - cram/cram_decode.o \ - cram/cram_encode.o \ - cram/cram_external.o \ - cram/cram_index.o \ - cram/cram_io.o \ - cram/cram_samtools.o \ - cram/cram_stats.o \ - cram/files.o \ - cram/mFILE.o \ - cram/open_trace_file.o \ - cram/pooled_alloc.o \ - cram/rANS_static.o \ - cram/sam_header.o \ - cram/string_alloc.o \ - cram/thread_pool.o \ - cram/vlen.o \ - cram/zfio.o - -PLUGIN_OBJS = - -cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h) -cram_io_h = cram/cram_io.h $(cram_misc_h) -cram_misc_h = cram/misc.h cram/os.h -cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) -cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h) -cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h) -cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h -hfile_internal_h = hfile_internal.h $(htslib_hfile_h) -hts_internal_h = hts_internal.h $(htslib_hts_h) - - -# To be effective, config.mk needs to appear after most Makefile variables are -# set but before most rules appear, so that it can both use previously-set -# variables in its own rules' prerequisites and also update variables for use -# in later rules' prerequisites. - -# If your make doesn't accept -include, change this to 'include' if you are -# using the configure script or just comment the line out if you are not. --include config.mk - -# Usually config.h is generated by running configure or config.status, -# but if those aren't used create a default config.h here. -config.h: - echo '/* Empty config.h generated by Makefile */' > $@ - - -lib-static: libhts.a - -# $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have -# GNU Make, comment out the parts of this conditional that don't apply. -PLATFORM := $(shell uname -s) -ifeq "$(PLATFORM)" "Darwin" -SHLIB_FLAVOUR = dylib -lib-shared: libhts.dylib -BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle) -else -SHLIB_FLAVOUR = so -lib-shared: libhts.so -BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so) -endif - -plugins: $(BUILT_PLUGINS) - - -libhts.a: $(LIBHTS_OBJS) - @-rm -f $@ - $(AR) -rc $@ $(LIBHTS_OBJS) - -$(RANLIB) $@ - - -# The target here is libhts.so, as that is the built file that other rules -# depend upon and that is used when -lhts appears in other program's recipes. -# As a byproduct invisible to make, libhts.so.NN is also created, as it is the -# file used at runtime (when $LD_LIBRARY_PATH includes the build directory). - -libhts.so: $(LIBHTS_OBJS:.o=.pico) - $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS) - ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) - -# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs -# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH -# includes this project's build directory). - -libhts.dylib: $(LIBHTS_OBJS) - $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS) - ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib - - -.pico.so: - $(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS) - -.o.bundle: - $(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS) - - -bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h) -kstring.o kstring.pico: kstring.c $(htslib_kstring_h) -knetfile.o knetfile.pico: knetfile.c $(htslib_knetfile_h) -hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h) -hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) -hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) -hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h) -hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h) -vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) -sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) -tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h) -faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) -synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) -vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h) -vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h) -kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h) -regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) -md5.o md5.pico: md5.c config.h $(htslib_hts_h) -plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h) - -cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h) -cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) -cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) -cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h) -cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h) -cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) -cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h) -cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h -cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h) -cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h -cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h) -cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h -cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h -cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h -cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h -cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h -cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h -cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h - - -bgzip: bgzip.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS) - -htsfile: htsfile.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS) - -tabix: tabix.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS) - -bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) -htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) -tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) - - -# For tests that might use it, set $REF_PATH explicitly to use only reference -# areas within the test suite (or set it to ':' to use no reference areas). -check test: htsfile $(BUILT_TEST_PROGRAMS) - test/fieldarith test/fieldarith.sam - test/hfile - test/sam test/ce.fa test/faidx.fa - test/test-regidx - cd test && REF_PATH=: ./test_view.pl - cd test && REF_PATH=: ./test.pl - -test/fieldarith: test/fieldarith.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS) - -test/hfile: test/hfile.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS) - -test/sam: test/sam.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS) - -test/test-regidx: test/test-regidx.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS) - -test/test_view: test/test_view.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS) - -test/test-vcf-api: test/test-vcf-api.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS) - -test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS) - -test/fieldarith.o: test/fieldarith.c $(htslib_sam_h) -test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h) -test/sam.o: test/sam.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) -test/test-regidx.o: test/test-regidx.c $(htslib_regidx_h) -test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h) -test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h) -test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h) - - -install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig - $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir) - if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi - $(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib - $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a - $(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir) - $(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir) - -installdirs: - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir) - if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi - -# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, -# with symlinks libhts.so (used via -lhts during linking of client programs) -# and libhts.so.NN (used by client executables at runtime). - -install-so: libhts.so installdirs - $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) - ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so - ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) - -install-dylib: libhts.dylib installdirs - $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib - ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib - ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib - -# Substitute these pseudo-autoconf variables only at install time -# so that "make install prefix=/prefix/path" etc continue to work. -install-pkgconfig: installdirs - sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc - chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc - -# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides -# flags for building against the uninstalled library in this build directory. -htslib-uninstalled.pc: htslib.pc.in - sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@ - - -testclean: - -rm -f test/*.tmp test/*.tmp.* - -mostlyclean: testclean - -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h - -clean: mostlyclean clean-$(SHLIB_FLAVOUR) - -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) - -distclean maintainer-clean: clean - -rm -f config.cache config.h config.log config.mk config.status - -rm -f TAGS *-uninstalled.pc - -clean-so: - -rm -f libhts.so libhts.so.* - -clean-dylib: - -rm -f libhts.dylib libhts.*.dylib - - -tags TAGS: - ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h - -# We recommend libhts-using programs be built against a separate htslib -# installation. However if you feel that you must bundle htslib source -# code with your program, this hook enables Automake-style "make dist" -# for this subdirectory. If you do bundle an htslib snapshot, please -# add identifying information to $(PACKAGE_VERSION) as appropriate. -# (The wildcards attempt to omit non-exported files (.git*, README.md, -# etc) and other detritus that might be in the top-level directory.) -distdir: - tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x) - +cd $(distdir) && $(MAKE) distclean - -force: - - -.PHONY: all check clean distclean distdir force -.PHONY: install install-pkgconfig installdirs lib-shared lib-static -.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean -.PHONY: clean-so install-so -.PHONY: clean-dylib install-dylib diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig deleted file mode 100644 index be2405e71c..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig +++ /dev/null @@ -1,426 +0,0 @@ -# Makefile for htslib, a C library for high-throughput sequencing data formats. -# -# Copyright (C) 2013-2015 Genome Research Ltd. -# -# Author: John Marshall -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -# DEALINGS IN THE SOFTWARE. - -CC = gcc -AR = ar -RANLIB = ranlib - -CPPFLAGS = -# TODO: probably update cram code to make it compile cleanly with -Wc++-compat -CFLAGS = -g -Wall -O2 -EXTRA_CFLAGS_PIC = -fpic -LDFLAGS = -LIBS = - -# For now these don't work too well as samtools also needs to know to -# add -lbz2 and -llzma if linking against the static libhts.a library. -# TODO This needs configury and adding to htslib.pc.in. -# -# # Bzip2 support; optionally used by CRAM. -# HAVE_LIBBZ2 := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes) -# ifeq "$(HAVE_LIBBZ2)" "yes" -# CPPFLAGS += -DHAVE_LIBBZ2 -# LIBS += -lbz2 -# endif -# -# # Lzma support; optionally used by CRAM. -# HAVE_LIBLZMA := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes) -# ifeq "$(HAVE_LIBLZMA)" "yes" -# CPPFLAGS += -DHAVE_LIBLZMA -# LIBS += -llzma -# endif - -prefix = /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin -includedir = $(prefix)/include -libdir = $(exec_prefix)/lib -libexecdir = $(exec_prefix)/libexec -datarootdir = $(prefix)/share -mandir = $(datarootdir)/man -man1dir = $(mandir)/man1 -man5dir = $(mandir)/man5 -pkgconfigdir= $(libdir)/pkgconfig - -MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_PROGRAM = $(INSTALL) -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 - -# Set by config.mk if plugins are enabled -plugindir = - -BUILT_PROGRAMS = \ - bgzip \ - htsfile \ - tabix - -BUILT_TEST_PROGRAMS = \ - test/fieldarith \ - test/hfile \ - test/sam \ - test/test-regidx \ - test/test_view \ - test/test-vcf-api \ - test/test-vcf-sweep - -all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) - -HTSPREFIX = -include htslib_vars.mk - - -PACKAGE_VERSION = 1.3 -LIBHTS_SOVERSION = 1 - - -# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string -# even if this is a dirty or untagged Git working tree. -NUMERIC_VERSION = $(PACKAGE_VERSION) - -# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git -# description of the working tree: either a release tag with the same value -# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. -# Much of this is also GNU Make-specific. If you don't have GNU Make and/or -# are not building from a Git repository, comment out this conditional. -ifneq "$(wildcard .git)" "" -original_version := $(PACKAGE_VERSION) -PACKAGE_VERSION := $(shell git describe --always --dirty) - -# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag -# with a numeric name, revert $(NUMERIC_VERSION) to the original version number -# written above, but with the patchlevel field bumped to 255. -ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "." -empty := -NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255) -endif - -# Force version.h to be remade if $(PACKAGE_VERSION) has changed. -version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) -endif - -version.h: - echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@ - -print-version: - @echo $(PACKAGE_VERSION) - - -.SUFFIXES: .bundle .c .o .pico .so - -.c.o: - $(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $< - -.c.pico: - $(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< - - -LIBHTS_OBJS = \ - kfunc.o \ - knetfile.o \ - kstring.o \ - bgzf.o \ - faidx.o \ - hfile.o \ - hfile_net.o \ - hts.o \ - md5.o \ - regidx.o \ - sam.o \ - synced_bcf_reader.o \ - vcf_sweep.o \ - tbx.o \ - vcf.o \ - vcfutils.o \ - cram/cram_codecs.o \ - cram/cram_decode.o \ - cram/cram_encode.o \ - cram/cram_external.o \ - cram/cram_index.o \ - cram/cram_io.o \ - cram/cram_samtools.o \ - cram/cram_stats.o \ - cram/files.o \ - cram/mFILE.o \ - cram/open_trace_file.o \ - cram/pooled_alloc.o \ - cram/rANS_static.o \ - cram/sam_header.o \ - cram/string_alloc.o \ - cram/thread_pool.o \ - cram/vlen.o \ - cram/zfio.o - -PLUGIN_OBJS = - -cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h) -cram_io_h = cram/cram_io.h $(cram_misc_h) -cram_misc_h = cram/misc.h cram/os.h -cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) -cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h) -cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h) -cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h -hfile_internal_h = hfile_internal.h $(htslib_hfile_h) -hts_internal_h = hts_internal.h $(htslib_hts_h) - - -# To be effective, config.mk needs to appear after most Makefile variables are -# set but before most rules appear, so that it can both use previously-set -# variables in its own rules' prerequisites and also update variables for use -# in later rules' prerequisites. - -# If your make doesn't accept -include, change this to 'include' if you are -# using the configure script or just comment the line out if you are not. --include config.mk - -# Usually config.h is generated by running configure or config.status, -# but if those aren't used create a default config.h here. -config.h: - echo '/* Empty config.h generated by Makefile */' > $@ - - -lib-static: libhts.a - -# $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have -# GNU Make, comment out the parts of this conditional that don't apply. -PLATFORM := $(shell uname -s) -ifeq "$(PLATFORM)" "Darwin" -SHLIB_FLAVOUR = dylib -lib-shared: libhts.dylib -BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle) -else -SHLIB_FLAVOUR = so -lib-shared: libhts.so -BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so) -endif - -plugins: $(BUILT_PLUGINS) - - -libhts.a: $(LIBHTS_OBJS) - @-rm -f $@ - $(AR) -rc $@ $(LIBHTS_OBJS) - -$(RANLIB) $@ - - -# The target here is libhts.so, as that is the built file that other rules -# depend upon and that is used when -lhts appears in other program's recipes. -# As a byproduct invisible to make, libhts.so.NN is also created, as it is the -# file used at runtime (when $LD_LIBRARY_PATH includes the build directory). - -libhts.so: $(LIBHTS_OBJS:.o=.pico) - $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS) - ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) - -# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs -# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH -# includes this project's build directory). - -libhts.dylib: $(LIBHTS_OBJS) - $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS) - ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib - - -.pico.so: - $(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS) - -.o.bundle: - $(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS) - - -bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h) -kstring.o kstring.pico: kstring.c $(htslib_kstring_h) -knetfile.o knetfile.pico: knetfile.c $(htslib_knetfile_h) -hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h) -hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) -hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) -hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h) -hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h) -vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) -sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) -tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h) -faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) -synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) -vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h) -vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h) -kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h) -regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) -md5.o md5.pico: md5.c config.h $(htslib_hts_h) -plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h) - -cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h) -cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) -cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) -cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h) -cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h) -cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) -cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h) -cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h -cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h) -cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h -cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h) -cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h -cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h -cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h -cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h -cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h -cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h -cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h - - -bgzip: bgzip.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS) - -htsfile: htsfile.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS) - -tabix: tabix.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS) - -bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) -htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) -tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) - - -# For tests that might use it, set $REF_PATH explicitly to use only reference -# areas within the test suite (or set it to ':' to use no reference areas). -check test: htsfile $(BUILT_TEST_PROGRAMS) - test/fieldarith test/fieldarith.sam - test/hfile - test/sam test/ce.fa test/faidx.fa - test/test-regidx - cd test && REF_PATH=: ./test_view.pl - cd test && REF_PATH=: ./test.pl - -test/fieldarith: test/fieldarith.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS) - -test/hfile: test/hfile.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS) - -test/sam: test/sam.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS) - -test/test-regidx: test/test-regidx.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS) - -test/test_view: test/test_view.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS) - -test/test-vcf-api: test/test-vcf-api.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS) - -test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS) - -test/fieldarith.o: test/fieldarith.c $(htslib_sam_h) -test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h) -test/sam.o: test/sam.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) -test/test-regidx.o: test/test-regidx.c $(htslib_regidx_h) -test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h) -test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h) -test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h) - - -install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig - $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir) - if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi - $(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib - $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a - $(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir) - $(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir) - -installdirs: - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir) - if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi - -# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, -# with symlinks libhts.so (used via -lhts during linking of client programs) -# and libhts.so.NN (used by client executables at runtime). - -install-so: libhts.so installdirs - $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) - ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so - ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) - -install-dylib: libhts.dylib installdirs - $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib - ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib - ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib - -# Substitute these pseudo-autoconf variables only at install time -# so that "make install prefix=/prefix/path" etc continue to work. -install-pkgconfig: installdirs - sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc - chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc - -# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides -# flags for building against the uninstalled library in this build directory. -htslib-uninstalled.pc: htslib.pc.in - sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@ - - -testclean: - -rm -f test/*.tmp test/*.tmp.* - -mostlyclean: testclean - -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h - -clean: mostlyclean clean-$(SHLIB_FLAVOUR) - -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) - -distclean maintainer-clean: clean - -rm -f config.cache config.h config.log config.mk config.status - -rm -f TAGS *-uninstalled.pc - -clean-so: - -rm -f libhts.so libhts.so.* - -clean-dylib: - -rm -f libhts.dylib libhts.*.dylib - - -tags TAGS: - ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h - -# We recommend libhts-using programs be built against a separate htslib -# installation. However if you feel that you must bundle htslib source -# code with your program, this hook enables Automake-style "make dist" -# for this subdirectory. If you do bundle an htslib snapshot, please -# add identifying information to $(PACKAGE_VERSION) as appropriate. -# (The wildcards attempt to omit non-exported files (.git*, README.md, -# etc) and other detritus that might be in the top-level directory.) -distdir: - tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x) - +cd $(distdir) && $(MAKE) distclean - -force: - - -.PHONY: all check clean distclean distdir force -.PHONY: install install-pkgconfig installdirs lib-shared lib-static -.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean -.PHONY: clean-so install-so -.PHONY: clean-dylib install-dylib diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/diff b/easybuild/easyconfigs/r/RSEM/sam/hts/diff deleted file mode 100644 index 97af9b3e44..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/hts/diff +++ /dev/null @@ -1,18 +0,0 @@ ---- Makefile.orig 2016-05-13 12:08:45.000000000 +0200 -+++ Makefile 2016-05-13 12:10:21.000000000 +0200 -@@ -22,13 +22,13 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc -+#CC = gcc - AR = ar - RANLIB = ranlib - - CPPFLAGS = - # TODO: probably update cram code to make it compile cleanly with -Wc++-compat --CFLAGS = -g -Wall -O2 -+#CFLAGS = -g -Wall -O2 - EXTRA_CFLAGS_PIC = -fpic - LDFLAGS = - LIBS = -- GitLab From 0254d8662fae60a862eafae16a99fa71776a81b2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 18 May 2016 09:50:12 +0200 Subject: [PATCH 1702/2133] provided author and reason for patch --- easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch index 483f79b1f2..4edfe60165 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch @@ -1,3 +1,5 @@ +# Remove preset CXX and CPPFLAGS for each makefile, such that it uses the ones defined by EB. +# Author: Bob Dröge - Rijksuniversiteit Groningen (RUG) --- RSEM-1.2.30/Makefile 2016-04-20 23:59:26.000000000 +0200 +++ RSEM-1.2.30.new/Makefile 2016-05-13 16:25:04.000000000 +0200 @@ -11,12 +11,12 @@ -- GitLab From 210ea5bae0fc66c42acbabfb2a162ca3e52fbb40 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 18 May 2016 09:53:02 +0200 Subject: [PATCH 1703/2133] removed files --- easybuild/easyconfigs/r/RSEM/Makefile | 173 --------------------- easybuild/easyconfigs/r/RSEM/Makefile.orig | 173 --------------------- 2 files changed, 346 deletions(-) delete mode 100644 easybuild/easyconfigs/r/RSEM/Makefile delete mode 100644 easybuild/easyconfigs/r/RSEM/Makefile.orig diff --git a/easybuild/easyconfigs/r/RSEM/Makefile b/easybuild/easyconfigs/r/RSEM/Makefile deleted file mode 100644 index 921b40b1b3..0000000000 --- a/easybuild/easyconfigs/r/RSEM/Makefile +++ /dev/null @@ -1,173 +0,0 @@ -SAMTOOLS = samtools-1.3 -HTSLIB = htslib-1.3 - -ifneq ($(cygwin), true) - SAMTOOLS_MAKEFILE = Makefile -else - SAMTOOLS_MAKEFILE = Makefile.cygwin -endif - -# overridable, defaulting to local copy -BOOST = ${EBROOTBOOST} - -# Compilation variables -CXX = g++ -CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) -CPPFLAGS = - -LDFLAGS = -LDLIBS = - -# Installation variables -INSTALL = install -INSTALL_PROGRAM = $(INSTALL) -p -INSTALL_DATA = $(INSTALL) -p -m 644 -INSTALL_DIR = $(INSTALL) -d -STRIP ?=strip - -prefix ?= /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin - -# Auxiliary variables for compilation -SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h -SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a -CONFIGURE = ./configure - -OBJS1 = parseIt.o -OBJS2 = extractRef.o synthesisRef.o preRef.o buildReadIndex.o wiggle.o tbam2gbam.o bam2wig.o bam2readdepth.o getUnique.o samValidator.o scanForPairedEndReads.o SamHeader.o -OBJS3 = EM.o Gibbs.o calcCI.o simulation.o - -PROGS1 = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads -PROGS2 = rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads -PROGS3 = rsem-run-gibbs rsem-calculate-credibility-intervals - -PROGRAMS = $(PROGS1) $(PROGS2) $(PROGS3) - -# Auxiliary variables for installation -SCRIPTS = rsem-prepare-reference rsem-calculate-expression rsem-refseq-extract-primary-assembly rsem-gff3-to-gtf rsem-plot-model \ - rsem-plot-transcript-wiggles rsem-gen-transcript-plots rsem-generate-data-matrix \ - extract-transcript-to-gene-map-from-trinity convert-sam-for-rsem - - - - -.PHONY : all ebseq clean - -all : $(PROGRAMS) $(SAMTOOLS)/samtools - -$(SAMTOOLS)/samtools : - cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools - -$(SAMLIBS) : $(SAMTOOLS)/samtools - - -# Compile objects -$(OBJS1) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O2 -c -o $@ $< - -$(OBJS2) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -c -o $@ $< - -$(OBJS3) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -ffast-math -c -o $@ $< - - -# Generate executables -$(PROGS1) : - $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) - -$(PROGS2) : - $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -L$(EBROOTZLIB)/lib -lz - -$(PROGS3) : - $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) - - -# Dependencies for executables -rsem-extract-reference-transcripts : extractRef.o -rsem-synthesis-reference-transcripts : synthesisRef.o -rsem-preref : preRef.o -rsem-build-read-index : buildReadIndex.o -rsem-simulate-reads : simulation.o - -rsem-parse-alignments : parseIt.o $(SAMLIBS) -rsem-run-em : EM.o SamHeader.o $(SAMLIBS) -rsem-tbam2gbam : tbam2gbam.o SamHeader.o $(SAMLIBS) -rsem-bam2wig : bam2wig.o wiggle.o $(SAMLIBS) -rsem-bam2readdepth : bam2readdepth.o wiggle.o $(SAMLIBS) -rsem-get-unique : getUnique.o $(SAMLIBS) -rsem-sam-validator : samValidator.o $(SAMLIBS) -rsem-scan-for-paired-end-reads : scanForPairedEndReads.o $(SAMLIBS) - -rsem-run-gibbs : Gibbs.o -rsem-calculate-credibility-intervals : calcCI.o $(LDLIBS) - -# Dependencies for objects -parseIt.o : parseIt.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h - -extractRef.o : extractRef.cpp utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h -synthesisRef.o : synthesisRef.cpp utils.h my_assert.h Transcript.h Transcripts.h -preRef.o : preRef.cpp utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h -buildReadIndex.o : buildReadIndex.cpp utils.h -wiggle.o: wiggle.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h wiggle.h -tbam2gbam.o : tbam2gbam.cpp $(SAMHEADERS) utils.h Transcripts.h Transcript.h BamConverter.h sam_utils.h SamHeader.hpp my_assert.h bc_aux.h -bam2wig.o : bam2wig.cpp utils.h my_assert.h wiggle.h -bam2readdepth.o : bam2readdepth.cpp utils.h my_assert.h wiggle.h -getUnique.o : getUnique.cpp $(SAMHEADERS) sam_utils.h utils.h -samValidator.o : samValidator.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h -scanForPairedEndReads.o : scanForPairedEndReads.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h -SamHeader.o : SamHeader.cpp $(SAMHEADERS) SamHeader.hpp - -EM.o : EM.cpp $(SAMHEADERS) utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_utils.h SamHeader.hpp sampling.h $(BOOST)/boost/random.hpp WriteResults.h -Gibbs.o : Gibbs.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h -calcCI.o : calcCI.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h -simulation.o : simulation.cpp utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h $(BOOST)/boost/random.hpp WriteResults.h - -# Dependencies for header files -Transcript.h : utils.h -Transcripts.h : utils.h my_assert.h Transcript.h -BowtieRefSeqPolicy.h : RefSeqPolicy.h -RefSeq.h : utils.h -Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h -SingleRead.h : Read.h -SingleReadQ.h : Read.h -PairedEndRead.h : Read.h SingleRead.h -PairedEndReadQ.h : Read.h SingleReadQ.h -PairedEndHit.h : SingleHit.h -HitContainer.h : GroupInfo.h -sam_utils.h : $(SAMHEADERS) Transcript.h Transcripts.h -SamParser.h : $(SAMHEADERS) sam_utils.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h -simul.h : $(BOOST)/boost/random.hpp -ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h -SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h -SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h -PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h -PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h -HitWrapper.h : HitContainer.h -BamWriter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h -sampling.h : $(BOOST)/boost/random.hpp -WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h -bc_aux.h : $(SAMHEADERS) -BamConverter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h bc_aux.h Transcript.h Transcripts.h -Buffer.h : my_assert.h -SamHeader.hpp : $(SAMHEADERS) - -# Compile EBSeq -ebseq : - cd EBSeq && $(MAKE) all - -# Install RSEM -install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) - $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) - $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools - $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools - $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) - $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm - -# Clean -clean : - rm -f *.o *~ $(PROGRAMS) - cd $(SAMTOOLS) && $(MAKE) clean-all - cd EBSeq && $(MAKE) clean diff --git a/easybuild/easyconfigs/r/RSEM/Makefile.orig b/easybuild/easyconfigs/r/RSEM/Makefile.orig deleted file mode 100644 index 09d2223b23..0000000000 --- a/easybuild/easyconfigs/r/RSEM/Makefile.orig +++ /dev/null @@ -1,173 +0,0 @@ -SAMTOOLS = samtools-1.3 -HTSLIB = htslib-1.3 - -ifneq ($(cygwin), true) - SAMTOOLS_MAKEFILE = Makefile -else - SAMTOOLS_MAKEFILE = Makefile.cygwin -endif - -# overridable, defaulting to local copy -BOOST = . - -# Compilation variables -CXX = g++ -CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) -CPPFLAGS = - -LDFLAGS = -LDLIBS = - -# Installation variables -INSTALL = install -INSTALL_PROGRAM = $(INSTALL) -p -INSTALL_DATA = $(INSTALL) -p -m 644 -INSTALL_DIR = $(INSTALL) -d -STRIP ?=strip - -prefix ?= /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin - -# Auxiliary variables for compilation -SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h -SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a -CONFIGURE = ./configure - -OBJS1 = parseIt.o -OBJS2 = extractRef.o synthesisRef.o preRef.o buildReadIndex.o wiggle.o tbam2gbam.o bam2wig.o bam2readdepth.o getUnique.o samValidator.o scanForPairedEndReads.o SamHeader.o -OBJS3 = EM.o Gibbs.o calcCI.o simulation.o - -PROGS1 = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads -PROGS2 = rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads -PROGS3 = rsem-run-gibbs rsem-calculate-credibility-intervals - -PROGRAMS = $(PROGS1) $(PROGS2) $(PROGS3) - -# Auxiliary variables for installation -SCRIPTS = rsem-prepare-reference rsem-calculate-expression rsem-refseq-extract-primary-assembly rsem-gff3-to-gtf rsem-plot-model \ - rsem-plot-transcript-wiggles rsem-gen-transcript-plots rsem-generate-data-matrix \ - extract-transcript-to-gene-map-from-trinity convert-sam-for-rsem - - - - -.PHONY : all ebseq clean - -all : $(PROGRAMS) $(SAMTOOLS)/samtools - -$(SAMTOOLS)/samtools : - cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools - -$(SAMLIBS) : $(SAMTOOLS)/samtools - - -# Compile objects -$(OBJS1) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O2 -c -o $@ $< - -$(OBJS2) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -c -o $@ $< - -$(OBJS3) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -ffast-math -c -o $@ $< - - -# Generate executables -$(PROGS1) : - $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) - -$(PROGS2) : - $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lz - -$(PROGS3) : - $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) - - -# Dependencies for executables -rsem-extract-reference-transcripts : extractRef.o -rsem-synthesis-reference-transcripts : synthesisRef.o -rsem-preref : preRef.o -rsem-build-read-index : buildReadIndex.o -rsem-simulate-reads : simulation.o - -rsem-parse-alignments : parseIt.o $(SAMLIBS) -rsem-run-em : EM.o SamHeader.o $(SAMLIBS) -rsem-tbam2gbam : tbam2gbam.o SamHeader.o $(SAMLIBS) -rsem-bam2wig : bam2wig.o wiggle.o $(SAMLIBS) -rsem-bam2readdepth : bam2readdepth.o wiggle.o $(SAMLIBS) -rsem-get-unique : getUnique.o $(SAMLIBS) -rsem-sam-validator : samValidator.o $(SAMLIBS) -rsem-scan-for-paired-end-reads : scanForPairedEndReads.o $(SAMLIBS) - -rsem-run-gibbs : Gibbs.o -rsem-calculate-credibility-intervals : calcCI.o - -# Dependencies for objects -parseIt.o : parseIt.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h - -extractRef.o : extractRef.cpp utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h -synthesisRef.o : synthesisRef.cpp utils.h my_assert.h Transcript.h Transcripts.h -preRef.o : preRef.cpp utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h -buildReadIndex.o : buildReadIndex.cpp utils.h -wiggle.o: wiggle.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h wiggle.h -tbam2gbam.o : tbam2gbam.cpp $(SAMHEADERS) utils.h Transcripts.h Transcript.h BamConverter.h sam_utils.h SamHeader.hpp my_assert.h bc_aux.h -bam2wig.o : bam2wig.cpp utils.h my_assert.h wiggle.h -bam2readdepth.o : bam2readdepth.cpp utils.h my_assert.h wiggle.h -getUnique.o : getUnique.cpp $(SAMHEADERS) sam_utils.h utils.h -samValidator.o : samValidator.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h -scanForPairedEndReads.o : scanForPairedEndReads.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h -SamHeader.o : SamHeader.cpp $(SAMHEADERS) SamHeader.hpp - -EM.o : EM.cpp $(SAMHEADERS) utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_utils.h SamHeader.hpp sampling.h $(BOOST)/boost/random.hpp WriteResults.h -Gibbs.o : Gibbs.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h -calcCI.o : calcCI.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h -simulation.o : simulation.cpp utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h $(BOOST)/boost/random.hpp WriteResults.h - -# Dependencies for header files -Transcript.h : utils.h -Transcripts.h : utils.h my_assert.h Transcript.h -BowtieRefSeqPolicy.h : RefSeqPolicy.h -RefSeq.h : utils.h -Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h -SingleRead.h : Read.h -SingleReadQ.h : Read.h -PairedEndRead.h : Read.h SingleRead.h -PairedEndReadQ.h : Read.h SingleReadQ.h -PairedEndHit.h : SingleHit.h -HitContainer.h : GroupInfo.h -sam_utils.h : $(SAMHEADERS) Transcript.h Transcripts.h -SamParser.h : $(SAMHEADERS) sam_utils.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h -simul.h : $(BOOST)/boost/random.hpp -ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h -SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h -SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h -PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h -PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h -HitWrapper.h : HitContainer.h -BamWriter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h -sampling.h : $(BOOST)/boost/random.hpp -WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h -bc_aux.h : $(SAMHEADERS) -BamConverter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h bc_aux.h Transcript.h Transcripts.h -Buffer.h : my_assert.h -SamHeader.hpp : $(SAMHEADERS) - -# Compile EBSeq -ebseq : - cd EBSeq && $(MAKE) all - -# Install RSEM -install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) - $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) - $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools - $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools - $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) - $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm - -# Clean -clean : - rm -f *.o *~ $(PROGRAMS) - cd $(SAMTOOLS) && $(MAKE) clean-all - cd EBSeq && $(MAKE) clean -- GitLab From 28666985979b191e3f3ff9c374b7beffa4298a8b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 18 May 2016 15:15:01 +0200 Subject: [PATCH 1704/2133] FIAT with foss 2016a --- .../FIAT-1.6.0-foss-2016a-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..b24555e505 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '1.6.0' + +homepage = 'https://bitbucket.org/fenics-project/fiat' +description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order + instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating + arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('sympy', '1.0', '-Python-%(pyver)s'), +] + +options = {'modulename': name} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From bf0d2b35fc9b19bb7e5a1d5ebb4445685ef1e995 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 May 2016 16:15:03 +0200 Subject: [PATCH 1705/2133] bump version to 2.9.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 64865babea..c52c2d0550 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.8.0' +VERSION = '2.9.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From c65b54690235513636e7619ce7fdab3bbfaf0bcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 May 2016 16:31:32 +0200 Subject: [PATCH 1706/2133] add easyconfig EasyBuild-2.8.0.eb --- .../e/EasyBuild/EasyBuild-2.8.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb new file mode 100644 index 0000000000..07bb77b453 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.8.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/1d/9e/9a69f54d7bdb4a75e78530d1ccdd66be5fd61e31ef289f167cf007e11089/', + 'https://pypi.python.org/packages/e9/c2/db36d5a92ddcb68645a64f9017a7056438aa40f224e09c3b6af374d58ebc/', + 'https://pypi.python.org/packages/c0/84/ebe0a2fc169370db663d82caf7c0224771028c79ec9a324b46d029840773/', + 'https://pypi.python.org/packages/ea/f2/a5556cc4e7f3dd4059d890b56a6af9ca80e9210993db65303aa0163806fd/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.4.18.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 81b7afc53a7220ab3196dd67f2ba2f81ec523bf5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 10:38:38 +0200 Subject: [PATCH 1707/2133] add easyconfig Spark-1.6.1.eb --- easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb | 28 ++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb b/easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb new file mode 100644 index 0000000000..e06636922a --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '1.6.1' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] +checksums = ['667a62d7f289479a19da4b563e7151d4'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['lib', 'python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' -- GitLab From 0e676c7588bcafcb57506cb3d124cf8dc67d076c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 10:47:51 +0200 Subject: [PATCH 1708/2133] fix source for snappy 1.1.3, drop autogen --- .../s/snappy/snappy-1.1.3-GCC-4.9.3-2.25.eb | 21 +++++++++++++++++++ .../s/snappy/snappy-1.1.3-GCC-4.9.3.eb | 13 +++--------- 2 files changed, 24 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..25d6fcc3ba --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'snappy' +version = '1.1.3' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['https://github.com/google/snappy/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libsnappy.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb index 36e8b8b902..5e495e1a26 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb @@ -3,22 +3,15 @@ easyblock = 'ConfigureMake' name = 'snappy' version = '1.1.3' -# snappy was migrated from code.google.com to github.com and this commit -# corresponds to release 1.1.2 (which they haven't tagged). -# see https://github.com/google/snappy/commit/1ff9be9 -commit = '1ff9be9' - -homepage = 'http://code.google.com/p/snappy/' +homepage = 'https://github.com/google/snappy' description = """Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.""" toolchain = {'name': 'GCC', 'version': '4.9.3'} -source_urls = ['https://github.com/google/snappy/archive'] -sources = ['%s.tar.gz' % commit] - -preconfigopts = "./autogen.sh && " +source_urls = ['https://github.com/google/snappy/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] sanity_check_paths = { 'files': ['lib/libsnappy.%s' % SHLIB_EXT], -- GitLab From 99f8995aa638826460dfb681ace651616c63f94b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 11:03:34 +0200 Subject: [PATCH 1709/2133] add testpath as dependency of IPython, rather than as extension --- ...IPython-4.0.0-intel-2015a-Python-2.7.10.eb | 17 ++++------- .../pip-8.1.2-intel-2015a-Python-2.7.10.eb | 19 ++++++++++++ .../testpath-0.2-intel-2015a-Python-2.7.10.eb | 30 +++++++++++++++++++ 3 files changed, 54 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/t/testpath/testpath-0.2-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb index aee1a02648..eacf19ae8d 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'IPython' version = '4.0.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -13,13 +14,9 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015a'} -python = 'Python' -pyver = '2.7.10' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.10'), + ('testpath', '0.2', versionsuffix), ] # this is a bundle of Python packages @@ -50,24 +47,20 @@ exts_list = [ ('requests', '2.7.0', { 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], }), - ('testpath', '0.2', { - 'source_urls': ['https://github.com/jupyter/testpath/archive/'], - 'source_tmpl': '%(version)s.tar.gz', - }), ('ipython', version, { 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'modulename': 'IPython', }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..f8c928ec85 --- /dev/null +++ b/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,19 @@ +easyblock = 'PythonPackage' + +name = 'pip' +version = '8.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pip.pypa.io' +description = """The PyPA recommended tool for installing Python packages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.10'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/testpath/testpath-0.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/t/testpath/testpath-0.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..90a7f21775 --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'testpath' +version = '0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jupyter/testpath' +description = """Test utilities for code working with files and commands""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://pypi.python.org/packages/py2.py3/t/testpath/'] +sources = ['testpath-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.10'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/testpath'], +} + +moduleclass = 'lib' -- GitLab From cd1f133df5a9a18ea5fe4c81d982725dde5da050 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 11:09:19 +0200 Subject: [PATCH 1710/2133] revert back to libreadline 6.3 in SQLite easyconfig --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb index 7b7e716a53..6a41f5863c 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb @@ -26,7 +26,7 @@ version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.spl sources = ['sqlite-autoconf-%s.tar.gz' % version_str] dependencies = [ - ('libreadline', '6.2'), + ('libreadline', '6.3'), ('Tcl', '8.6.4'), ] -- GitLab From dcd8260522e4ed83259fcf39bdd52f0986d3c6e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 11:28:07 +0200 Subject: [PATCH 1711/2133] downgrade to SQLite to fix libreadline conflict --- ...IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 2 +- .../s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb | 37 +++++++++++++++++++ 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index af763e233d..fcbae3463e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -25,7 +25,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), - ('SQLite', '3.8.10.2'), + ('SQLite', '3.8.5'), ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), ] diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb new file mode 100644 index 0000000000..6f7046c321 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.5' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2013'] +sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.4'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From c4880662bf3b1931681e4aaf13e7ed33b1d15e79 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 11:31:17 +0200 Subject: [PATCH 1712/2133] fix modulenam for path.py extension --- .../i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb index eacf19ae8d..4ba4b8c0f8 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -36,6 +36,7 @@ exts_list = [ }), ('path.py', '7.6', { 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + 'modulename': 'path', }), ('pickleshare', '0.5', { 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], -- GitLab From 7b0872b489226825cb57886dce2cfa89bdc40fba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 12:20:22 +0200 Subject: [PATCH 1713/2133] add testpath as a dependency to IPython --- ...IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 9 ++---- .../pip-8.1.2-goolf-1.4.10-Python-2.7.5.eb | 19 ++++++++++++ .../testpath-0.3-goolf-1.4.10-Python-2.7.5.eb | 30 +++++++++++++++++++ 3 files changed, 52 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/p/pip/pip-8.1.2-goolf-1.4.10-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/t/testpath/testpath-0.3-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index fcbae3463e..614af5bd06 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -27,6 +27,7 @@ dependencies = [ (python, pyver), ('SQLite', '3.8.5'), ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('testpath', '0.3', versionsuffix), ] # this is a bundle of Python packages @@ -131,10 +132,6 @@ exts_list = [ ('ipykernel', '4.2.2', { 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], }), - #('testpath', '0.3', { - #'source_urls': ['https://github.com/jupyter/testpath/archive/'], #this extension doesn't provide a setup.py and it's required for the sanity checks (iptest, iptest2) - #'source_tmpl': '0.3.tar.gz', - #}), ('ipython', version, { 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'modulename': 'IPython', @@ -151,8 +148,8 @@ sanity_check_paths = { sanity_check_commands = [ ('ipython -h', ''), ('ipython notebook --help', ''), - #('iptest', ''), # this test fails with 'ImportError: No module named testpath'. testpath cannot be installed with easyconfig - #('iptest2', ''), + ('iptest', ''), + ('iptest2', ''), ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pip/pip-8.1.2-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/pip/pip-8.1.2-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..79cbce5e37 --- /dev/null +++ b/easybuild/easyconfigs/p/pip/pip-8.1.2-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,19 @@ +easyblock = 'PythonPackage' + +name = 'pip' +version = '8.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pip.pypa.io' +description = """The PyPA recommended tool for installing Python packages.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.5'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/testpath/testpath-0.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/t/testpath/testpath-0.3-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..8d9a62a9e3 --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.3-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'testpath' +version = '0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jupyter/testpath' +description = """Test utilities for code working with files and commands""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/py2.py3/t/testpath/'] +sources = ['testpath-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.5'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/testpath'], +} + +moduleclass = 'lib' -- GitLab From c3d233d23d2151c9c98a341051b666b239af129d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 12:22:20 +0200 Subject: [PATCH 1714/2133] add easyconfig netCDF-Fortran-4.4.4-intel-2016a.eb, add easyconfig netCDF-C++4-4.3.0-intel-2016a.eb --- .../netCDF-C++4-4.3.0-intel-2016a.eb | 24 +++++++++++++++++++ .../netCDF-Fortran-4.4.4-intel-2016a.eb | 17 +++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016a.eb new file mode 100644 index 0000000000..3243613e15 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.0')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2016a.eb new file mode 100644 index 0000000000..947f018cb3 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2016a.eb @@ -0,0 +1,17 @@ +name = 'netCDF-Fortran' +version = '4.4.4' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' -- GitLab From 912898e31a7dc99effb7c7fc9610b9a497354cf9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 12:24:58 +0200 Subject: [PATCH 1715/2133] fix source URL for SQLite --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb index 6f7046c321..72f8da9d34 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb @@ -18,8 +18,7 @@ version = '3.8.5' homepage = 'http://www.hwaci.com/sw/sqlite/' description = "SQLite: SQL Database Engine in a C Library" -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2013'] +source_urls = ['http://www.sqlite.org/2014'] sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 389d679cd6e983b0025c75444b23641daa4835f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 13:03:04 +0200 Subject: [PATCH 1716/2133] add missing extension pexpect --- .../i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index 614af5bd06..deb444d50b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -132,6 +132,9 @@ exts_list = [ ('ipykernel', '4.2.2', { 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], }), + ('pexpect', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), ('ipython', version, { 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'modulename': 'IPython', -- GitLab From 31d3406af466b7af5c2fa8c85af5e2e95c0612d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 13:07:17 +0200 Subject: [PATCH 1717/2133] add SQLite dep in Python 2.7.5 easyconfig --- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index b8e12d524c..7844382331 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('SQLite', '3.8.5'), # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -- GitLab From 2a80620861105a62c9dda56080ae9efff2a38dcb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 13:25:34 +0200 Subject: [PATCH 1718/2133] drop explicit dep on SQLite, use %(pyver)s and %(pyshortver)s --- .../IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index deb444d50b..3aa3ecb170 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -7,6 +7,7 @@ easyblock = 'Bundle' name = 'IPython' version = '4.1.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -18,14 +19,8 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'goolf', 'version': '1.4.10'} -python = 'Python' -pyver = '2.7.5' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), - ('SQLite', '3.8.5'), + ('Python', '2.7.5'), ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), ('testpath', '0.3', versionsuffix), ] @@ -141,11 +136,11 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ -- GitLab From 8b6dae32e5e96d91f6f3ac3af5001e44c48cf7a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 13:36:43 +0200 Subject: [PATCH 1719/2133] don't hardcode versions in source templates for extensions --- .../i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index 3aa3ecb170..cc3235c707 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -90,11 +90,11 @@ exts_list = [ }), ('setuptools_scm', '1.10.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], - 'source_tmpl': 'setuptools_scm-1.10.1.tar.bz2', + 'source_tmpl': 'setuptools_scm-%(version)s.tar.bz2', }), ('simplegeneric', '0.8.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], - 'source_tmpl': 'simplegeneric-0.8.1.zip', + 'source_tmpl': 'simplegeneric-%(version)s.zip', }), ('path.py', '8.1.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], -- GitLab From 40d159d417f8257e8820be35477abdf1d873eac7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 19 May 2016 13:58:01 +0200 Subject: [PATCH 1720/2133] Add likwid 4.1.0 --- .../l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb | 33 ++++++++++++++ .../l/likwid/likwid-4.1.0-config-mk.patch | 43 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb new file mode 100644 index 0000000000..cda484e29c --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '4.1.0' + +homepage = 'http://code.google.com/p/likwid/' +description = """Likwid stands for Like I knew what I am doing. This project contributes easy to use + command line tools for Linux to support programmers in developing high performance multi threaded programs.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] + +patches = ['likwid-%(version)s-config-mk.patch'] + +builddependencies = [('binutils', '2.25', '', ('GCCcore', '4.9.3'))] + +skipsteps = ['configure'] +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", + "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", "bin/likwid-topology", + "lib/liblikwidpin.%s" % SHLIB_EXT, "lib/liblikwid.%s" % SHLIB_EXT], + 'dirs': ["man/man1"] +} + +maxparallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch new file mode 100644 index 0000000000..735ec88bea --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch @@ -0,0 +1,43 @@ +# Patches the build system +# Ward Poelmans +diff -ur likwid-likwid-4.1.0.orig/config.mk likwid-likwid-4.1.0/config.mk +--- likwid-likwid-4.1.0.orig/config.mk 2016-05-19 13:16:28.000000000 +0200 ++++ likwid-likwid-4.1.0/config.mk 2016-05-19 13:46:33.345284562 +0200 +@@ -9,7 +9,7 @@ + COLOR = BLUE#NO SPACE + + # Path were to install likwid +-PREFIX = /usr/local#NO SPACE ++#PREFIX = /usr/local#NO SPACE + + ################################################################# + # Common users do not need to change values below this comment! # +@@ -33,7 +33,7 @@ + # chown installed tools to this user/group + # if you change anything here, make sure that the user/group can access + # the MSR devices and (on Intel) the PCI devices. +-INSTALL_CHOWN = -g root -o root ++INSTALL_CHOWN = + + # For the daemon based secure msr/pci access configure + # the absolute path to the msr daemon executable. +@@ -44,7 +44,7 @@ + # Build the accessDaemon. Have a look in the WIKI for details. + BUILDDAEMON = true#NO SPACE + #Build the setFrequencies tool +-BUILDFREQ = true#NO SPACE ++BUILDFREQ = false#NO SPACE + + # Set the default mode for MSR access. + # This can usually be overriden on the commandline. +@@ -71,8 +71,8 @@ + # a proper config file at CFG_FILE_PATH) + MAX_NUM_THREADS = 263 + MAX_NUM_NODES = 64 +-CFG_FILE_PATH = /etc/likwid.cfg +-TOPO_FILE_PATH = /etc/likwid_topo.cfg ++CFG_FILE_PATH = $(PREFIX)/etc/likwid.cfg ++TOPO_FILE_PATH = $(PREFIX)/etc/likwid_topo.cfg + + # Versioning Information + VERSION = 4 -- GitLab From 24083ad232dca9485aa4be1c83a4b964881437d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 14:05:28 +0200 Subject: [PATCH 1721/2133] add easyconfig IPython-4.2.0-intel-2016a-Python-2.7.11.eb --- ...IPython-4.2.0-intel-2016a-Python-2.7.11.eb | 144 ++++++++++++++++++ 1 file changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0b3b531cf3 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,144 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'IPython' +version = '4.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), + ('testpath', '0.3', versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysqlite', '2.8.2', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2016.2.28', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('jupyter_client', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools_scm', '1.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('path.py', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + 'modulename': 'path', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pickleshare', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('pathlib2', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' -- GitLab From 59986fa63491a504f0e21e652ca0ca661e125d60 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 19 May 2016 14:10:35 +0200 Subject: [PATCH 1722/2133] Fix filename --- ...ikwid-4.1.0-GCCCore-4.9.3.eb => likwid-4.1.0-GCCcore-4.9.3.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/likwid/{likwid-4.1.0-GCCCore-4.9.3.eb => likwid-4.1.0-GCCcore-4.9.3.eb} (100%) diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb similarity index 100% rename from easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb rename to easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb -- GitLab From ffea8d3c28fb854c18aacd99afe3733257c26717 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 14:16:18 +0200 Subject: [PATCH 1723/2133] modify easyconfig Maven-3.2.3.eb, modify easyconfig Maven-3.3.3.eb, add easyconfig Maven-3.3.9.eb --- easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb | 1 - easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb | 1 - easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb | 22 ++++++++++++++++++++ 3 files changed, 22 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb index c78d5ecd63..ae08a0b454 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb @@ -14,7 +14,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['apache-maven-%(version)s-bin.tar.gz'] source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] - sanity_check_paths = { 'files': ["bin/mvn"], 'dirs': [], diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb index a18f09ae41..642c9d91d2 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb @@ -14,7 +14,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['apache-maven-%(version)s-bin.tar.gz'] source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] - sanity_check_paths = { 'files': ["bin/mvn"], 'dirs': [], diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb b/easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb new file mode 100644 index 0000000000..f38f753af8 --- /dev/null +++ b/easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb @@ -0,0 +1,22 @@ +easyblock = 'PackedBinary' + +name = 'Maven' +version = '3.3.9' + +homepage = 'http://maven.apache.org/index.html' +description = """Binary maven install, Apache Maven is a software project management and comprehension tool. Based on +the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a +central piece of information. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['apache-maven-%(version)s-bin.tar.gz'] +source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] + +sanity_check_paths = { + 'files': ["bin/mvn"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 6e368670a4e2d50b06252cae0871853e408cc454 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 14:30:56 +0200 Subject: [PATCH 1724/2133] add easyconfig Hadoop-2.6.0-cdh5.7.0-native.eb, add easyconfig CMake-3.5.2.eb --- easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb | 22 ++++++++++++++ .../h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb | 30 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb create mode 100644 easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb new file mode 100644 index 0000000000..412e055df6 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb new file mode 100644 index 0000000000..b5884a562e --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb @@ -0,0 +1,30 @@ +name = 'Hadoop' +version = '2.6.0-cdh5.7.0' +versionsuffix = '-native' + +homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' +description = """Hadoop MapReduce by Cloudera""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] + +patches = ['Hadoop-TeraSort-on-local-filesystem.patch'] + +builddependencies = [ + ('Maven', '3.3.9'), + ('protobuf', '2.5.0'), # *must* be this version + ('CMake', '3.5.2'), + ('snappy', '1.1.3', '', ('GCC', '4.9.3-2.25')), +] + +dependencies = [('Java', '1.7.0_80')] + +build_native_libs = True + +extra_native_libs = [('snappy', 'lib/libsnappy.so*')] + +parallel = 1 + +moduleclass = 'tools' -- GitLab From 7de330213bf1ef16b9ecc5d3d981f6233a69e18f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 17:17:14 +0200 Subject: [PATCH 1725/2133] add easyconfig Yade-1.20.0-intel-2016a-Python-2.7.11.eb, add easyconfig Qt-4.8.7-intel-2016a-GLib-2.48.0.eb, add easyconfig PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb, add easyconfig minieigen-0.5.3-intel-2016a-Python-2.7.11.eb, add easyconfig libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb, add easyconfig IPython-3.2.3-intel-2016a-Python-2.7.11.eb, add easyconfig GTS-0.7.6-intel-2016a.eb, add easyconfig GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb, add easyconfig Loki-0.1.7-intel-2016a.eb, add easyconfig matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb, add easyconfig freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb --- .../freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb | 40 ++++++++ .../GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb | 37 ++++++++ .../g/GTS/GTS-0.7.6-intel-2016a.eb | 25 +++++ ...IPython-3.2.3-intel-2016a-Python-2.7.11.eb | 94 +++++++++++++++++++ .../l/Loki/Loki-0.1.7-intel-2016a.eb | 24 +++++ ...QGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb | 23 +++++ ...ntel-2016a-Python-2.7.11-freetype-2.6.3.eb | 47 ++++++++++ ...nieigen-0.5.3-intel-2016a-Python-2.7.11.eb | 26 +++++ .../PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb | 30 ++++++ .../q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb | 27 ++++++ .../Yade-1.20.0-intel-2016a-Python-2.7.11.eb | 60 ++++++++++++ 11 files changed, 433 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb create mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb create mode 100644 easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..fceaa15cbb --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', mesa_ver), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..3f9a18be1e --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', mesa_ver), + ('libGLU', '9.0.0', versionsuffix), + ('freeglut', '3.0.0', versionsuffix), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb new file mode 100644 index 0000000000..fa9873619a --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.48.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..b9c58c257f --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,94 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb new file mode 100644 index 0000000000..353bbfd940 --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Loki' +version = '0.1.7' + +homepage = 'http://loki-lib.sourceforge.net/' +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and + idioms. """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths={ + 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], + 'dirs': ['include/loki'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..3e6a70b031 --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,23 @@ +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('libGLU', '9.0.0', versionsuffix), +] + +builddependencies = [('Qt', '4.8.7', '-GLib-2.48.0')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb new file mode 100644 index 0000000000..85c6625096 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -0,0 +1,47 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +freetype_ver = '2.6.3' +versionsuffix = '-Python-%%(pyver)s-freetype-%s' % freetype_ver + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', freetype_ver), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..32173fca1a --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'minieigen' +version = '0.5.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://launchpad.net/minieigen/' +description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Boost', '1.60.0', versionsuffix), + ('Eigen', '3.2.7'), + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/minieigen.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..7383e08e64 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyGTS' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourceforge.net/projects/pygts/' +description = """ PyGTS is a python package used to construct, manipulate, + and perform computations on triangulated surfaces. + It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('GLib', '2.48.0'), + ('GTS' ,'0.7.6'), +] + +options = {'modulename': 'gts'} + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], + 'dirs':[], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000..ada4c2ab36 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb @@ -0,0 +1,27 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +glib_ver = '2.48.0' +versionsuffix = '-GLib-%s' % glib_ver + +dependencies = [ + ('GLib', glib_ver), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXrender', '0.9.9'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..cecf209b8a --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,60 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '1.20.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://yade-dem.org/doc/' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] + +mesaver = '11.2.1' +dependencies = [ + ('Boost', '1.60.0', versionsuffix), + ('CGAL', '4.8', versionsuffix), + ('Eigen', '3.2.7'), + ('GDB', '7.10.1', versionsuffix), + ('GL2PS', '1.3.9', '-Mesa-%s' % mesaver), + ('GTS', '0.7.6'), + ('IPython', '3.2.3', versionsuffix), + ('libQGLViewer', '2.6.3', '-Mesa-%s' % mesaver), + ('Loki', '0.1.7'), + ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3'), + ('minieigen', '0.5.3', versionsuffix), + ('PyGTS', '0.3.1', versionsuffix), + ('Python', '2.7.11'), + ('Qt', '4.8.7', '-GLib-2.48.0'), + ('SQLite', '3.9.2'), + ('VTK', '6.3.0', versionsuffix), + ('zlib', '1.2.8'), +] + +builddependencies = [('CMake', '3.5.2')] + +separate_build_dir = True + +configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' +configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'PYTHONPATH': ['lib/x86_64-linux-gnu/yade-%(version)s/py', 'lib64/yade-%(version)s/py'], +} + +sanity_check_paths = { + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', + ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, + 'lib64/yade-%%(version)s/libyade.%s' %SHLIB_EXT)], + 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], +} + +moduleclass = 'devel' -- GitLab From fad10b526d2974383d5ef3e840c431c976e78df6 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 20 May 2016 11:58:49 +0200 Subject: [PATCH 1726/2133] add easyconfig Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb --- .../Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..61ca6bdf28 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'Pysam' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +parallel = 1 + +dependencies = [ + ('Python', '2.7.11'), + ('ncurses', '5.9'), + ('zlib', '1.2.8'), + ('cURL', '7.44.0'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('Cython', '0.23.4', { + 'source_urls': ['http://cython.org/release/'], + }), + ('pysam', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pysam-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], +} + +moduleclass = 'bio' -- GitLab From dde9b3d04fa8f6bd4005ba98c8ef9727dad8a0dd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 20 May 2016 12:33:19 +0200 Subject: [PATCH 1727/2133] Boost 1.60 without Python --- .../b/Boost/Boost-1.60.0-intel-2016a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb new file mode 100644 index 0000000000..c6b8b5f02f --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.60.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From bfe9230346a9a22c61b0b49c5f04ee3aefdd5bce Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 20 May 2016 12:33:46 +0200 Subject: [PATCH 1728/2133] GROMACS 5.1.2 for intel/2016a --- .../GROMACS-5.1.2-intel-2016a-hybrid.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb new file mode 100644 index 0000000000..1d0b356a9e --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +# +# Version 5.1.2 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.2' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.5.2'), + ('libxml2', '2.9.3') +] + +dependencies = [('Boost', '1.60.0')] + +moduleclass = 'bio' -- GitLab From 218d926848f15ab39e8d32f6b80d79d3c30f1ddc Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 20 May 2016 13:21:39 +0200 Subject: [PATCH 1729/2133] Python-2.7.11-goolf-1.7.20.eb and dependencies --- .../g/GMP/GMP-6.1.0-goolf-1.7.20.eb | 30 ++++ .../libreadline-6.2-goolf-1.7.20.eb | 30 ++++ .../p/Python/Python-2.7.11-goolf-1.7.20.eb | 137 ++++++++++++++++++ .../s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb | 40 +++++ .../easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20.eb | 25 ++++ 5 files changed, 262 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..7a5dd73b3c --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215', '', True), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..be707f2f9d --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.2' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb new file mode 100644 index 0000000000..244af3a298 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb @@ -0,0 +1,137 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.4' +scipyversion = '0.17.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), + ('SQLite', '3.9.2'), + #('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4'), + ('GMP', '6.1.0'), +# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..5b3197813b --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20.eb new file mode 100644 index 0000000000..b613bb1182 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 20344e023efd16e234068988d34a357d4fed7f8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 May 2016 13:38:44 +0200 Subject: [PATCH 1730/2133] {bio}[intel/2016a] MRtrix 0.3.14 --- ...MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb | 26 ++++++++++++ .../m/MRtrix/MRtrix-0.3.14_intel-fixes.patch | 41 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..020ed91a4c --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +name = 'MRtrix' +version = '0.3.14' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] + +#patches = ['MRtrix-%(version)s.patch'] +patches = ['MRtrix-%(version)s_intel-fixes.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + ('Mesa', '11.2.1'), + ('Qt', '4.8.7'), + ('Eigen', '3.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch new file mode 100644 index 0000000000..bbc46048db --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch @@ -0,0 +1,41 @@ +fix compilation with Intel compilers, cfr. https://github.com/MRtrix3/mrtrix3/pull/622 +author: Kenneth Hoste (HPC-UGent) +diff --git a/src/dwi/tractography/seeding/base.h b/src/dwi/tractography/seeding/base.h +--- a/src/dwi/tractography/seeding/base.h ++++ b/src/dwi/tractography/seeding/base.h +@@ -62,7 +62,7 @@ namespace MR + uint32_t get_count (ImageType& data) + { + std::atomic count (0); +- ThreadedLoop (data).run ([&] (decltype(data)& v) { if (v.value()) count.fetch_add (1, std::memory_order_relaxed); }, data); ++ ThreadedLoop (data).run ([&] (ImageType& v) { if (v.value()) count.fetch_add (1, std::memory_order_relaxed); }, data); + return count; + } + + +diff --git a/lib/adapter/base.h b/lib/adapter/base.h +--- a/lib/adapter/base.h ++++ b/lib/adapter/base.h +@@ -25,7 +25,7 @@ namespace MR + namespace Adapter + { + +- template